Contacts of the strand formed by residues 97 - 107 (chain A) in PDB entry 3I7O


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 SER 97 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  GLN*     3.1     3.5    -      -       -      +
     94A  SER*     2.5    45.5    +      -       -      -
     96A  GLU*     1.3    96.3    +      -       -      +
     98A  ILE*     1.3    66.1    +      -       -      +
     99A  ASP*     4.0     9.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  VAL*     4.6     7.9    -      -       +      +
     53A  LYS*     3.7    40.9    +      -       +      +
     91A  TYR*     2.8    31.9    -      -       +      +
     92A  LYS      3.6     2.2    -      -       -      -
     93A  GLN*     3.7    27.8    -      -       +      +
     96A  GLU      4.0     6.7    -      -       -      +
     97A  SER*     1.3    80.5    -      -       -      +
     99A  ASP*     1.3    70.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  LYS*     5.1     1.6    -      -       -      +
     91A  TYR*     5.3     1.1    -      -       -      -
     92A  LYS*     2.7    54.6    +      -       +      +
     94A  SER*     5.7     3.2    +      -       -      +
     97A  SER*     4.0     9.6    +      -       -      +
     98A  ILE*     1.3    88.4    +      -       -      +
    100A  ILE*     1.3    67.6    +      -       -      +
    101A  ILE*     5.3     7.0    -      -       +      -
   1063A  LYS*     5.3    12.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  PHE*     4.8     4.7    -      -       +      -
     39A  LEU*     4.6     2.5    -      -       +      -
     41A  ILE*     3.8    14.4    -      -       +      -
     53A  LYS*     3.8    16.8    -      -       +      +
     55A  VAL*     3.3    46.4    -      -       +      -
     89A  LEU*     4.0    37.2    -      -       +      -
     90A  GLU      3.5     7.9    -      -       -      +
     91A  TYR*     4.2    17.7    -      -       +      -
     99A  ASP*     1.3    77.5    +      -       -      +
    101A  ILE*     1.3    64.3    +      -       -      +
    102A  THR*     4.3     1.7    +      -       -      -
   1065A  VAL*     4.2    19.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  ILE      3.6     0.5    -      -       -      +
     89A  LEU*     3.2    11.3    -      -       -      +
     90A  GLU*     2.8    54.3    +      -       +      +
     92A  LYS*     3.7    39.9    -      -       +      +
     99A  ASP*     3.8     8.0    +      -       +      +
    100A  ILE*     1.3    75.6    -      -       -      +
    102A  THR*     1.3    66.2    +      -       -      +
    103A  ARG*     3.9    19.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  CYS*     4.3     0.7    -      -       +      -
     88A  ILE      3.5     4.9    -      -       -      +
     89A  LEU*     3.9     3.8    -      -       +      +
    100A  ILE      4.9     0.3    +      -       -      -
    101A  ILE*     1.3    78.2    -      -       -      +
    103A  ARG*     1.3    62.8    +      -       -      +
    104A  ALA*     3.3    26.4    +      -       -      +
    105A  HIS*     4.2     0.7    -      -       +      +
   1065A  VAL      2.6    26.9    +      -       -      -
   1066A  GLY*     3.7    17.7    -      -       -      +
   1067A  LYS*     3.7    45.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  GLU*     2.9    28.5    +      -       -      -
     76A  LEU*     3.5    19.6    -      -       +      +
     88A  ILE*     2.9    26.0    +      -       +      +
     90A  GLU*     3.0    34.8    +      -       +      -
    101A  ILE*     3.9    17.5    -      -       +      -
    102A  THR*     1.3    72.9    -      -       -      +
    104A  ALA*     1.3    62.9    +      -       +      +
    147A  ARG*     6.0     4.2    -      -       -      +
    150A  LYS*     3.8    34.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  CYS*     3.3     0.9    -      -       -      -
     88A  ILE*     2.9    33.0    +      -       +      -
    102A  THR*     3.3     8.4    -      -       -      +
    103A  ARG*     1.3    82.6    -      -       -      +
    105A  HIS*     1.3    71.5    +      -       -      +
    149A  ASN      4.1     2.2    -      -       -      +
    150A  LYS*     3.0    27.8    -      -       -      +
    152A  LEU*     3.7    20.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  ALA      3.3     9.2    -      -       -      +
     87A  CYS*     4.1     1.1    -      -       +      -
    102A  THR*     4.2     1.2    -      -       +      +
    104A  ALA*     1.3    84.9    -      -       -      +
    106A  GLY*     1.3    61.4    +      -       -      +
    150A  LYS      2.9     6.4    +      -       -      +
    151A  GLU*     3.0    27.0    -      -       +      +
    152A  LEU*     3.2    15.2    -      -       -      +
   1066A  GLY      3.7    13.2    -      -       -      +
   1067A  LYS*     3.4    59.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  ASN*     3.9     1.4    -      -       -      -
     86A  ALA*     2.9    29.8    +      -       -      +
    105A  HIS*     1.3    85.2    -      -       -      +
    107A  ASN*     1.3    62.5    +      -       -      -
    108A  VAL*     4.6     2.7    -      -       -      -
    151A  GLU*     3.6    12.8    -      -       -      -
    152A  LEU*     3.9     3.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  LYS      3.2    21.0    +      -       -      -
     84A  TYR*     3.3     5.7    -      -       -      +
     85A  ASN*     3.6    16.9    -      -       -      +
    106A  GLY*     1.3    73.8    -      -       -      -
    108A  VAL*     1.3    61.7    +      -       -      +
    109A  GLN*     2.8    49.7    +      -       +      +
   1072A  PHE*     3.6    22.4    -      -       -      -
----------------------------------------------------------
 Back to top of page


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