Contacts of the strand formed by residues 157 - 162 (chain B) in PDB entry 3GW5


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 VAL 157 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  PHE*     3.3    14.3    -      -       -      -
    155B  GLU*     2.7    19.7    +      -       +      +
    156B  ASP*     1.3    79.2    -      -       -      +
    158B  PHE*     1.3    57.9    +      -       -      +
    179B  GLY*     2.8    30.5    +      -       -      +
    180B  GLY*     3.3    37.5    -      -       -      +
    326B  GLU*     4.0    21.1    -      -       +      +
    327B  PHE      3.2    10.8    -      -       -      +
    328B  ASP*     3.8    31.0    -      -       +      +
    330B  ARG*     5.7     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 158 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  THR*     3.7    13.5    -      -       +      -
    130B  MET*     3.6    39.5    -      -       +      -
    144B  PHE*     3.5    34.8    -      +       +      -
    157B  VAL*     1.3    76.5    -      -       -      +
    159B  SER*     1.3    60.8    +      -       -      +
    160B  PHE*     3.7    19.5    -      +       -      -
    176B  ILE*     4.8     0.9    -      -       +      -
    177B  VAL      3.0    14.4    -      -       -      +
    178B  LEU*     3.4    17.5    -      -       +      -
    180B  GLY      4.1     1.6    -      -       -      -
    201B  TRP*     3.9    20.2    -      +       -      -
    326B  GLU*     3.6     2.4    -      -       -      +
    327B  PHE*     2.8    62.5    +      +       +      -
    329B  ARG*     4.9     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 159 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158B  PHE*     1.3    73.4    -      -       -      +
    160B  PHE*     1.3    63.5    +      -       -      +
    161B  TYR      4.3     0.2    -      -       -      -
    175B  GLN      4.4     0.2    -      -       -      -
    176B  ILE*     3.1    12.8    -      -       -      +
    177B  VAL*     2.7    32.6    +      -       -      -
    180B  GLY      3.1    18.2    -      -       -      -
    181B  SER*     2.5    23.4    +      -       -      -
    324B  TYR*     2.7    32.5    -      -       -      -
    325B  THR      3.4     5.8    +      -       -      -
    326B  GLU*     3.8     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 160 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  LEU*     4.7     0.9    -      -       +      -
     37B  PHE*     3.6    17.3    -      -       +      -
     39B  THR*     4.3     2.0    -      -       +      -
    130B  MET*     4.8     3.8    -      -       +      -
    158B  PHE*     3.7    28.0    -      +       -      -
    159B  SER*     1.3    80.0    +      -       -      +
    161B  TYR*     1.3    59.0    +      -       -      +
    162B  TYR*     3.8    23.3    -      +       -      -
    175B  GLN      3.6     1.3    -      -       -      -
    176B  ILE*     3.4    37.7    -      -       +      -
    227B  THR*     3.5    43.3    -      -       +      -
    320B  ILE*     4.3    14.8    -      -       +      +
    324B  TYR*     3.7    11.4    -      -       -      -
    325B  THR*     2.9    34.4    +      -       -      +
    327B  PHE*     3.7    17.0    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 161 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160B  PHE*     1.3    73.8    -      -       -      +
    162B  TYR*     1.3    83.9    +      -       -      +
    163B  ASN*     3.3    42.6    +      -       +      -
    172B  LEU*     4.1     9.9    -      -       +      -
    174B  GLY*     3.2     2.0    -      -       -      -
    175B  GLN*     2.7    50.1    +      -       +      +
    185B  HIS*     3.4    48.8    +      +       +      -
    320B  ILE      5.7     0.4    -      -       -      -
    321B  ARG      5.3     0.2    -      -       -      -
    324B  TYR*     3.6    19.9    -      +       +      +
    339B  ALA*     4.3    14.6    -      -       +      -
    340B  ARG*     3.3    29.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 162 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  LEU*     3.6    25.9    -      -       +      +
     20B  TYR*     3.5    46.2    +      +       +      +
     36B  VAL*     5.9     0.7    -      -       -      +
     37B  PHE      4.4     2.1    +      -       -      -
    160B  PHE*     3.8    20.7    +      +       -      -
    161B  TYR*     1.3    93.4    -      -       -      +
    163B  ASN*     1.3    63.7    +      -       -      +
    164B  ARG*     5.2     0.3    -      -       -      +
    173B  GLY      4.2     0.4    -      -       -      -
    227B  THR*     2.7    34.5    +      -       -      -
    317B  ALA*     3.9    32.8    -      -       +      -
    320B  ILE*     3.7    34.1    +      -       +      +
    321B  ARG*     3.5    31.0    -      -       +      +
    400B  72X      4.1     1.0    -      -       -      -
----------------------------------------------------------
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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