Contacts of the strand formed by residues 135 - 147 (chain B) in PDB entry 4R95


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 GLY 135 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131B  PRO*     4.4     0.2    -      -       -      +
    132B  TYR*     2.8    48.3    +      -       -      +
    133B  THR      3.3     2.0    -      -       -      -
    134B  GLN*     1.3    77.8    -      -       -      +
    136B  LYS*     1.4    67.4    +      -       -      +
    167B  ASP*     3.1    16.8    -      -       -      -
    168B  LYS*     4.3     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A  LEU      4.9     9.3    +      -       -      -
    275A  LYS      6.3     0.2    -      -       -      -
    276A  MET*     5.0     8.1    -      -       -      +
    304A  ALA*     4.6    17.8    -      -       -      +
    129B  TYR*     3.7    29.7    +      -       +      +
    130B  VAL      3.5     7.6    -      -       -      +
    131B  PRO*     3.9    18.2    -      -       +      -
    132B  TYR*     3.5     6.6    -      -       -      -
    135B  GLY*     1.4    79.5    -      -       -      +
    137B  TRP*     1.3    63.6    +      -       -      +
    138B  GLU*     6.2     0.2    -      -       +      -
    166B  SER*     3.3     6.1    -      -       -      -
    167B  ASP*     2.8    58.3    +      -       +      +
    169B  PHE*     3.8     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  ASN*     3.8    31.2    -      -       +      -
    100B  ALA*     3.8    13.6    -      -       +      +
    128B  VAL*     3.6    20.6    -      -       +      -
    129B  TYR*     4.3     0.3    -      -       -      -
    130B  VAL*     2.7    77.0    +      -       +      +
    132B  TYR*     4.0     8.5    -      +       -      -
    136B  LYS*     1.3    75.2    -      -       -      +
    138B  GLU*     1.3    63.6    +      -       -      +
    139B  GLY*     4.4     2.7    -      -       -      -
    161B  ALA*     3.4    34.5    -      -       +      -
    163B  ILE*     3.8    22.7    -      -       +      -
    165B  GLU      3.6     6.5    -      -       -      +
    166B  SER*     4.5     0.2    -      -       -      -
    169B  PHE*     3.5    39.0    -      +       +      -
    179B  ILE*     4.8     6.6    -      -       +      +
    502B  3KW      5.3     5.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 138 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307A  LYS*     3.0    41.2    +      -       -      -
    128B  VAL      3.3    13.8    -      -       -      +
    129B  TYR*     3.9    14.3    -      -       +      +
    136B  LYS*     6.2     0.7    -      -       +      -
    137B  TRP*     1.3    80.4    -      -       -      +
    139B  GLY*     1.3    64.9    +      -       -      +
    163B  ILE*     3.5     4.0    -      -       -      -
    164B  THR*     2.9    26.4    +      -       -      +
    165B  GLU*     2.8    42.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 139 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  GLY*     3.3     5.4    -      -       -      -
    128B  VAL*     2.9    44.1    +      -       -      +
    137B  TRP*     4.3     1.5    -      -       -      -
    138B  GLU*     1.3    78.6    -      -       -      +
    140B  GLU*     1.3    64.6    +      -       -      +
    162B  ALA      3.1    15.5    -      -       -      -
    163B  ILE*     4.2     0.2    -      -       -      -
    164B  THR*     3.9     8.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 140 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115B  ARG*     2.7    38.6    +      -       -      +
    121B  TYR*     5.8     0.7    -      -       -      +
    123B  ASP*     5.7     3.1    -      -       -      +
    126B  LYS      3.7     7.2    -      -       -      +
    127B  GLY*     5.2     3.4    -      -       -      -
    139B  GLY*     1.3    78.1    -      -       -      +
    141B  LEU*     1.3    65.5    +      -       -      +
    160B  ILE      3.7     0.7    -      -       -      +
    161B  ALA*     4.4     1.3    -      -       -      -
    162B  ALA*     2.8    38.3    +      -       -      +
    164B  THR*     4.1    20.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 141 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121B  TYR*     4.7     3.2    +      -       -      -
    123B  ASP*     3.7     8.1    -      -       -      +
    124B  LEU*     3.1    34.3    +      -       +      +
    125B  ARG      4.0     2.1    +      -       -      -
