Contacts of the strand formed by residues 31 - 39 (chain B) in PDB entry 4FAO


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 GLU 31 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  ARG*     4.0    34.3    +      -       +      +
     15B  VAL      3.2    16.2    -      -       -      +
     16B  ASN*     3.6    25.1    +      -       +      +
     17B  PHE*     4.6     2.2    -      -       -      +
     29B  PRO*     3.3    10.3    -      -       -      +
     30B  LYS*     1.3    80.7    -      -       +      +
     32B  TYR*     1.3    62.7    +      -       -      +
     64F  PHE*     4.1    12.3    -      -       +      -
     65F  ASN*     3.1    27.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 32 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  HIS*     5.2     0.3    -      -       -      -
     57A  VAL*     4.0    12.8    -      -       +      +
     14B  ARG*     3.5     2.6    -      -       -      -
     15B  VAL*     2.9    51.8    +      -       +      -
     17B  PHE*     3.5    34.1    -      +       -      -
     29B  PRO*     3.9    14.4    -      -       +      -
     31B  GLU*     1.3    77.4    -      -       -      +
     33B  GLU*     1.3    68.0    +      -       -      +
     34B  ALA*     3.3    24.4    +      -       +      +
     82B  ILE*     3.6    28.5    -      -       +      -
    102B  MET*     2.9    50.8    +      -       +      +
     63F  ASP*     4.7     5.8    -      -       +      +
     64F  PHE*     3.7    12.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 33 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  SER*     2.9    21.2    +      -       -      -
     13B  LEU      2.6    22.5    +      -       -      -
     14B  ARG*     3.2    17.5    +      -       -      +
     32B  TYR*     1.3    79.6    -      -       -      +
     34B  ALA*     1.3    81.4    +      -       -      +
     35B  TYR*     3.4    39.5    +      -       +      +
     82B  ILE*     5.2     0.7    -      -       -      +
    103B  SER*     3.0    18.4    +      -       -      -
     63F  ASP*     5.4     0.2    +      -       -      -
     64F  PHE*     3.4    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 34 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  HIS*     4.0    11.9    -      -       +      +
     57A  VAL*     5.4     1.8    -      -       +      -
     13B  LEU*     2.6    22.3    +      -       +      +
     15B  VAL*     4.0    10.3    -      -       +      -
     32B  TYR*     3.3    21.5    +      -       +      +
     33B  GLU*     1.3    97.3    -      -       -      +
     35B  TYR*     1.3    61.3    +      -       -      +
    102B  MET      3.3    23.1    -      -       -      +
    103B  SER*     4.0     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 35 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  HIS*     2.9    22.3    +      -       -      -
     10B  LYS*     3.3    34.9    +      -       +      -
     11B  THR      3.1    22.2    -      -       -      +
     12B  SER*     4.5     3.4    -      -       -      -
     13B  LEU*     3.7    10.1    -      -       -      +
     33B  GLU*     3.4    35.4    +      -       +      +
     34B  ALA*     1.3    78.6    -      -       -      +
     36B  GLU*     1.3    59.8    +      -       -      +
    103B  SER*     3.6    13.9    -      -       -      -
    104B  VAL*     3.1    49.0    -      -       +      +
     37F  LYS*     5.9     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 36 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  GLN*     4.3    20.4    +      -       -      +
     68A  LYS      4.1     4.5    -      -       -      +
     69A  VAL*     3.8     9.5    -      -       -      -
     70A  GLY*     3.5    24.6    +      -       -      -
     10B  LYS*     3.5     5.4    -      -       -      -
     11B  THR*     2.9    42.7    +      -       -      +
     12B  SER      4.7     0.5    -      -       -      +
     13B  LEU*     4.0    21.7    -      -       +      +
     35B  TYR*     1.3    76.4    -      -       -      +
     37B  CYS*     1.3    70.4    +      -       -      +
     38B  LYS*     3.0    45.2    +      -       +      +
    104B  VAL*     4.9     0.7    -      -       -      -
    107B  CYS*     4.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 37 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  GLN*     5.0     6.3    +      -       -      +
      9B  GLN      3.7     2.9    -      -       -      -
     36B  GLU*     1.3    77.4    -      -       -      +
     38B  LYS*     1.3    60.6    +      -       -      +
     39B  GLY      4.4     0.2    +      -       -      -
     74B  CYS*     3.5    32.2    -      -       -      +
     75B  VAL*     3.5     5.4    -      -       -      -
     76B  PRO*     3.4    34.6    -      -       +      +
    104B  VAL*     3.9    10.9    -      -       -      +
    107B  CYS*     2.0    44.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 38 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  LYS      4.0    14.8    +      -       -      -
      7B  HIS      3.7     0.3    -      -       -      +
      8B  CYS*     3.4     1.0    -      -       -      -
      9B  GLN*     2.9    37.1    +      -       +      +
     11B  THR*     3.7    34.2    -      -       +      +
     12B  SER      5.1     0.6    +      -       -      -
     36B  GLU*     3.0    42.3    +      -       +      +
     37B  CYS*     1.3    75.1    -      -       -      +
     39B  GLY*     1.3    59.7    +      -       -      +
     74B  CYS*     3.7     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  SER      5.4     1.8    -      -       -      -
      7B  HIS      2.5    18.2    -      -       -      -
      8B  CYS*     4.0     2.7    -      -       -      -
     37B  CYS      4.4     0.2    +      -       -      -
     38B  LYS*     1.3    74.2    -      -       -      +
     40B  GLY*     1.3    61.5    +      -       -      -
     74B  CYS*     3.4    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