Contacts of the strand formed by residues 432 - 438 (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 GLN 432 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  LYS*     3.5    38.4    +      -       +      +
     75A  PHE      2.8    25.1    +      -       -      +
     76A  GLN      3.3     5.4    -      -       -      +
     77A  LYS*     4.0    30.1    -      -       +      +
    430A  GLY      3.7     2.0    +      -       -      +
    431A  SER*     1.3    74.4    -      -       -      +
    433A  ARG*     1.3    76.5    +      -       -      +
    434A  VAL*     3.4     7.6    +      -       +      +
    449A  LEU*     4.0     3.4    -      -       -      -
    450A  MET*     2.8    41.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 433 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  PHE*     2.8    73.0    +      -       -      +
     76A  GLN*     2.9    43.0    +      -       -      +
    371A  LEU*     2.8    33.9    +      -       +      -
    372A  LEU*     3.4    34.5    +      -       -      +
    374A  HIS*     3.8    14.3    +      -       -      +
    432A  GLN*     1.3    74.6    -      -       -      +
    434A  VAL*     1.3    63.9    +      -       -      +
    447A  VAL*     3.9    13.5    -      -       +      -
    448A  ALA      3.5    13.9    -      -       -      +
    449A  LEU*     3.9    14.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 434 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  LEU*     3.9    29.6    -      -       +      -
     70A  GLN      3.9     5.8    -      -       -      +
     71A  PRO*     4.0     4.5    -      -       +      +
     73A  GLN      3.1     9.2    -      -       -      +
     74A  LYS*     4.0    26.9    -      -       +      +
     75A  PHE*     3.9     5.6    -      -       -      -
    372A  LEU*     6.2     0.2    -      -       -      +
    432A  GLN*     3.5    15.3    -      -       +      +
    433A  ARG*     1.3    84.3    +      -       -      +
    435A  GLY*     1.3    65.2    +      -       -      +
    436A  LEU*     3.8     1.2    +      -       -      +
    447A  VAL*     5.6     0.2    -      -       -      +
    448A  ALA*     3.0    29.5    +      -       -      +
    449A  LEU*     4.2     6.5    -      -       -      -
    450A  MET*     4.0    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 435 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  LEU*     3.6     3.5    -      -       -      -
     70A  GLN*     2.8    49.6    +      -       -      +
     73A  GLN*     2.9    14.0    +      -       -      -
     75A  PHE*     3.7    13.9    -      -       -      -
    434A  VAL*     1.3    80.2    -      -       -      +
    436A  LEU*     1.3    58.9    +      -       -      +
    448A  ALA*     4.2     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 436 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  LEU*     4.3    25.1    -      -       +      +
     68A  THR      3.4     4.9    -      -       -      -
     69A  LEU*     3.7    29.8    -      -       +      +
     70A  GLN*     4.2     2.0    +      -       -      -
    372A  LEU*     6.1     3.5    -      -       +      +
    434A  VAL      3.8     1.9    +      -       -      +
    435A  GLY*     1.3    71.9    -      -       -      +
    437A  VAL*     1.3    65.7    +      -       -      +
    446A  ALA*     3.8    32.8    -      -       +      +
    447A  VAL*     4.1    19.1    -      -       -      +
    448A  ALA*     3.9    20.4    -      -       +      +
    458A  VAL*     4.3    13.5    -      -       +      -
    472A  ILE*     5.0     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 437 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  LEU      3.6     1.0    -      -       -      +
     67A  LEU*     3.2     6.7    -      -       -      -
     68A  THR*     2.7    60.2    +      -       -      +
     70A  GLN*     3.5    36.3    -      -       +      +
    436A  LEU*     1.3    77.5    -      -       -      +
    438A  ALA*     1.3    63.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 438 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  LEU*     4.1     1.3    -      -       +      -
     66A  LEU      3.4     4.7    -      -       -      -
     67A  LEU*     3.9    14.4    -      -       +      -
    436A  LEU      4.4     0.2    +      -       -      -
    437A  VAL*     1.3    76.7    -      -       -      +
    439A  SER*     1.3    64.4    +      -       -      +
    440A  GLN      3.4     6.8    +      -       -      +
    442A  ASN*     3.4    29.4    -      -       -      +
----------------------------------------------------------
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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