Contacts of the strand formed by residues 464 - 470 (chain C) in PDB entry 3V81


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 464 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    457C  TYR*     3.4    18.3    +      -       -      +
    458C  VAL*     4.0    23.1    -      -       +      +
    462C  GLY*     3.4    15.4    +      -       -      +
    463C  ARG*     1.3    83.9    -      -       -      +
    465C  LYS*     1.3    65.9    +      -       -      +
    551C  LEU*     3.7    23.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 465 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    456C  GLY*     3.1     2.6    -      -       -      -
    457C  TYR*     3.0    47.8    +      -       +      +
    464C  GLN*     1.3    77.6    -      -       -      +
    466C  VAL*     1.3    72.6    +      -       -      +
    467C  VAL*     3.9    22.0    -      -       +      -
    484C  LEU*     4.0    27.5    -      -       +      +
    487C  GLN*     5.9     0.8    -      -       -      +
    488C  ASP*     3.3    32.5    +      -       -      +
    551C  LEU*     4.9     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 466 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454C  LYS*     3.7    39.9    -      -       +      -
    455C  ALA      3.9     3.4    -      -       -      +
    456C  GLY*     4.2     0.2    -      -       -      -
    464C  GLN*     6.4     0.2    -      -       +      -
    465C  LYS*     1.3    81.5    -      -       -      +
    467C  VAL*     1.3    69.3    +      -       -      +
    468C  PRO*     4.1     4.4    -      -       -      +
    551C  LEU*     3.8    42.4    -      -       +      +
    552C  VAL*     4.5     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 467 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454C  LYS*     3.4     2.9    -      -       -      -
    455C  ALA*     3.0    36.2    +      -       +      +
    465C  LYS*     3.9    18.6    -      -       +      -
    466C  VAL*     1.3    79.6    -      -       -      +
    468C  PRO*     1.4    79.2    -      -       +      +
    469C  LEU*     3.7    16.2    -      -       +      +
    480C  GLN*     5.8     1.3    -      -       +      +
    484C  LEU*     3.9    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 468 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    452C  LEU*     6.2     2.5    -      -       +      -
    453C  GLY      3.8     4.9    -      -       -      +
    454C  LYS*     4.6    16.6    -      -       +      +
    466C  VAL*     4.1     5.9    -      -       -      +
    467C  VAL*     1.4    95.3    -      -       +      +
    469C  LEU*     1.3    65.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 469 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    451C  LYS      4.4     0.2    -      -       -      +
    452C  LEU*     3.2     9.1    -      -       -      +
    453C  GLY      2.8    41.5    +      -       -      +
    455C  ALA*     3.5    31.9    -      -       +      +
    467C  VAL*     3.7    14.1    -      -       +      +
    468C  PRO*     1.3    82.7    -      -       -      +
    470C  THR*     1.3    64.2    +      -       -      +
    472C  THR*     4.6    13.7    -      -       +      +
    477C  THR*     3.9    18.4    -      -       +      -
    480C  GLN*     3.9    31.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 470 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    451C  LYS      4.1     1.1    -      -       -      -
    452C  LEU*     3.6    23.8    -      -       +      -
    469C  LEU*     1.3    76.7    -      -       -      +
    471C  ASN*     1.3    75.8    +      -       -      +
    472C  THR*     3.6     3.7    -      -       -      -
----------------------------------------------------------
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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