Contacts of the strand formed by residues 142 - 152 (chain B) in PDB entry 1MWA


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 LYS 142 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  MET*     3.6    22.5    -      -       +      +
    172A  ALA*     5.4     4.0    -      -       -      +
    175A  SER*     4.3    13.6    +      -       -      +
    136B  GLU*     3.5     7.5    -      -       -      +
    137B  ILE*     3.1    28.3    +      -       -      +
    140B  LYS*     3.0    23.6    -      -       +      +
    141B  GLN*     1.3    81.6    -      -       -      +
    143B  ALA*     1.3    60.0    +      -       -      +
    197B  ARG*     3.2    45.8    -      -       +      +
    198B  VAL      3.4     9.9    -      -       -      +
    199B  SER*     4.5     2.9    -      -       -      -
    200B  ALA      4.2     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132B  PRO*     4.0    20.9    -      -       +      -
    136B  GLU*     3.8     2.2    -      -       -      -
    137B  ILE*     4.1     5.8    -      -       +      -
    142B  LYS*     1.3    76.6    -      -       -      +
    144B  THR*     1.3    61.2    +      -       -      +
    145B  LEU*     3.6     3.0    +      -       +      +
    196B  LEU      3.3     2.9    -      -       -      +
    197B  ARG*     3.0    23.3    -      -       -      -
    198B  VAL*     2.6    22.6    +      -       +      +
    199B  SER      3.8    10.1    -      -       -      +
    200B  ALA*     4.9     0.2    -      -       -      -
    203B  TRP*     3.9    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  LEU*     3.4    19.6    -      -       -      +
    142A  LEU*     3.5    23.4    -      -       +      +
    144A  THR*     5.1     0.5    +      -       -      +
    132B  PRO*     3.7    10.3    -      -       -      +
    136B  GLU*     2.6    35.2    +      -       -      +
    143B  ALA*     1.3    72.3    -      -       -      +
    145B  LEU*     1.3    72.1    +      -       -      +
    146B  VAL*     5.1     2.0    -      -       +      -
    195B  ARG*     3.8    31.3    +      -       +      +
    196B  LEU      3.6     4.5    -      -       -      +
    197B  ARG*     3.1    21.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 145 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129B  LEU*     4.4    17.0    -      -       +      -
    130B  PHE      3.8     7.4    -      -       -      +
    131B  GLU*     5.2     0.7    -      -       -      -
    132B  PRO*     4.1    17.0    -      -       +      -
    143B  ALA*     4.1    10.1    -      -       +      +
    144B  THR*     1.3    75.7    -      -       -      +
    146B  VAL*     1.3    59.2    +      -       -      +
    161B  TRP*     4.1    17.3    -      -       +      -
    195B  ARG*     3.4     4.2    -      -       -      -
    196B  LEU*     2.8    44.0    +      -       +      +
    198B  VAL*     4.4    13.0    -      -       +      -
    203B  TRP*     4.1    27.1    -      -       +      -
    210B  PHE*     3.8    38.6    -      -       +      -
    241B  ALA*     4.6     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 146 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  LEU*     3.3    25.4    -      -       +      -
    140A  LEU*     3.8    24.0    -      -       +      -
    142A  LEU*     5.7     2.0    -      -       +      -
    181A  ILE*     3.7    26.7    -      -       +      -
    129B  LEU*     3.8     3.9    -      -       -      -
    130B  PHE*     2.9    65.8    +      -       +      +
    144B  THR*     4.8     5.2    -      -       +      +
    145B  LEU*     1.3    75.1    -      -       -      +
    147B  CYS*     1.3    69.1    +      -       -      +
    148B  LEU*     5.0     0.2    -      -       +      -
    193B  SER*     4.9     1.1    -      -       -      -
    194B  SER      3.3     9.6    -      -       -      +
    195B  ARG*     5.1     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 147 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  VAL*     4.4     8.5    -      -       -      -
    128B  SER      3.9     9.2    -      -       -      -
    129B  LEU*     4.3     1.3    -      -       -      -
    146B  VAL*     1.3    72.3    -      -       -      +
    148B  LEU*     1.3    68.6    +      -       -      +
    159B  LEU*     4.0    12.2    -      -       +      +
    161B  TRP*     3.4    20.0    -      -       +      -
