Contacts of the strand formed by residues 176 - 187 (chain A) in PDB entry 2VIG


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 SER 176 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172A  ALA*     3.5     6.6    -      -       -      +
    173A  GLU      3.0    28.0    +      -       -      -
    174A  GLY      3.2     2.2    -      -       -      +
    175A  ASP*     1.3    94.1    +      -       -      +
    177A  TRP*     1.3    68.2    +      -       -      +
    178A  VAL*     5.1     1.6    -      -       -      -
    247A  ARG*     3.1    39.8    +      -       -      +
    248A  ILE      3.4    15.2    +      -       -      -
    249A  PRO*     4.5     4.5    -      -       -      +
    250A  LYS*     4.3     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 177 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  ALA*     4.5     5.6    -      -       +      -
    171A  ARG      3.4     7.2    -      -       -      -
    172A  ALA*     3.8    36.6    -      -       +      -
    176A  SER*     1.3    78.0    -      -       -      +
    178A  VAL*     1.3    63.0    +      -       -      +
    179A  LEU*     4.1    10.3    -      -       +      -
    201A  THR*     4.2    19.3    -      -       +      -
    213A  PHE*     3.5    29.4    -      +       +      -
    246A  CYS      3.4     1.6    -      -       -      +
    247A  ARG*     3.4     3.8    -      -       -      -
    248A  ILE*     3.0    42.1    +      -       +      +
    249A  PRO      3.8    19.3    -      -       -      -
    250A  LYS*     3.2    25.7    +      -       +      +
    253A  ILE*     3.9    28.8    -      -       +      +
    257A  PRO*     4.7    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 178 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  THR*     3.6     2.4    +      -       -      +
    170A  ALA*     3.3     2.6    -      -       -      -
    171A  ARG*     2.9    55.9    +      -       -      +
    173A  GLU*     3.7    29.4    -      -       +      -
    176A  SER*     5.1     0.7    -      -       -      -
    177A  TRP*     1.3    78.5    -      -       -      +
    179A  LEU*     1.3    64.3    +      -       -      +
    180A  ASN*     4.0    12.0    +      -       -      +
    245A  ASP*     3.9    32.3    -      -       +      +
    246A  CYS      3.4     3.6    -      -       -      +
    247A  ARG*     4.7    16.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 179 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168A  THR*     5.2     2.2    -      -       +      -
    169A  THR      3.2     8.5    -      -       -      +
    170A  ALA*     3.8    21.8    -      -       +      -
    177A  TRP*     4.1     9.0    -      -       +      -
    178A  VAL*     1.3    80.0    -      -       -      +
    180A  ASN*     1.3    66.5    +      -       -      +
    197A  VAL*     4.3    14.1    -      -       +      -
    199A  ALA*     4.7     4.7    -      -       +      -
    213A  PHE*     4.7     8.3    -      -       +      -
    215A  VAL*     4.2     9.4    -      -       +      -
    243A  PHE*     3.6    42.1    -      -       +      +
    245A  ASP      3.5     1.9    +      -       -      -
    246A  CYS      2.9    34.0    +      -       -      +
    248A  ILE*     3.9    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 180 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  SER      4.3     1.7    -      -       -      +
    168A  THR*     3.4     5.0    -      -       -      -
    169A  THR*     2.9    46.1    +      -       -      +
    171A  ARG*     4.3    13.5    -      -       -      +
    178A  VAL*     4.0    16.0    +      -       -      +
    179A  LEU*     1.3    80.1    +      -       -      +
    181A  GLY*     1.3    59.1    +      -       -      +
    243A  PHE*     3.5     3.7    -      -       -      +
    244A  GLU*     3.5     9.4    -      -       -      +
    245A  ASP*     2.9    35.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  SER      5.4     0.7    -      -       -      -
    168A  THR*     3.4    15.9    -      -       -      -
    180A  ASN*     1.3    75.1    -      -       -      +
    182A  THR*     1.3    61.6    +      -       -      -
    183A  LYS      4.2     0.2    -      -       -      -
    242A  ILE*     3.7     0.8    -      -       -      -
    243A  PHE*     2.8    42.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  GLU*     3.5    14.7    -      -       -      +
    157A  PRO*     3.6    22.5    -      -       +      +
    168A  THR*     3.3    11.2    +      -       -      -
