Contacts of the strand formed by residues 93 - 104 (chain I) in PDB entry 6XAV


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 93 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78I  PRO*     3.5    22.0    -      -       -      +
     79I  VAL*     4.2     5.2    +      -       -      +
     91I  THR*     3.4    23.8    +      -       -      +
     92I  TYR*     1.3    75.1    -      -       -      +
     94I  ALA*     1.3    62.5    +      -       -      +
     95I  PRO*     4.6     0.3    -      -       -      +
    126I  GLU*     3.2    31.7    +      -       -      +
    127I  ILE      3.2    19.1    -      -       -      -
    128I  PRO*     3.7     9.2    -      -       -      -
    129I  LEU*     4.0     4.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 94 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75I  LEU*     5.1     6.8    -      -       +      +
     76I  GLY      3.4    26.9    -      -       -      +
     77I  GLU      4.2     6.3    -      -       -      -
     78I  PRO*     4.2     2.0    -      -       +      -
     93I  SER*     1.3    74.6    -      -       -      +
     95I  PRO*     1.3    70.8    -      -       +      +
     96I  LEU      3.7     1.2    +      -       -      -
    126I  GLU*     3.1    10.6    -      -       -      +
    127I  ILE*     3.5    18.2    +      -       -      +
    129I  LEU*     3.4    29.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 95 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75I  LEU*     3.3     3.7    -      -       -      +
     76I  GLY*     2.4    41.4    +      -       -      -
     77I  GLU      3.4    20.6    -      -       -      +
     79I  VAL*     5.4     8.5    -      -       +      -
     93I  SER      4.6     0.7    -      -       -      +
     94I  ALA*     1.3    87.4    -      -       +      +
     96I  LEU*     1.3    59.7    +      -       -      +
     97I  ARG*     3.5    37.0    -      -       -      +
    123I  TYR*     4.0     5.6    -      -       +      -
    126I  GLU*     3.3    21.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 96 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49I  LEU*     5.3     4.3    -      -       +      -
     53I  PHE*     4.5     3.8    -      -       +      -
     73I  TYR*     4.0    14.4    -      -       +      -
     74I  ARG      3.7     7.0    -      -       -      +
     75I  LEU*     3.7    26.0    -      -       +      -
     94I  ALA      3.7     2.0    +      -       -      +
     95I  PRO*     1.3    73.7    -      -       -      +
     97I  ARG*     1.3    61.4    +      -       -      +
     98I  VAL*     3.8    25.3    +      -       +      -
    122I  VAL      3.6     0.7    -      -       -      +
    123I  TYR*     3.4     7.4    -      -       -      -
    124I  MET*     3.2    46.5    +      -       +      +
    125I  GLY*     4.2     9.4    +      -       -      +
    127I  ILE*     4.9    16.8    -      -       +      -
    464I  PHE*     4.3    28.7    -      -       +      -
    498I  ILE*     5.6     1.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 97 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73I  TYR*     3.2     1.2    -      -       -      -
     74I  ARG*     2.5    82.9    +      -       -      +
     76I  GLY*     4.5     7.5    -      -       -      +
     95I  PRO*     3.5    28.2    -      -       -      +
     96I  LEU*     1.3    73.4    -      -       -      +
     98I  VAL*     1.3    59.7    +      -       -      +
     99I  LYS*     4.2     1.4    +      -       -      +
    121I  GLU*     3.8    21.7    -      -       +      +
    122I  VAL      3.5     8.7    -      -       -      +
    123I  TYR*     3.2    40.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 98 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53I  PHE*     3.9    13.9    -      -       +      -
     57I  PHE*     6.1     0.7    -      -       +      -
     70I  TYR*     3.6    30.5    -      -       +      -
     72I  SER      3.6     4.5    -      -       -      +
     73I  TYR*     3.8    11.4    -      -       +      -
     96I  LEU*     3.8    19.5    -      -       +      -
     97I  ARG*     1.3    76.5    -      -       -      +
     99I  LYS*     1.3    62.2    +      -       -      +
    100I  LEU*     3.4    18.8    +      -       +      -
    121I  GLU*     4.0     0.2    -      -       -      -
    122I  VAL*     2.8    37.2    +      -       -      +
    124I  MET*     3.7    31.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 99 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70I  TYR*     4.0     0.3    -      -       -      -
     71I  VAL*     3.0    37.9    +      -       +      +
