Contacts of the strand formed by residues 478 - 484 (chain B) in PDB entry 2V3D


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 478 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  ILE*     3.7     5.8    -      -       -      +
     57B  GLN      3.2     9.9    -      -       -      -
     58B  ALA*     4.7     4.9    -      -       -      -
    472B  ILE      3.9     0.7    -      -       -      +
    473B  LYS*     3.7     1.5    -      -       -      -
    474B  ASP*     2.8    39.2    +      -       -      +
    475B  PRO      4.8     0.8    -      -       -      -
    477B  VAL*     1.3    81.7    -      -       -      +
    479B  PHE*     1.3    70.6    -      -       -      -
    480B  LEU*     4.5     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 479 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  PRO      4.1     0.2    -      -       -      +
     56B  ILE*     3.4     4.7    -      -       -      +
     57B  GLN*     2.7    46.2    +      -       +      +
     58B  ALA      3.5    26.9    -      -       -      -
     59B  ASN*     3.6    11.9    -      -       -      +
     60B  HIS*     3.3    42.6    -      +       +      -
     66B  LEU*     4.2     5.8    -      -       +      -
    471B  THR*     3.9    18.2    -      -       +      -
    472B  ILE      3.3     3.8    -      -       -      -
    473B  LYS*     3.5    51.1    -      -       +      -
    478B  GLY*     1.3    77.4    -      -       -      -
    480B  LEU*     1.3    63.7    +      -       -      +
    481B  GLU*     4.0     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 480 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  PHE*     3.5    47.8    -      -       +      -
     55B  PRO      4.5     0.4    -      -       -      -
     56B  ILE*     4.2    17.0    -      -       +      -
    471B  THR*     3.2     7.4    -      -       -      +
    472B  ILE*     2.8    51.4    +      -       +      +
    477B  VAL*     5.2     0.7    -      -       +      -
    478B  GLY      4.5     4.7    -      -       -      +
    479B  PHE*     1.3    77.2    -      -       -      +
    481B  GLU*     1.3    61.6    +      -       -      +
    482B  THR*     3.8     4.6    +      -       +      +
    492B  TYR*     4.1    12.8    -      -       +      -
    494B  TRP*     3.7    47.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 481 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  PHE*     4.4    12.8    -      -       -      -
     39B  ARG*     4.4     2.8    +      -       -      -
     55B  PRO*     4.8     3.1    +      -       -      +
     57B  GLN*     4.5    20.4    -      -       +      +
     59B  ASN      4.6     2.4    -      -       -      +
     60B  HIS*     2.6    40.1    +      -       -      +
    470B  LEU      3.9     2.1    -      -       -      +
    471B  THR*     2.8    27.6    +      -       +      +
    479B  PHE*     4.0     2.4    +      -       -      +
    480B  LEU*     1.3    70.4    -      -       -      +
    482B  THR*     1.3    62.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 482 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  PHE*     5.0     2.0    -      -       -      -
     39B  ARG*     3.0    23.5    +      -       -      +
    469B  PRO*     3.7     5.0    -      -       -      +
    470B  LEU*     2.8    54.2    +      -       +      +
    472B  ILE*     4.7     7.6    -      -       +      -
    480B  LEU*     4.6     7.0    -      -       +      +
    481B  GLU*     1.3    77.6    -      -       -      +
    483B  ILE*     1.3    70.5    +      -       -      +
    492B  TYR*     2.6    42.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 483 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  ARG*     5.6     3.6    -      -       -      +
    467B  ASP*     3.7    25.4    -      -       +      +
    468B  VAL      3.4     9.4    -      -       -      +
    469B  PRO*     3.3    37.7    -      -       +      -
    470B  LEU*     3.8     4.5    -      -       -      -
    482B  THR*     1.3    83.9    +      -       -      +
    484B  SER*     1.3    59.2    +      -       -      +
    485B  PRO*     3.3    18.0    -      -       +      +
    490B  HIS*     3.2    26.3    +      -       +      -
    492B  TYR*     3.8     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 484 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444B  LEU*     3.7    16.6    -      -       -      +
    460B  VAL*     4.0    13.5    +      -       -      +
    462B  ASN*     2.8    42.6    +      -       -      +
    468B  VAL      2.7    30.6    +      -       -      -
    470B  LEU*     3.6    11.2    -      -       -      +
    483B  ILE*     1.3    72.3    -      -       -      +
    485B  PRO*     1.3    62.1    -      -       -      +
    488B  SER*     3.8     5.0    +      -       -      -
    490B  HIS*     4.6     5.2    +      -       -      -
    492B  TYR*     6.0     0.2    -      -       -      -
----------------------------------------------------------
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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