Contacts of the strand formed by residues 54 - 59 (chain A) in PDB entry 3V4V


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 ALA 54 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  ALA*     3.0    33.8    +      -       -      +
     41A  ALA*     3.9     6.3    -      -       +      +
     43A  TRP*     3.7    14.1    -      -       +      +
     53A  GLY*     1.3    75.8    -      -       -      -
     55A  ILE*     1.3    66.6    +      -       -      +
     56A  TYR*     4.1     6.0    -      -       +      -
     70A  GLN*     3.6    39.0    -      -       +      +
     71A  LEU      3.9     5.8    -      -       -      +
     94A  LEU*     4.0     6.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LEU*     5.3     8.1    -      -       +      -
     36A  VAL      3.2    12.8    -      -       -      +
     37A  GLY*     4.6     1.1    -      -       -      -
     54A  ALA*     1.3    77.2    -      -       -      +
     56A  TYR*     1.3    68.4    +      -       -      +
     70A  GLN*     3.9     0.5    -      -       -      +
     71A  LEU*     2.9    53.2    +      -       +      +
     73A  LEU*     4.1    14.1    -      -       +      +
     94A  LEU*     4.7     5.5    -      -       +      +
     95A  GLY*     3.7    16.2    -      -       -      +
     98A  LEU*     4.3    15.0    -      -       +      -
    108A  ILE*     5.7     2.5    -      -       +      -
    110A  THR*     3.6    42.8    -      -       +      +
    135A  VAL*     5.3     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  PRO*     3.4    31.4    -      -       +      +
     17A  THR*     5.0     0.3    -      -       -      +
     19A  PHE*     3.9    26.7    -      +       +      -
     34A  LEU      4.6     0.2    -      -       -      -
     35A  LEU*     3.5     8.7    -      -       -      +
     36A  VAL*     2.7    32.2    +      -       +      +
     38A  ALA*     4.1    19.3    -      -       +      -
     41A  ALA*     4.1    13.3    -      -       +      +
     42A  ASN      4.9     0.3    +      -       -      -
     54A  ALA      4.1     7.0    -      -       -      -
     55A  ILE*     1.3    84.6    -      -       -      +
     57A  ARG*     1.3    63.6    +      -       -      +
     58A  CYS*     5.2     0.2    -      -       -      -
     68A  CYS*     4.3    16.4    -      -       +      -
     69A  GLU      3.4    12.6    -      -       -      +
     70A  GLN*     3.2    54.4    +      -       +      -
     71A  LEU*     3.7     3.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  TRP*     3.7    29.5    -      -       +      -
     34A  LEU      3.6     4.9    -      -       -      -
     35A  LEU*     3.6    17.7    -      -       +      -
     56A  TYR*     1.3    77.7    -      -       -      +
     58A  CYS*     1.3    62.5    +      -       -      +
     59A  ARG      4.3     0.3    +      -       -      -
     67A  THR      4.3     0.2    -      -       -      +
     68A  CYS*     3.6     1.6    -      -       -      -
     69A  GLU*     3.0    65.3    +      -       +      +
     71A  LEU*     3.5    23.8    -      -       +      +
    138A  ASP      4.2     5.3    +      -       -      -
    139A  LEU*     3.5    44.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  TYR*     3.6    26.5    -      -       +      -
     19A  PHE*     4.4     8.7    -      -       -      -
     33A  TRP*     3.6     4.2    -      -       -      -
     34A  LEU*     2.9    44.1    +      -       +      +
     36A  VAL*     4.4     5.4    -      -       -      -
     56A  TYR*     5.1     0.2    -      -       -      -
     57A  ARG*     1.3    77.0    -      -       -      +
     59A  ARG*     1.3    66.4    +      -       -      +
     60A  ILE*     3.4     4.2    +      -       -      +
     67A  THR      3.9     5.4    -      -       -      +
     68A  CYS*     2.0    49.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  TYR*     2.8    21.5    +      -       -      -
     30A  ALA      5.6     0.6    +      -       -      -
     31A  ASN*     2.7    40.9    +      -       -      +
     32A  ARG      3.8     8.4    -      -       -      +
     33A  TRP*     3.4    43.5    -      -       +      -
     57A  ARG      4.3     0.2    +      -       -      -
     58A  CYS*     1.3    72.6    -      -       -      +
     60A  ILE*     1.3    68.3    +      -       -      +
     62A  LYS*     3.4    47.5    -      -       -      +
     63A  ASN*     3.1    28.8    +      -       -      +
     67A  THR      4.4     0.6    +      -       -      -
----------------------------------------------------------
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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