Contacts of the helix formed by residues 125 - 145 (chain B) in PDB entry 2M8L


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with PRO 125 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118B  MET*     4.7    12.3    -      -       +      -
    123B  PRO*     3.5    21.1    -      -       +      +
    124B  ILE*     1.3    81.4    -      -       +      +
    126B  VAL*     1.3    59.0    +      -       -      +
    127B  GLY      3.2     3.8    -      -       -      -
    128B  GLU*     3.0    27.9    +      -       +      +
    129B  ILE*     3.0    44.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  PRO*     3.7    25.6    -      -       +      +
     99B  PRO*     3.8    18.2    -      -       +      -
    104B  ILE*     3.8    15.4    -      -       +      +
    114B  GLN*     3.9    32.3    -      -       -      +
    117B  TRP*     3.9    11.9    -      -       +      -
    118B  MET*     4.9     3.5    -      -       +      +
    124B  ILE*     2.8    37.4    +      -       +      +
    125B  PRO*     1.3    70.4    -      -       -      +
    127B  GLY*     1.3    65.1    +      -       -      +
    129B  ILE*     3.8     9.4    -      -       +      -
    130B  TYR*     3.1    26.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 127 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  ALA      3.4    25.1    -      -       -      -
     48B  THR*     4.5     1.6    -      -       -      -
     49B  PRO*     3.9    13.0    -      -       -      +
     52B  LEU*     3.5     6.7    -      -       -      +
    118B  MET*     5.3     7.3    -      -       -      +
    125B  PRO      3.2     1.0    -      -       -      -
    126B  VAL*     1.3    83.6    -      -       -      +
    128B  GLU*     1.3    56.7    +      -       -      +
    131B  LYS*     3.0    31.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 128 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125B  PRO*     3.0    28.7    +      -       +      +
    127B  GLY*     1.3    76.1    -      -       -      +
    129B  ILE*     1.3    60.2    +      -       +      +
    131B  LYS*     3.4    14.2    +      -       +      +
    132B  ARG*     3.0    27.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 129 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80B  TRP*     4.2    29.8    -      -       +      -
    104B  ILE*     4.0    13.2    -      -       +      -
    124B  ILE*     5.4     2.7    -      -       +      -
    125B  PRO*     3.0    43.5    +      -       +      +
    126B  VAL*     4.1     7.6    -      -       +      +
    128B  GLU*     1.3    76.1    -      -       +      +
    130B  TYR*     1.3    66.3    +      -       -      +
    132B  ARG*     3.3     8.8    +      -       +      +
    133B  TRP*     3.2    53.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  PRO*     4.0    13.9    -      -       +      -
     52B  LEU*     3.4    32.3    -      -       +      -
     53B  ASN*     4.5    10.9    +      -       +      +
     56B  LEU*     4.2     8.7    -      -       -      +
     73B  ILE*     3.6    34.5    -      -       +      +
    104B  ILE*     3.3    20.8    -      -       +      +
    105B  ALA*     3.5    43.7    +      -       +      +
    126B  VAL      3.1    18.8    +      -       -      +
    129B  ILE*     1.3    75.9    -      -       -      +
    131B  LYS*     1.3    62.8    +      -       -      +
    133B  TRP*     3.1    15.7    +      +       -      +
    134B  ILE*     3.1    37.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 131 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  PHE*     4.3     8.1    -      -       +      -
     41B  SER*     3.9    11.2    +      -       -      +
     44B  SER*     2.9    53.3    +      -       -      +
     45B  GLU*     3.6    10.1    -      -       -      +
     46B  GLY      4.2     3.6    -      -       -      +
     47B  ALA*     5.2     2.5    -      -       -      +
     52B  LEU*     3.6    13.4    -      -       +      +
    127B  GLY      3.0    20.8    +      -       -      +
    128B  GLU*     3.5    14.5    -      -       +      +