    181A  GLY*     1.3    74.0    +      -       -      -
    183A  LYS*     1.3    73.4    +      -       -      +
    240A  ASN*     3.7    27.4    -      -       +      +
    241A  LEU      3.4     4.7    -      -       -      +
    242A  ILE*     4.0    20.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  ALA*     3.4    40.6    +      -       +      -
    154A  LEU*     3.2    27.1    +      -       -      +
    155A  SER      3.3     9.0    -      -       -      +
    156A  GLU*     2.7    21.3    +      -       -      +
    166A  ALA*     4.2     4.6    -      -       -      +
    168A  THR*     3.4    25.5    -      -       +      +
    182A  THR*     1.3    75.1    -      -       -      +
    184A  ALA*     1.3    60.0    +      -       -      +
    186A  ILE*     4.0     7.6    -      -       +      -
    197A  VAL*     4.5     3.1    -      -       +      -
    198A  PHE*     2.6    27.8    +      -       -      +
    240A  ASN*     3.1    11.1    -      -       -      +
    241A  LEU*     2.8    32.3    +      -       +      +
    243A  PHE*     4.1    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  SER*     2.9    17.5    +      -       -      +
    156A  GLU*     3.6     5.3    -      -       -      +
    157A  PRO*     3.5    32.8    -      -       +      -
    183A  LYS*     1.3    71.5    -      -       -      +
    185A  TRP*     1.3    84.3    +      -       +      +
    186A  ILE*     3.2    17.8    -      -       -      +
    228A  GLU*     5.9     0.4    -      -       -      +
    240A  ASN*     3.3    17.3    -      -       -      +
    501A  FAD      4.2     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 185 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  SER*     4.0     8.7    -      -       -      -
    156A  GLU      4.4     6.6    +      -       -      -
    157A  PRO*     5.3     3.6    +      -       +      +
    184A  ALA*     1.3    96.6    -      -       +      +
    186A  ILE*     1.3    61.9    +      -       -      +
    187A  THR      3.2     0.2    +      -       -      -
    228A  GLU*     4.0    27.0    +      -       +      -
    230A  LYS*     6.6     0.2    -      -       +      -
    238A  THR*     3.4    16.6    -      -       +      +
    239A  ALA*     3.8     6.3    +      -       -      +
    240A  ASN*     3.9     3.6    +      -       -      -
    501A  FAD      2.9    89.5    +      +       +      +
    297B  ARG*     6.0     0.6    -      -       -      +
    369B  GLY*     3.4    35.2    -      -       -      -
    370B  MET*     3.7    27.1    -      -       +      -
    373B  VAL*     3.8    26.0    -      -       +      -
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Residues in contact with ILE 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  CYS*     3.6    35.7    -      -       +      -
    152A  PHE      3.7    16.4    -      -       -      +
    153A  ALA*     3.6    31.4    -      -       +      -
    154A  LEU      4.3     0.9    -      -       -      +
    155A  SER      4.5     0.2    -      -       -      +
    183A  LYS*     4.0    11.7    -      -       +      -
    184A  ALA      3.2    25.4    -      -       -      +
    185A  TRP*     1.3    74.6    -      -       -      +
    187A  THR*     1.3    63.3    +      -       -      +
    189A  ALA*     3.2    17.7    +      -       +      +
    238A  THR*     3.3     3.7    -      -       -      -
    239A  ALA      3.0    27.1    +      -       -      +
    241A  LEU*     3.9    20.4    -      -       +      -
    501A  FAD      3.8    10.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  VAL*     4.2    17.6    -      -       +      +
    118A  VAL*     3.7    25.8    -      -       +      +
    151A  CYS*     3.3    19.6    -      -       -      +
    185A  TRP      3.2     1.8    +      -       -      -
    186A  ILE*     1.3    70.9    -      -       -      +
    188A  ASN*     1.3    81.0    +      -       -      +
    189A  ALA      3.2     0.4    -      -       -      -
    233A  ILE*     5.6     0.9    -      -       -      +
    236A  SER*     4.1    18.1    +      -       -      +
    237A  SER      3.1     9.9    -      -       -      +
    238A  THR*     4.5     2.9    +      -       -      +
    391A  TYR*     4.9     0.5    -      -       -      -
    501A  FAD      3.0    43.4    +      -       -      +
----------------------------------------------------------
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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