Contacts of the strand formed by residues 238 - 249 (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 THR 238 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  TRP*     3.4    39.7    -      -       +      +
    186A  ILE      3.3     4.0    -      -       -      +
    187A  THR*     4.4     1.3    +      -       -      +
    227A  LYS*     3.4     3.5    -      -       -      +
    228A  GLU*     2.8    44.6    +      -       +      +
    230A  LYS*     2.8    34.8    +      -       -      +
    236A  SER*     3.9     2.7    +      -       -      -
    237A  SER*     1.3    76.1    +      -       -      +
    239A  ALA*     1.3    63.2    +      -       -      +
    501A  FAD      3.9    23.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  TRP      3.8     2.6    +      -       -      +
    186A  ILE*     3.0    36.0    +      -       -      +
    189A  ALA*     3.9     6.1    -      -       +      +
    190A  TRP*     3.4    22.0    -      -       +      +
    224A  LEU*     5.3     0.2    -      -       +      -
    225A  GLY      3.4    23.3    -      -       -      +
    226A  LYS      3.4     9.6    -      -       -      +
    228A  GLU*     4.7     5.6    -      -       -      -
    238A  THR*     1.3    79.8    -      -       -      +
    240A  ASN*     1.3    69.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157A  PRO*     4.6     6.5    -      -       -      +
    182A  THR*     3.7    20.7    -      -       +      +
    183A  LYS      3.1    14.8    -      -       -      +
    184A  ALA*     3.3    23.0    -      -       -      +
    185A  TRP      3.9     1.4    +      -       -      -
    224A  LEU*     3.4     8.8    -      -       -      +
    225A  GLY*     2.7    40.5    +      -       -      +
    226A  LYS      4.7     1.0    +      -       -      -
    228A  GLU*     4.3    11.7    +      -       -      +
    239A  ALA*     1.3    75.7    -      -       -      +
    241A  LEU*     1.3    57.7    -      -       -      +
    242A  ILE*     4.0     7.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  CYS*     4.5     2.2    -      -       -      -
    153A  ALA*     4.1    22.0    -      -       +      -
    181A  GLY      3.7     2.4    -      -       -      +
    182A  THR*     3.4     2.3    -      -       -      -
    183A  LYS*     2.8    41.0    +      -       +      -
    186A  ILE*     3.9    14.3    -      -       +      +
    189A  ALA*     3.7    32.1    -      -       +      -
    195A  ALA*     4.2    21.1    -      -       +      -
    217A  MET*     4.3    10.5    -      -       +      -
    222A  LEU*     3.9    17.5    -      -       +      -
    223A  THR      3.8     4.5    -      -       -      -
    224A  LEU*     3.8    12.6    -      -       +      -
    239A  ALA      3.8     0.6    +      -       -      -
    240A  ASN*     1.3    69.5    -      -       -      +
    242A  ILE*     1.3    60.5    +      -       -      +
    243A  PHE*     3.9    21.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  GLY      3.7     2.5    -      -       -      -
    182A  THR*     4.0    27.8    -      -       +      +
    221A  GLY      3.4     4.3    -      -       -      +
    222A  LEU*     3.4     2.3    -      -       -      +
    223A  THR*     2.8    56.7    +      -       -      +
    224A  LEU      4.0     2.5    -      -       -      +
    225A  GLY*     3.8    29.6    -      -       -      +
    240A  ASN*     4.3     6.1    -      -       +      +
    241A  LEU*     1.3    73.7    -      -       -      +
    243A  PHE*     1.3    69.2    +      -       -      +
    244A  GLU*     4.0     5.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168A  THR*     4.8     6.7    -      -       +      -
    179A  LEU*     3.6    39.3    -      -       +      +
    180A  ASN*     3.5     2.0    -      -       -      +
    181A  GLY*     2.8    45.6    +      -       -      +
    183A  LYS*     4.1     9.6    -      -       +      -
    197A  VAL*     3.9    37.2    -      -       +      -
    215A  VAL*     4.1    18.4    -      -       +      -
    221A  GLY      3.2     4.7    -      -       -      +
    222A  LEU*     3.9    23.3    -      -       +      -