    129B  ILE      3.2     0.2    -      -       -      -
    130B  TYR*     1.3    75.9    -      -       -      +
    132B  ARG*     1.3    57.2    +      -       -      +
    134B  ILE*     3.3     6.7    +      -       -      +
    135B  ILE*     2.9    50.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  GLU*     3.0    13.1    +      -       +      +
    129B  ILE*     3.5    12.1    -      -       -      +
    131B  LYS*     1.3    77.6    -      -       -      +
    133B  TRP*     1.3    68.9    +      -       +      +
    135B  ILE*     3.7     9.5    -      -       +      +
    136B  LEU*     2.9    45.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  THR*     3.6     7.8    -      -       -      +
     73B  ILE*     4.4    23.9    -      -       +      +
     76B  GLU*     3.6    36.7    -      -       +      +
     77B  ALA*     3.8    23.1    -      -       +      -
     80B  TRP*     4.0    19.7    -      +       +      -
    101B  GLY*     3.7    16.6    -      -       -      -
    104B  ILE*     3.6    32.8    -      -       +      -
    105B  ALA*     4.4     5.6    -      -       +      -
    129B  ILE*     3.2    35.8    +      -       +      +
    130B  TYR*     3.1    22.9    +      +       +      +
    132B  ARG*     1.3    83.4    -      -       +      +
    134B  ILE*     1.3    63.5    +      -       -      +
    136B  LEU*     3.2    14.0    +      -       +      +
    137B  GLY*     3.0    17.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  PHE*     3.5    31.9    -      -       +      -
     52B  LEU*     3.8    20.4    -      -       +      -
     56B  LEU*     3.7    27.4    -      -       +      -
     69B  LEU*     3.6    21.1    -      -       +      +
     73B  ILE*     4.5     7.2    -      -       +      -
    130B  TYR*     3.1    46.0    +      -       +      +
    131B  LYS*     3.6     6.5    -      -       -      +
    133B  TRP*     1.3    75.1    -      -       -      +
    135B  ILE*     1.3    57.3    +      -       -      +
    137B  GLY*     3.0     4.7    +      -       -      -
    138B  LEU*     2.8    33.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  ILE*     4.1    24.5    -      -       +      -
     40B  PHE*     4.2    16.6    -      -       +      -
     41B  SER*     4.4    19.7    -      -       -      -
    131B  LYS*     2.9    38.7    +      -       +      +
    132B  ARG*     3.7     9.0    -      -       +      +
    134B  ILE*     1.3    73.1    -      -       -      +
    136B  LEU*     1.3    66.5    +      -       +      +
    138B  LEU*     3.2     9.7    +      -       +      +
    139B  ASN*     3.0    24.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  THR*     3.9     8.3    -      -       +      -
     76B  GLU*     3.5    35.7    -      -       +      +
    132B  ARG*     2.9    44.0    +      -       +      +
    133B  TRP*     3.3    11.9    -      -       +      +
    135B  ILE*     1.3    77.4    -      -       +      +
    137B  GLY*     1.3    61.2    +      -       -      +
    139B  ASN*     3.5     6.4    +      -       -      +
    140B  LYS*     3.2    27.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  MET*     3.8     2.9    -      -       -      +
     69B  LEU*     4.3     8.5    -      -       -      -
     72B  THR*     3.6    25.7    -      -       -      +
    133B  TRP      3.0     7.6    +      -       -      -
    134B  ILE      3.0     8.7    +      -       -      -
    136B  LEU*     1.3    74.7    -      -       -      +
    138B  LEU*     1.3    59.1    +      -       -      +
    140B  LYS*     3.2     4.7    +      -       -      +
    141B  ILE*     2.9    36.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 138 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  TRP*     5.0     7.6    -      -       +      -
     36B  VAL*     4.9    13.0    -      -       +      -
     37B  ILE*     3.6    29.2    -      -       +      -
     40B  PHE*     3.8    42.2    -      -       +      -
     56B  LEU*     6.0     3.4    -      -       +      -
     69B  LEU*     4.5    11.0    -      -       +      -