    126B  LYS*     2.9    44.7    +      -       +      +
    127B  GLY      4.2     3.6    -      -       -      +
    128B  VAL*     3.9    22.4    -      -       +      -
    140B  GLU*     1.3    74.9    -      -       -      +
    142B  GLY*     1.3    57.5    +      -       -      +
    159B  ASN*     5.8     0.2    -      -       +      -
    160B  ILE      3.7     3.8    -      -       -      +
    161B  ALA*     4.1    15.5    -      -       +      +
    189B  ARG      4.8     0.9    -      -       -      +
    190B  PRO*     3.7    23.8    -      -       +      -
    194B  LEU*     3.6    36.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 142 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121B  TYR*     4.4     9.6    -      -       -      -
    122B  ARG      3.0    15.5    -      -       -      -
    124B  LEU*     3.8    10.3    -      -       -      +
    141B  LEU*     1.3    76.6    -      -       -      +
    143B  THR*     1.3    64.8    +      -       -      +
    159B  ASN*     3.4     7.6    -      -       -      +
    160B  ILE*     2.8    32.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113B  TYR*     5.0     0.2    -      -       -      -
    121B  TYR*     3.6     4.1    -      -       -      -
    122B  ARG*     2.8    47.5    +      -       -      +
    124B  LEU*     4.1    16.8    -      -       +      -
    142B  GLY*     1.3    74.1    -      -       -      -
    144B  ASP*     1.3    64.7    +      -       -      +
    157B  ARG*     3.2    29.7    +      -       +      -
    158B  ALA      3.2    13.0    -      -       -      +
    159B  ASN*     3.4    25.1    -      -       -      +
    160B  ILE*     4.5     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  GLY*     3.3    12.7    -      -       -      +
    113B  TYR*     2.5    28.0    +      -       -      +
    118B  SER*     2.8    24.8    +      -       -      -
    120B  THR*     2.6    30.3    +      -       -      -
    121B  TYR*     3.6    10.0    -      -       -      -
    143B  THR*     1.3    73.9    +      -       -      +
    145B  LEU*     1.3    72.6    +      -       -      +
    146B  VAL*     3.6     3.5    -      -       -      +
    157B  ARG*     3.5    13.1    -      -       -      +
    158B  ALA      3.0    31.2    +      -       -      +
    160B  ILE*     3.6    14.0    -      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
     80B  THR      4.0     0.3    -      -       -      +
     81B  VAL*     3.4     3.6    -      -       -      -
     82B  GLY      2.9    28.6    +      -       -      +
     83B  SER*     4.0     9.4    -      -       -      +
    120B  THR*     3.9    32.5    -      -       +      +
    144B  ASP*     1.3    79.3    +      -       -      +
    146B  VAL*     1.3    59.2    +      -       -      +
    155B  THR*     3.8    21.5    -      -       +      -
    156B  VAL      3.4     4.3    -      -       -      +
    157B  ARG*     3.8    39.0    -      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
     79B  MET*     3.6    29.6    -      -       +      -
     80B  THR      3.4    10.8    -      -       -      +
     81B  VAL*     4.1     2.5    -      -       +      -
     99B  PHE*     3.8    26.2    -      -       +      -
    144B  ASP      3.6    12.1    -      -       -      +
    145B  LEU*     1.3    79.4    -      -       -      +
    147B  SER*     1.4    68.5    +      -       -      +
    154B  VAL      4.2     0.3    -      -       -      +
    155B  THR*     3.5     1.3    -      -       -      -
    156B  VAL*     2.8    38.4    +      -       -      +
    158B  ALA*     4.0    12.1    -      -       +      -
    160B  ILE*     3.9    12.8    -      -       +      -
    197B  PHE*     3.8    17.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 147 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79B  MET*     3.4     8.3    -      -       -      +
     80B  THR*     2.9    43.2    +      -       -      +
    145B  LEU      5.4     0.2    -      -       -      -
    146B  VAL*     1.4    75.2    +      -       -      +
    148B  ILE*     1.3    66.1    +      -       -      +
    149B  PRO*     4.0     4.5    -      -       -      -
    154B  VAL      3.7    11.7    -      -       -      -
    155B  THR*     2.9    28.5    +      -       -      +
    197B  PHE*     6.1     0.7    -      -       -      -
----------------------------------------------------------
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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