Contacts of the strand formed by residues 954 - 959 (chain A) in PDB entry 3I7H


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 MET 954 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    912A  LEU*     5.2     0.7    -      -       -      +
    913A  TYR*     2.9    22.9    +      -       +      -
    925A  ASP*     2.9    33.6    +      -       +      +
    928A  ARG*     5.2     1.3    -      -       -      +
    930A  VAL*     3.7    12.8    -      -       +      -
    952A  ASN*     3.0    25.5    +      -       +      +
    953A  TRP*     1.3    78.8    -      -       -      +
    955A  SER*     1.3    59.4    +      -       -      +
    956A  ALA      3.2    27.1    -      -       -      +
    957A  VAL*     3.4    18.4    -      -       +      -
    967A  GLY*     3.7     8.7    -      -       -      -
    968A  ALA      3.4     6.1    -      -       -      +
    969A  GLU*     4.6     0.9    -      -       -      -
    975A  PHE*     3.6    36.1    -      -       +      -
     96B  ARG*     2.8    19.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 955 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    913A  TYR*     3.3    26.2    +      -       -      -
    954A  MET*     1.3    73.0    -      -       -      +
    956A  ALA*     1.3    64.0    +      -       -      +
    968A  ALA*     2.9    22.6    +      -       -      +
    969A  GLU*     3.8     3.9    +      -       -      -
   1003A  PHE*     3.3    35.4    -      -       -      -
   1004A  VAL      2.9    22.5    +      -       -      +
   1005A  ASN*     4.3     9.7    -      -       -      +
     96B  ARG*     3.8     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 956 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    913A  TYR*     4.2    11.9    -      -       -      -
    954A  MET*     3.2    22.9    -      -       -      +
    955A  SER*     1.3    83.8    +      -       -      +
    957A  VAL*     1.3    62.6    +      -       -      +
    968A  ALA*     3.3    11.4    +      -       +      -
   1004A  VAL*     3.7    21.1    -      -       +      +
   1005A  ASN      4.2    10.5    -      -       -      +
   1006A  VAL*     4.3     1.8    -      -       -      +
   1007A  PHE*     3.6    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 957 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    913A  TYR*     4.3    22.4    -      -       +      +
    914A  LEU      4.7     0.2    -      -       -      +
    915A  LYS*     3.2    40.6    +      -       +      +
    923A  VAL*     4.1    34.8    -      -       +      +
    924A  GLY      4.9     8.3    -      -       -      +
    925A  ASP*     5.3     1.3    -      -       +      -
    930A  VAL*     4.9     4.7    -      -       +      -
    954A  MET*     3.4    23.3    -      -       +      -
    956A  ALA*     1.3    79.9    -      -       -      +
    958A  GLU*     1.3    63.2    +      -       -      +
    966A  LEU      3.5     8.7    -      -       -      +
   1007A  PHE*     3.5     8.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 958 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    915A  LYS*     2.9    39.3    +      -       -      +
    923A  VAL*     4.7     4.9    -      -       -      +
    957A  VAL*     1.3    77.4    -      -       -      +
    959A  ILE*     1.3    87.6    +      -       -      +
    960A  LEU*     4.5     2.2    -      -       +      -
    965A  PHE*     3.3     6.8    -      -       -      +
    966A  LEU*     2.7    49.7    +      -       +      +
   1007A  PHE*     3.9    22.2    -      -       +      -
   1008A  CYS*     4.2     5.2    -      -       -      -
   1009A  HIS*     2.7    42.7    +      -       +      +
   1028A  VAL*     4.4    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 959 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    915A  LYS*     3.5    12.5    -      -       +      +
    916A  THR*     3.2    51.1    -      -       -      +
    917A  LYS*     3.5    28.5    -      -       +      +
    923A  VAL*     3.1    24.0    -      -       +      +
    958A  GLU*     1.3    82.5    +      -       -      +
    960A  LEU*     1.3    57.9    +      -       -      +
    961A  ASP*     3.2    27.6    -      -       -      +
    964A  ASN      3.9     4.5    -      -       -      -
    965A  PHE*     4.5     1.6    -      -       +      -
   1009A  HIS*     3.0    29.3    +      -       +      +
----------------------------------------------------------
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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