     72I  SER*     2.5    35.3    +      -       -      +
     73I  TYR*     5.5     1.3    -      -       -      -
     74I  ARG*     5.8     9.0    -      -       +      +
     97I  ARG      5.3     2.0    -      -       -      +
     98I  VAL*     1.3    68.7    -      -       -      +
    100I  LEU*     1.3    64.9    +      -       -      +
    119I  GLU*     5.5     8.5    -      -       +      +
    120I  GLN*     3.4    11.6    -      -       -      +
    121I  GLU*     3.4    41.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 100 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57I  PHE*     3.7    28.7    -      -       +      -
     68I  LEU*     3.7    28.5    -      -       +      -
     69I  GLN      3.6     8.7    -      -       -      +
     70I  TYR*     4.0     7.9    -      -       +      -
     71I  VAL*     4.6     0.4    -      -       -      +
     98I  VAL*     3.4    23.1    +      -       +      -
     99I  LYS*     1.3    73.8    -      -       -      +
    101I  ARG*     1.3    65.8    +      -       -      +
    118I  LYS      4.0     0.6    -      -       -      +
    119I  GLU*     3.8     4.2    -      -       -      +
    120I  GLN*     3.1    37.0    +      -       -      +
    122I  VAL*     4.2    10.5    -      -       +      -
    124I  MET*     3.9    11.2    -      -       +      -
    489I  PRO*     5.1     2.9    -      -       +      +
    493I  ILE*     3.7    31.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 101 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67I  GLU      3.6     1.9    -      -       -      +
     68I  LEU*     3.3     6.9    -      -       -      +
     69I  GLN*     3.1    61.1    +      -       +      +
     71I  VAL*     3.5    27.9    -      -       +      +
    100I  LEU*     1.3    80.6    -      -       -      +
    102I  LEU*     1.3    59.8    +      -       -      +
    103I  VAL*     4.1    11.4    +      -       +      +
    117I  ILE*     3.6    35.7    -      -       +      +
    118I  LYS      3.3     6.7    -      -       -      +
    119I  GLU*     3.1    39.2    +      -       +      -
    489I  PRO*     5.3     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 102 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67I  GLU      3.4    18.2    -      -       -      +
     68I  LEU*     3.9     3.7    -      -       +      +
    101I  ARG*     1.3    73.6    -      -       -      +
    103I  VAL*     1.3    75.4    +      -       -      +
    104I  ILE*     4.8    13.7    -      -       +      -
    116I  ASP      4.3     0.3    -      -       -      +
    117I  ILE*     4.0     1.2    -      -       -      -
    118I  LYS*     3.1    40.2    +      -       +      +
    479I  LEU*     3.7    31.2    -      -       +      -
    485I  ASP*     6.2     2.9    -      -       -      -
    487I  LEU*     4.7    12.1    -      -       +      +
    489I  PRO*     3.9    30.8    -      -       +      +
    492I  MET*     4.0    22.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 103 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65I  ASN      3.8     2.3    -      -       -      +
     67I  GLU*     3.2    52.9    +      -       +      +
     69I  GLN*     5.4     6.7    -      -       +      +
    101I  ARG*     4.1    20.9    -      -       +      +
    102I  LEU*     1.3    81.8    -      -       -      +
    104I  ILE*     1.3    76.0    +      -       -      +
    105I  TYR*     4.1    10.3    -      -       +      +
    114I  VAL*     3.8    30.1    -      -       +      -
    116I  ASP      4.9     0.4    -      -       -      -
    117I  ILE*     4.1    13.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 104 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64I  GLY      5.1     2.0    -      -       -      +
     65I  ASN*     3.9     3.6    -      -       +      +
     66I  SER*     3.8    26.9    -      -       -      +
    102I  LEU*     4.8    14.8    -      -       +      -
    103I  VAL*     1.3    82.9    -      -       -      +
    105I  TYR*     1.3    72.6    +      -       -      +
    107I  ARG*     4.5     4.5    -      -       -      +
    114I  VAL*     3.4     8.4    -      -       +      +
    115I  LYS*     3.2    36.8    +      -       +      +
    116I  ASP*     4.9     9.3    +      -       -      +
    479I  LEU*     6.0     0.7    -      -       +      -
    483I  ASP      4.4    13.0    -      -       -      +
    484I  LEU*     3.8    27.8    -      -       +      -
    485I  ASP*     4.7    17.0    -      -       +      +
----------------------------------------------------------
 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