    241A  LEU*     3.9    27.8    -      -       +      -
    242A  ILE*     1.3    74.1    -      -       -      +
    244A  GLU*     1.3    60.1    +      -       -      +
    246A  CYS*     3.8    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 244 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  ASN*     3.5     7.4    -      -       -      +
    221A  GLY*     2.8    25.0    +      -       -      +
    242A  ILE*     4.0     6.4    +      -       +      -
    243A  PHE*     1.3    74.0    -      -       -      +
    245A  ASP*     1.3    84.3    +      -       -      +
    246A  CYS      3.2     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 245 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171A  ARG*     6.3     0.4    -      -       -      -
    178A  VAL*     3.9    19.0    -      -       +      +
    179A  LEU      3.5     0.4    +      -       -      -
    180A  ASN*     2.9    23.2    +      -       -      +
    220A  PRO      4.9     0.9    -      -       -      +
    221A  GLY*     4.6     2.3    -      -       -      -
    244A  GLU*     1.3    87.3    -      -       +      +
    246A  CYS*     1.3    61.4    +      -       -      +
    247A  ARG*     3.4     5.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 246 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  TRP      3.4     4.3    -      -       -      +
    178A  VAL*     4.2     0.9    -      -       -      -
    179A  LEU*     2.9    43.2    +      -       +      +
    215A  VAL*     4.9     0.2    -      -       -      -
    219A  THR*     3.6    23.6    -      -       -      -
    220A  PRO      3.5    21.1    -      -       -      -
    221A  GLY      3.7    19.7    -      -       -      +
    243A  PHE*     3.8    24.9    -      -       +      -
    244A  GLU      4.0     0.4    -      -       -      -
    245A  ASP*     1.3    72.7    -      -       -      +
    247A  ARG*     1.3    59.6    +      -       -      +
    248A  ILE*     3.8    13.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  GLU*     4.1    11.1    +      -       -      +
    174A  GLY*     5.8     0.4    -      -       -      -
    175A  ASP*     3.2    23.4    +      -       -      -
    176A  SER*     3.1    35.3    +      -       -      +
    177A  TRP      3.4     6.3    -      -       -      +
    178A  VAL*     4.5    12.3    -      -       +      +
    219A  THR*     4.8     5.5    +      -       -      -
    220A  PRO*     4.4     5.7    +      -       -      +
    245A  ASP      3.4     7.0    +      -       -      +
    246A  CYS*     1.3    74.2    -      -       -      +
    248A  ILE*     1.3    67.3    +      -       -      +
    249A  PRO*     4.8     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  SER*     3.4     5.7    -      -       -      -
    177A  TRP*     3.0    45.0    +      -       +      +
    179A  LEU*     3.9    25.6    -      -       +      -
    213A  PHE*     3.9    24.0    -      -       +      -
    214A  LEU      4.4     1.3    -      -       -      +
    215A  VAL*     4.0    22.4    -      -       +      -
    216A  PRO*     4.9     7.6    -      -       +      -
    219A  THR*     5.0     4.0    -      -       +      +
    246A  CYS*     4.2    20.0    -      -       -      +
    247A  ARG*     1.3    80.8    -      -       -      +
    249A  PRO*     1.3    70.9    -      -       +      +
    252A  SER*     3.7    23.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175A  ASP      4.5     0.2    -      -       -      +
    176A  SER*     4.5     7.0    -      -       -      +
    177A  TRP*     3.8     3.5    -      -       -      -
    216A  PRO*     6.1     2.9    -      -       +      -
    247A  ARG      4.8     0.7    -      -       -      +
    248A  ILE*     1.3    88.3    -      -       +      +
    250A  LYS*     1.3    65.2    +      -       -      +
    251A  ASP*     3.3     4.5    -      -       +      +
    252A  SER*     2.6    38.3    +      -       -      +
----------------------------------------------------------
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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