Contacts of the strand formed by residues 584 - 588 (chain C) in PDB entry 1P4V


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 GLY 584 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    580C  HIS*     3.3    13.6    -      -       -      -
    581C  ASP      2.9    27.2    +      -       -      -
    582C  GLN      3.3     0.8    -      -       -      -
    583C  LYS*     1.3    82.7    -      -       -      +
    585C  ASN*     1.3    60.9    +      -       -      -
    586C  ARG*     3.3    13.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 585 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315C  LEU*     2.8    51.2    +      -       +      +
    318C  ASN*     3.2    26.0    +      -       -      +
    319C  VAL*     4.0    12.4    -      -       +      +
    579C  VAL      3.2     5.2    -      -       -      +
    580C  HIS*     3.2    28.0    +      -       +      +
    584C  GLY*     1.3    72.1    -      -       -      -
    586C  ARG*     1.3    64.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 586 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303C  ASN*     4.9     0.2    -      -       -      +
    315C  LEU*     3.9     7.2    -      -       -      -
    566C  TYR*     3.3    21.0    +      -       -      -
    578C  ALA*     3.3     2.6    -      -       -      -
    579C  VAL*     2.8    54.9    +      -       +      +
    581C  ASP*     2.7    43.8    +      -       -      -
    583C  LYS*     4.0    25.0    -      -       -      +
    584C  GLY      3.3    18.4    +      -       -      +
    585C  ASN*     1.3    76.8    +      -       -      +
    587C  LEU*     1.3    63.7    +      -       -      +
    588C  GLU*     2.8    27.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 587 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    311C  TRP      4.5     0.7    -      -       -      +
    312C  ASN*     3.7    50.3    -      -       +      +
    315C  LEU*     4.1    19.3    -      -       +      +
    576C  ASN*     3.7    22.9    -      -       +      +
    577C  PHE      3.6    13.2    -      -       -      +
    578C  ALA*     4.5     6.5    -      -       +      +
    586C  ARG*     1.3    74.0    -      -       -      +
    588C  GLU*     1.3    63.2    +      -       -      +
    589C  THR*     5.3     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 588 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    566C  TYR*     2.9    33.4    +      -       -      -
    576C  ASN*     3.2     7.0    -      -       -      +
    577C  PHE*     2.9    53.0    +      -       +      +
    579C  VAL*     4.0     5.8    -      -       +      -
    586C  ARG*     2.8    42.1    +      -       +      +
    587C  LEU*     1.3    79.7    -      -       -      +
    589C  THR*     1.3    62.8    +      -       -      +
----------------------------------------------------------
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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