Contacts of the strand formed by residues 163 - 171 (chain B) in PDB entry 4A12


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 HIS 163 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134B  HIS*     3.1    29.8    +      +       +      -
    159B  GLN*     3.4     2.3    -      -       -      -
    160B  THR*     2.8    46.1    +      -       -      +
    162B  LYS*     1.4    96.0    -      -       +      +
    164B  TYR*     1.3    58.8    +      -       -      +
    165B  TYR*     4.1    17.8    +      -       +      -
    183B  LYS*     3.6    41.3    -      -       +      -
    184B  MSE      3.3     4.3    -      -       -      +
    185B  PHE*     3.7    24.8    -      +       +      +
    186B  TYR*     3.4     8.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 164 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  ASN*     3.4    43.1    +      -       +      +
    126B  ILE*     3.8    42.2    -      -       +      -
    128B  GLN*     4.0    10.5    +      -       +      -
    156B  VAL*     3.7    25.4    -      -       +      -
    158B  ASN      3.7     2.2    -      -       -      -
    159B  GLN*     3.0    36.0    +      -       +      -
    163B  HIS*     1.3    70.7    -      -       -      +
    165B  TYR*     1.3    61.8    -      -       -      +
    166B  VAL*     3.8     1.5    +      -       +      -
    182B  PHE      3.5     2.3    -      -       -      +
    183B  LYS*     3.8     1.2    -      -       -      -
    184B  MSE      2.7    38.5    +      -       +      +
    186B  TYR*     3.4    46.4    -      +       +      -
    188B  LYS*     5.7     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 165 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156B  VAL*     3.5     3.5    -      -       -      -
    157B  VAL*     2.7    40.8    +      -       +      -
    158B  ASN*     2.7    49.6    +      -       +      +
    159B  GLN      4.4     0.7    -      -       -      -
    160B  THR*     3.7    29.0    +      -       +      +
    163B  HIS*     4.1    18.0    +      -       +      +
    164B  TYR*     1.3    72.0    -      -       -      +
    166B  VAL*     1.3    55.8    +      -       -      +
    182B  PHE      3.4     6.5    -      -       -      +
    183B  LYS*     3.6    47.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 166 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122B  CYS*     3.8    19.3    -      -       -      -
    125B  LEU*     3.8     7.9    -      -       +      -
    126B  ILE*     3.8    28.9    -      -       +      -
    154B  ALA*     3.8    28.9    -      -       +      -
    155B  ARG      3.4    11.2    -      -       -      +
    156B  VAL*     4.4    11.9    -      -       +      -
    157B  VAL*     4.7     1.1    -      -       -      -
    164B  TYR      4.3     3.1    -      -       -      +
    165B  TYR*     1.3    76.9    -      -       -      +
    167B  GLU*     1.3    65.9    +      -       -      +
    168B  VAL*     5.0     0.2    -      -       -      -
    180B  GLY      3.7     0.9    -      -       -      +
    181B  ASN*     3.4     4.0    -      -       -      +
    182B  PHE*     2.7    42.4    +      -       +      +
    184B  MSE      4.1    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 167 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153B  GLU      3.7     1.7    -      -       -      +
    154B  ALA*     3.4     1.4    -      -       -      -
    155B  ARG*     2.9    38.5    +      -       +      +
    157B  VAL*     3.7    35.4    -      -       +      +
    166B  VAL*     1.3    72.3    -      -       -      +
    168B  VAL*     1.3    62.3    +      -       -      +
    169B  LYS*     3.5    25.9    +      -       -      +
    180B  GLY      3.5     2.9    -      -       -      +
    181B  ASN*     3.3    26.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 168 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118B  ALA*     3.9    24.7    -      -       +      +
    121B  LEU*     4.7     2.2    -      -       +      -
    122B  CYS*     3.7    30.1    -      -       -      -
    152B  ALA*     4.5     6.5    -      -       +      -
    153B  GLU      3.4    12.1    -      -       -      +
    154B  ALA*     3.8    11.2    -      -       +      -
    166B  VAL*     4.3     1.1    -      -       +      -
    167B  GLU*     1.3    76.6    -      -       -      +
    169B  LYS*     1.3    66.5    +      -       -      +
    170B  SER*     4.1    15.0    -      -       -      +
    178B  PHE*     4.5     3.1    -      -       +      -
    179B  LYS*     3.4     5.8    -      -       -      +
    180B  GLY*     2.6    38.6    +      -       -      +
    182B  PHE*     3.8    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 169 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153B  GLU*     2.9    42.2    +      -       +      +
    155B  ARG*     4.5    15.5    -      -       -      +
    167B  GLU*     3.5    31.2    +      -       -      +
    168B  VAL*     1.3    77.3    -      -       -      +
    170B  SER*     1.3    60.5    +      -       -      +
    171B  TYR*     3.4    32.8    -      -       +      +
    176B  LEU*     3.8    12.8    -      -       +      -
    178B  PHE      3.6     3.8    -      -       -      -
    179B  LYS*     3.8    29.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 170 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  LEU*     4.8     3.1    +      -       -      +
    117B  GLN*     4.4     2.3    +      -       -      -
    118B  ALA*     5.3     0.9    -      -       -      +
    150B  VAL*     3.6    22.2    -      -       -      +
    151B  ARG      3.4     4.3    -      -       -      -
    152B  ALA*     3.3    20.9    -      -       -      +
    168B  VAL*     4.1     3.3    -      -       -      +
    169B  LYS*     1.3    73.0    -      -       -      +
    171B  TYR*     1.3    61.0    +      -       -      +
    176B  LEU*     3.6     5.2    -      -       -      +
    177B  VAL*     3.0    25.1    +      -       -      -
    178B  PHE*     2.9    41.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 171 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149B  THR      3.7     0.7    -      -       -      +
    150B  VAL*     3.5     4.9    -      -       -      -
    151B  ARG*     2.8    77.4    +      -       -      +
    153B  GLU*     3.3    24.5    +      -       +      -
    169B  LYS*     3.4    42.6    -      -       +      +
    170B  SER*     1.3    72.5    -      -       -      +
    172B  VAL*     1.3    63.2    +      -       -      +
    173B  LYS      4.2     0.6    +      -       -      -
    174B  HIS*     4.3     7.2    -      -       +      -
    175B  THR      3.3    16.6    -      -       -      +
    176B  LEU*     3.5    39.5    -      -       +      +
    177B  VAL*     4.1     0.9    -      -       -      -
----------------------------------------------------------
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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