Contacts of the strand formed by residues 52 - 59 (chain B) in PDB entry 5VSW


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 PRO 52 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  GLU      6.4     0.4    -      -       -      +
      8A  PHE*     5.6     2.7    -      -       +      -
     50B  SER      3.2     8.7    -      -       -      +
     51B  MET*     1.3    97.4    -      -       +      +
     53B  GLY*     1.3    60.1    +      -       -      +
    148B  ARG*     5.6    10.1    -      -       -      +
    149B  GLY      3.7     5.8    -      -       -      +
    150B  ARG*     3.9    20.4    -      -       +      +
    177B  TYR      3.8     3.6    -      -       -      +
    179B  PRO*     4.0     9.2    -      -       -      +
    219B  ARG*     5.7    12.8    -      -       +      +
    223B  ILE*     4.7     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  PRO*     1.3    77.0    -      -       -      +
     54B  CYS*     1.3    64.8    +      -       -      -
    148B  ARG*     3.3     8.3    -      -       -      +
    149B  GLY      2.7    38.5    +      -       -      +
    177B  TYR*     2.9    26.1    -      -       -      +
    179B  PRO*     5.3     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  GLY*     1.3    73.7    -      -       -      -
     55B  ALA*     1.3    64.5    +      -       -      +
     89B  ALA*     5.5     0.5    -      -       -      -
     90B  VAL*     3.0    29.8    +      -       +      +
     91B  ARG*     3.8     7.4    -      -       -      -
     92B  VAL*     3.2    39.3    -      -       +      +
    146B  VAL*     4.4     8.5    -      -       +      -
    147B  GLN      3.6    15.5    -      -       -      +
    148B  ARG*     3.6    27.8    -      -       +      -
    176B  CYS      4.8     0.2    -      -       -      +
    177B  TYR*     4.0     3.5    +      -       -      +
    208B  ASN*     5.9     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  CYS*     1.3    77.1    -      -       -      +
     56B  VAL*     1.3    69.6    +      -       -      +
     57B  THR*     3.1     4.2    +      -       -      -
     86B  LYS      4.9     2.0    -      -       -      +
     88B  LEU      4.7    10.5    -      -       -      +
     90B  VAL*     5.4     1.8    -      -       -      +
    146B  VAL*     3.6    11.9    -      -       -      +
    147B  GLN      3.6     2.3    +      -       -      +
    176B  CYS*     3.2    46.2    -      -       -      +
    177B  TYR*     3.1    23.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 56 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  ALA*     1.3    73.0    -      -       -      +
     57B  THR*     1.3    60.7    +      -       -      +
     59B  VAL*     4.0    11.2    -      -       +      -
     85B  LEU*     3.7    32.4    +      -       +      +
     86B  LYS*     5.5     1.3    +      -       -      +
     88B  LEU*     4.3    16.8    -      -       +      +
     90B  VAL*     4.9     2.7    -      -       +      -
    144B  ILE*     3.6    42.4    -      -       +      -
    145B  LYS      4.0     4.0    -      -       -      +
    146B  VAL*     4.0    13.9    -      -       +      +
    173B  VAL*     3.0    30.9    -      -       +      +
    174B  ASP      3.9     9.9    -      -       -      +
    175B  ALA*     3.9     5.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 57 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  ALA      3.1     2.8    +      -       -      -
     56B  VAL*     1.3    72.7    -      -       -      +
     58B  GLU*     1.3    68.9    +      -       +      +
    145B  LYS      3.2     7.1    +      -       -      -
    146B  VAL*     4.2     0.2    -      -       -      +
    147B  GLN*     3.2    43.6    +      -       -      +
    158B  ARG*     6.3     3.4    -      -       -      +
    172B  LEU*     4.0     6.3    -      -       +      +
    173B  VAL*     3.0    26.9    +      -       -      +
    175B  ALA*     4.6     4.4    -      -       +      +
    177B  TYR*     2.6    41.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 58 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  VAL*     4.0     0.9    -      -       -      +
     57B  THR*     1.3    91.1    -      -       +      +
     59B  VAL*     1.3    72.9    +      -       -      +
    145B  LYS*     3.0    57.7    +      -       +      +
    147B  GLN*     3.2    18.3    -      -       -      +
    158B  ARG*     4.8    13.3    +      -       -      -
    172B  LEU*     4.1    25.1    -      -       +      +
    173B  VAL      4.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 59 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  VAL*     4.0     8.7    -      -       +      -
     58B  GLU*     1.3    87.8    -      -       -      +
     60B  GLU*     1.3    62.7    +      -       -      +
     61B  ILE*     3.6    29.8    +      -       +      +
     82B  LEU*     5.1     7.0    -      -       +      -
     85B  LEU*     3.6    30.3    -      -       +      -
    142B  MET*     4.4    10.1    -      -       -      -
    143B  ARG      4.7     4.3    -      -       -      -
    144B  ILE*     4.2    10.5    -      -       +      -
    145B  LYS*     5.9     0.2    -      -       -      -
    172B  LEU*     4.0    19.2    +      -       -      +
    173B  VAL*     4.4    12.3    -      -       +      -
----------------------------------------------------------
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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