Contacts of the strand formed by residues 8 - 16 (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 CYS 8 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  HIS*     1.3    83.0    -      -       -      +
      9B  GLN*     1.3    65.4    +      -       -      +
     38B  LYS      3.4     3.1    -      -       -      -
     39B  GLY*     3.9     0.4    -      -       -      -
     40B  GLY      3.4    22.1    +      -       -      +
     49B  VAL*     4.5    21.1    -      -       +      +
     74B  CYS*     2.0    46.9    -      -       +      -
    107B  CYS*     4.7     2.4    -      -       -      +
    108B  GLY      4.3    12.3    -      -       -      -
    109B  CYS*     4.3    13.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 9 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  SER*     3.3    40.4    -      -       -      +
      7B  HIS*     3.7    21.3    +      -       +      +
      8B  CYS*     1.3    81.6    -      -       -      +
     10B  LYS*     1.3    69.4    +      -       -      +
     11B  THR*     4.3     6.1    +      -       -      +
     37B  CYS*     3.7     4.0    -      -       -      -
     38B  LYS*     2.9    37.3    +      -       +      +
    107B  CYS*     3.7    10.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 10 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  GLN*     1.3    82.3    -      -       -      +
     11B  THR*     1.3    63.2    +      -       -      +
     35B  TYR*     3.3    54.5    +      -       +      -
     36B  GLU      3.5     3.4    -      -       -      +
    104B  VAL*     3.8    21.9    +      -       +      +
    105B  ALA*     3.1    27.4    +      -       -      +
    106B  GLU*     5.1     0.9    -      -       -      +
    107B  CYS*     3.7    13.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 11 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  GLN*     4.3     6.6    +      -       -      +
     10B  LYS*     1.3    76.4    +      -       -      +
     12B  SER*     1.3    76.4    +      -       -      +
     35B  TYR*     3.1    13.3    -      -       -      -
     36B  GLU*     2.9    43.3    +      -       +      -
     38B  LYS*     3.7    43.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 12 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  THR*     1.3    90.6    -      -       -      +
     13B  LEU*     1.3    62.9    +      -       -      +
     14B  ARG*     3.9    16.3    +      -       -      +
     33B  GLU*     2.9    26.9    +      -       -      -
     35B  TYR*     4.0     3.8    -      -       -      -
     36B  GLU*     4.7     1.4    -      -       -      +
     38B  LYS*     5.1     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 13 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  HIS*     5.2     0.7    -      -       -      +
     58A  GLN*     4.8    20.6    -      -       +      +
     61A  VAL*     4.7     8.1    -      -       +      -
     69A  VAL*     3.6    32.1    -      -       +      -
     11B  THR      3.5     0.2    +      -       -      -
     12B  SER*     1.3    75.1    -      -       -      +
     14B  ARG*     1.3    67.8    +      -       -      +
     15B  VAL*     3.0    26.4    +      -       +      +
     33B  GLU*     2.6    11.4    +      -       -      -
     34B  ALA*     2.6    35.7    +      -       +      +
     35B  TYR      3.7    22.9    -      -       -      +
     36B  GLU*     4.0    19.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 14 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  VAL*     6.2     0.3    -      -       -      +
     12B  SER*     3.9    10.8    +      -       -      +
     13B  LEU*     1.3    77.0    -      -       -      +
     15B  VAL*     1.3    61.3    +      -       -      +
     16B  ASN*     3.7     3.1    +      -       -      +
     31B  GLU*     4.0    25.4    +      -       -      +
     32B  TYR      3.5     2.9    -      -       -      +
     33B  GLU*     3.2    27.5    +      -       -      +
     64F  PHE*     3.2    56.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 15 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  VAL*     4.0    23.3    -      -       +      -
     61A  VAL*     4.0    26.2    -      -       +      -
     13B  LEU*     3.0    24.2    +      -       +      +
     14B  ARG*     1.3    72.5    -      -       -      +
     16B  ASN*     1.3    70.9    -      -       -      +
     17B  PHE*     4.5     2.5    -      -       +      +
     20B  ILE*     4.3    11.2    -      -       +      -
     31B  GLU*     3.2     3.8    -      -       -      +
     32B  TYR*     2.9    51.1    +      -       +      -
     34B  ALA*     4.0    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  ARG      3.7     3.1    +      -       -      +
     15B  VAL*     1.3    78.7    -      -       -      +
     17B  PHE*     1.3    59.9    +      -       -      +
     18B  GLU*     2.9    32.9    +      -       -      +
     19B  ASP*     2.8    50.9    +      -       -      +
     20B  ILE      3.6     2.4    +      -       -      -
     30B  LYS*     3.3    12.2    -      -       -      +
     31B  GLU*     3.6    25.5    +      -       -      +
----------------------------------------------------------
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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