Contacts of the strand formed by residues 488 - 494 (chain A) in PDB entry 2V3E


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 488 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  SER      3.3    12.1    -      -       -      -
     43A  THR*     4.0    13.9    -      -       -      -
    357A  TRP*     4.1     4.5    -      -       -      -
    460A  VAL      4.6     0.4    +      -       -      -
    461A  LEU*     3.6     3.9    -      -       -      +
    462A  ASN      3.0    27.3    +      -       -      +
    484A  SER*     3.9     6.4    +      -       -      -
    485A  PRO*     2.7    43.4    +      -       -      +
    487A  TYR*     1.3    79.4    -      -       -      +
    489A  ILE*     1.3    63.8    +      -       -      +
    490A  HIS*     3.8    10.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 489 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  SER*     3.0    44.3    +      -       -      +
    364A  SER*     3.5    32.3    -      -       -      -
    419A  HIS*     3.7    24.9    -      -       +      +
    422A  HIS*     3.3    42.0    -      -       +      +
    423A  PHE*     4.1     2.2    -      -       +      -
    459A  VAL*     3.8    23.1    -      -       +      -
    460A  VAL      3.4     8.5    -      -       -      +
    461A  LEU*     3.8    12.3    -      -       +      -
    488A  SER*     1.3    75.6    -      -       -      +
    490A  HIS*     1.3    68.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 490 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ARG*     3.8    18.0    -      -       +      -
     40A  TYR      3.0     8.3    -      -       -      +
     41A  GLU*     2.8    39.0    +      -       +      +
    422A  HIS*     3.8     1.8    -      -       -      -
    458A  VAL      3.8     0.4    -      -       -      +
    459A  VAL*     3.3     7.8    -      -       -      +
    460A  VAL*     2.9    36.8    +      -       +      +
    483A  ILE*     3.1    26.8    +      -       +      -
    484A  SER*     4.5     4.9    -      -       -      -
    485A  PRO*     3.5     9.7    -      -       +      +
    488A  SER*     3.8     9.1    +      -       -      -
    489A  ILE*     1.3    82.9    -      -       -      +
    491A  THR*     1.3    62.2    +      -       -      +
    492A  TYR*     2.5    41.3    +      +       +      -
----------------------------------------------------------
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Residues in contact with THR 491 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  SER      3.8     0.9    -      -       -      +
     39A  ARG*     3.4     3.5    -      -       -      -
     40A  TYR*     2.8    36.6    +      -       -      +
    422A  HIS*     2.7    42.3    +      -       -      +
    426A  PHE*     3.5    31.4    -      -       +      -
    457A  VAL*     3.6    28.0    -      -       +      -
    458A  VAL      3.4     4.0    -      -       -      +
    459A  VAL*     3.8     4.6    -      -       +      +
    490A  HIS*     1.3    73.2    +      -       -      +
    492A  TYR*     1.3    62.6    +      -       -      +
    493A  LEU*     3.8     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 492 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  PHE*     3.8    25.1    -      +       -      -
     38A  SER      3.3     3.4    -      -       -      -
     39A  ARG*     3.5    21.7    +      -       +      -
    456A  ALA      3.8     0.5    -      -       -      +
    457A  VAL*     3.2     7.1    -      -       -      -
    458A  VAL*     2.7    45.5    +      -       +      +
    460A  VAL*     4.1    17.3    -      -       +      -
    470A  LEU*     5.4     1.0    -      -       +      +
    472A  ILE*     3.9    16.2    -      -       +      -
    480A  LEU*     4.2     7.0    -      -       +      -
    482A  THR*     2.6    41.0    +      -       +      +
    483A  ILE      3.9     1.4    +      -       -      -
    490A  HIS*     2.5    45.3    +      -       +      -
    491A  THR*     1.3    72.9    -      -       -      +
    493A  LEU*     1.3    63.3    +      -       -      +
    494A  TRP*     4.1    19.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 493 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  THR*     6.5     0.9    -      -       +      -
     36A  THR      4.6     0.2    -      -       -      +
     37A  PHE*     3.5     2.1    -      -       -      +
     38A  SER*     2.8    47.0    +      -       -      +
     40A  TYR*     3.8    21.3    -      -       +      +
    426A  PHE*     3.7    38.6    -      -       +      +
    451A  HIS*     4.8     8.1    -      -       +      +
    456A  ALA      3.5     5.4    -      -       -      +
    457A  VAL*     3.8    24.2    -      -       +      -
    491A  THR*     3.8     6.5    -      -       +      -
    492A  TYR*     1.3    84.1    -      -       -      +
    494A  TRP*     1.3    66.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 494 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  PRO*     6.3     1.1    -      -       -      -
     36A  THR      3.9     9.9    -      -       -      +
     37A  PHE*     4.1     2.2    -      -       +      -
     56A  ILE*     3.9    19.5    -      -       +      -
     69A  LEU*     4.5     6.7    -      -       +      -
    455A  SER*     3.5     3.2    -      -       -      -
    456A  ALA*     2.8    61.0    +      -       +      +
    458A  VAL*     3.8    31.2    -      -       +      -
    472A  ILE*     3.8    15.7    -      -       +      -
    474A  ASP*     2.9    41.2    +      -       +      -
    477A  VAL*     3.5    15.4    -      -       +      +
    480A  LEU*     3.7    31.4    -      -       +      -
    492A  TYR*     4.1    11.4    -      -       +      -
    493A  LEU*     1.3    85.2    -      -       -      +
    495A  HIS*     1.3    81.2    +      -       -      +
    496A  ARG*     3.9     1.3    +      -       +      +
----------------------------------------------------------
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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