    134B  ILE*     2.8    26.9    +      -       +      +
    135B  ILE*     3.2     7.8    +      -       +      +
    137B  GLY*     1.3    72.3    -      -       -      +
    139B  ASN*     1.3    58.8    +      -       -      +
    141B  ILE*     3.2    15.7    +      -       +      +
    142B  VAL*     2.9    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 139 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  ILE*     4.4     7.9    -      -       +      +
    135B  ILE*     3.0    19.8    +      -       +      +
    136B  LEU*     3.7     6.6    +      -       -      +
    138B  LEU*     1.3    75.2    -      -       -      +
    140B  LYS*     1.3    61.8    +      -       -      +
    142B  VAL*     3.1    15.5    -      -       -      +
    143B  ARG*     3.0    43.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 140 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  MET*     3.6    34.1    -      -       +      +
     71B  GLU*     4.6     4.8    +      -       -      -
     72B  THR*     4.5     7.8    +      -       +      +
    136B  LEU*     3.2    17.0    +      -       +      +
    137B  GLY      3.2     9.3    +      -       -      +
    139B  ASN*     1.3    79.1    -      -       -      +
    141B  ILE*     1.3    58.3    +      -       -      +
    143B  ARG*     3.1    36.3    -      -       -      +
    144B  MET*     2.7    49.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 141 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  PHE*     3.6    32.5    -      -       +      -
     65B  ALA*     3.4    38.1    -      -       +      +
     68B  MET*     3.7    22.7    -      -       +      -
     69B  LEU*     4.5     7.9    -      -       +      +
    137B  GLY      2.9    24.6    +      -       -      +
    138B  LEU*     3.2    21.5    +      -       +      +
    140B  LYS*     1.3    73.7    -      -       -      +
    142B  VAL*     1.3    68.7    +      -       +      +
    144B  MET*     3.2     5.4    +      -       -      +
    145B  TYR*     3.0    25.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 142 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  PHE*     3.3    31.7    -      -       +      +
     33B  SER      3.8    15.3    -      -       -      +
     34B  PRO*     4.3    14.6    -      -       +      -
     36B  VAL*     5.6     0.7    -      -       +      -
     37B  ILE*     3.8    15.3    -      -       +      -
    138B  LEU      2.9    19.2    +      -       -      +
    139B  ASN*     3.1    23.8    -      -       -      +
    141B  ILE*     1.3    76.7    -      -       +      +
    143B  ARG*     1.3    77.9    +      -       +      +
    145B  TYR      3.2    20.0    +      -       -      +
    146B  SER*     4.8     1.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199A  LYS*     5.8     6.1    -      -       -      +
    139B  ASN*     3.0    28.2    +      -       -      +
    140B  LYS*     3.1    36.9    -      -       -      +
    142B  VAL*     1.3    85.0    -      -       +      +
    144B  MET*     1.3    84.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  MET*     5.5     7.6    -      -       +      -
    140B  LYS*     2.7    53.4    +      -       +      +
    141B  ILE*     3.2     4.9    +      -       -      +
    143B  ARG*     1.3   117.4    -      -       -      +
    145B  TYR*     1.3    65.8    +      -       +      +
    146B  SER      4.1     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 145 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  PHE*     3.8    34.7    -      +       +      +
    141B  ILE*     3.0    16.2    +      -       +      +
    142B  VAL*     3.2    13.4    +      -       -      +
    144B  MET*     1.3    85.0    -      -       +      +
    146B  SER*     1.3    90.4    +      -       -      +
    147B  PRO*     4.3     1.6    -      -       -      +
    148B  THR*     5.7     3.6    -      -       -      -
    152B  ASP*     2.8    35.1    +      -       -      -
    153B  ILE*     6.0     1.2    -      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il