Contacts of the strand formed by residues 664 - 669 (chain A) in PDB entry 4FOV


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 ILE 664 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    596A  ILE*     4.2    12.1    -      -       +      -
    598A  TYR*     3.6    35.2    -      -       +      -
    609A  ILE*     3.9    19.7    -      -       +      -
    624A  LEU*     4.2    12.8    -      -       +      -
    656A  ILE*     4.7     9.4    -      -       +      -
    657A  THR      3.5     6.3    -      -       -      +
    658A  GLU*     4.3     1.8    -      -       -      -
    659A  LEU*     3.9     3.8    -      -       -      +
    662A  HIS      4.8     0.4    -      -       -      +
    663A  HIS*     1.3    77.9    -      -       -      +
    665A  GLY*     1.3    70.2    +      -       -      +
    666A  VAL*     4.0    14.6    +      -       +      +
    688A  ILE      3.9     0.5    -      -       -      +
    689A  ASP*     3.5     5.2    -      -       -      -
    690A  LEU*     2.6    48.2    +      -       +      +
    692A  ILE*     4.5    12.3    -      -       +      +
    695A  LEU*     4.7     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 665 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249A  LEU*     3.8     7.2    -      -       -      +
    656A  ILE*     3.2     7.6    -      -       -      +
    657A  THR*     2.9    36.0    +      -       -      +
    659A  LEU*     3.7     9.6    -      -       -      +
    664A  ILE*     1.3    73.8    -      -       -      +
    666A  VAL*     1.3    61.9    +      -       -      +
    687A  TYR*     3.6    25.4    -      -       -      -
    688A  ILE      3.7     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 666 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    611A  SER*     4.6     0.7    -      -       -      +
    624A  LEU*     4.0    16.6    -      -       +      -
    644A  ILE*     4.8     2.5    -      -       +      -
    651A  TYR*     3.6    24.0    -      -       -      +
    654A  SER*     5.0     0.4    -      -       -      -
    655A  ALA      3.3    10.5    -      -       -      +
    656A  ILE*     3.9    16.8    -      -       +      -
    664A  ILE*     4.0    12.6    -      -       +      +
    665A  GLY*     1.3    77.3    -      -       -      +
    667A  LEU*     1.3    60.8    +      -       -      +
    668A  PHE*     3.8    16.8    -      -       +      -
    686A  GLN      3.6     1.9    -      -       -      +
    687A  TYR*     3.1     7.4    -      -       -      -
    688A  ILE*     2.8    48.0    +      -       +      +
    690A  LEU*     4.2    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 667 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  ILE*     3.7    31.6    -      -       +      +
    233A  PHE*     4.5     9.9    -      -       +      +
    247A  PRO*     3.5    30.2    -      -       +      +
    248A  THR      4.0     4.3    -      -       -      +
    249A  LEU*     3.6    18.4    -      -       +      +
    259A  SER*     3.3    26.7    -      -       -      +
    261A  ILE*     4.8     0.2    -      -       +      -
    655A  ALA*     2.8    34.7    +      -       +      -
    666A  VAL*     1.3    70.9    -      -       -      +
    668A  PHE*     1.3    61.2    +      -       -      +
    685A  VAL*     4.0    15.7    -      -       +      +
    686A  GLN*     3.3    23.1    -      -       -      +
    687A  TYR*     3.7     5.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 668 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  TRP*     3.8    28.0    -      +       -      -
    247A  PRO*     4.1     2.2    -      -       -      -
    644A  ILE*     4.0     7.9    -      -       +      -
    651A  TYR*     3.3    38.4    -      +       +      +
    653A  TYR      3.5    11.9    -      -       -      +
    654A  SER*     3.9     8.1    -      -       -      -
    666A  VAL*     3.8    17.5    -      -       +      -
    667A  LEU*     1.3    76.6    -      -       -      +
    669A  GLU*     1.3    68.2    +      -       -      +
    670A  LYS*     3.2    33.0    +      -       +      -
    685A  VAL*     3.2     5.5    -      -       -      -
    686A  GLN*     2.8    48.1    +      -       +      -
    688A  ILE*     4.0    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 669 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  ARG*     2.8    32.0    +      -       -      +
    246A  ILE      3.0    19.6    +      -       -      -
    247A  PRO*     4.2     5.6    -      -       +      +
    651A  TYR*     3.4     3.1    -      -       -      -
    652A  ALA*     2.9    28.9    +      -       +      -
    653A  TYR*     3.0    39.3    +      -       +      +
    668A  PHE*     1.3    71.4    -      -       -      +
    670A  LYS*     1.3    57.0    +      -       -      +
    671A  TYR*     3.0    20.3    +      -       +      -
    673A  SER*     2.7    27.8    +      -       -      -
    684A  VAL      4.0     2.5    -      -       -      -
    685A  VAL*     4.0    20.4    -      -       +      -
----------------------------------------------------------
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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