    192B  LEU      4.7     0.2    -      -       -      -
    193B  SER*     3.0     5.5    -      -       -      -
    194B  SER*     2.6    39.3    +      -       -      +
    212B  CYS*     2.0    52.0    -      -       +      -
    214B  VAL*     4.7     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 148 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  LEU*     3.8    26.5    -      -       +      -
    183A  TRP*     4.0    32.5    -      -       +      -
    126B  LYS      3.8     0.9    -      -       -      +
    127B  VAL*     3.4     4.3    -      -       -      +
    128B  SER*     3.2    30.9    +      -       -      +
    130B  PHE*     4.0    25.6    -      -       +      -
    146B  VAL      3.9     0.2    +      -       -      -
    147B  CYS*     1.3    79.4    -      -       -      +
    149B  ALA*     1.3    72.8    +      -       -      +
    150B  ARG*     3.9    28.8    +      -       +      +
    191B  CYS*     4.8     0.2    -      -       +      -
    192B  LEU      3.5    12.6    -      -       -      +
    193B  SER*     3.9    14.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 149 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125B  PRO*     4.5     4.5    -      -       +      -
    126B  LYS      3.4     5.8    -      -       -      +
    127B  VAL*     4.4     1.6    -      -       +      +
    147B  CYS*     5.1     0.2    -      -       -      -
    148B  LEU*     1.3    73.9    -      -       -      +
    150B  ARG*     1.3    62.1    +      -       -      +
    152B  PHE*     3.4    18.1    -      -       +      -
    159B  LEU*     5.0     2.7    -      -       +      -
    191B  CYS*     3.0     7.3    -      -       -      +
    192B  LEU*     2.7    47.0    +      -       +      +
    214B  VAL*     4.2    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 150 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  THR*     6.1     0.8    -      -       -      +
    183A  TRP*     3.1    40.9    -      -       -      +
    184A  SER      6.1     1.0    -      -       -      -
    185A  ASN*     6.1     1.0    -      -       -      +
    125B  PRO*     3.5     0.9    -      -       -      +
    126B  LYS*     2.6    48.5    +      -       +      +
    148B  LEU*     3.9    21.0    -      -       +      +
    149B  ALA*     1.3    79.0    -      -       -      +
    151B  GLY*     1.3    60.3    +      -       -      +
    152B  PHE*     3.5     4.6    +      -       -      -
    181B  GLU*     2.5    40.9    +      -       -      +
    190B  TYR      3.8     4.7    -      -       -      -
    191B  CYS*     4.1     6.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 151 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  THR*     3.5    21.3    -      -       -      +
    124B  PRO      3.5     7.2    -      -       -      +
    126B  LYS*     4.9     4.3    -      -       -      -
    150B  ARG*     1.3    74.1    -      -       -      +
    152B  PHE*     1.3    62.4    +      -       -      +
    181B  GLU*     3.6     6.3    +      -       -      -
    187B  TYR      4.9     1.9    -      -       -      +
    189B  SER*     3.6    16.2    +      -       -      -
    190B  TYR      3.4     6.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 152 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  THR      2.9    15.9    -      -       -      +
    124B  PRO      3.7     1.1    +      -       -      -
    125B  PRO*     3.5    30.1    -      -       +      -
    149B  ALA*     3.4    27.1    -      -       +      -
    150B  ARG      3.5     4.9    +      -       -      -
    151B  GLY*     1.3    74.7    -      -       -      +
    153B  PHE*     1.3    64.1    +      -       -      +
    154B  PRO      4.4     0.4    -      -       -      -
    155B  ASP*     4.1     8.3    -      -       -      -
    157B  VAL*     4.0    30.7    -      -       +      -
    178B  ALA*     4.2     4.5    -      -       +      -
    189B  SER*     3.6     1.0    -      -       -      -
    190B  TYR*     2.7    73.8    +      +       +      -
    191B  CYS      3.7    10.3    -      -       -      -
    192B  LEU*     4.1    10.1    -      -       +      -
    216B  PHE*     3.9    11.0    -      -       +      -
----------------------------------------------------------
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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