Contacts of the strand formed by residues 93 - 99 (chain I) in PDB entry 1G3I


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 ALA 93 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47I  ALA      3.3    13.2    -      -       -      +
     48I  GLY*     4.0     3.4    -      -       -      -
     52I  ASP*     3.9     5.8    -      -       +      +
     53I  ALA*     3.6    36.1    -      -       -      +
     56I  LEU*     3.9     9.6    -      -       +      -
     91I  LEU      3.0     3.8    +      -       -      +
     92I  GLU*     1.3    79.1    -      -       -      +
     94I  MET*     1.3    71.5    +      -       -      +
    108I  GLY*     2.9    25.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 94 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46I  PHE*     3.4     4.0    -      -       -      +
     47I  ALA*     2.8    34.1    +      -       +      +
     56I  LEU*     4.0     1.7    -      -       -      +
     93I  ALA*     1.3    81.1    -      -       -      +
     95I  LEU*     1.3    66.5    +      -       -      +
    105I  ILE*     4.8     1.8    -      -       +      -
    106I  ILE      3.1    10.5    -      -       -      +
    107I  THR*     4.1    22.9    -      -       +      -
    123I  ILE*     3.4    42.2    -      -       +      +
    124I  GLY*     4.1    10.8    -      -       -      +
     22J  LEU*     5.3     9.4    -      -       +      -
     27J  MET*     4.7    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 95 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44I  ALA*     5.1     0.9    -      -       +      -
     45I  GLY      3.2     7.6    -      -       -      +
     46I  PHE*     3.1    35.4    -      -       +      +
     53I  ALA      4.9     0.2    -      -       -      +
     56I  LEU*     3.6    28.0    -      -       +      -
     57I  PHE*     3.4    40.8    -      -       +      +
     60I  PHE*     4.0    21.1    -      -       +      -
     94I  MET*     1.3    74.4    -      -       -      +
     96I  ILE*     1.3    62.5    +      -       -      +
     97I  VAL*     3.9    13.5    -      -       +      -
    105I  ILE*     3.2    10.0    -      -       -      +
    106I  ILE*     2.6    42.0    +      -       +      +
    123I  ILE*     4.0     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 96 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3I  ILE*     3.5    35.7    -      -       +      +
      4I  VAL*     4.5     1.1    -      -       -      -
      5I  SER*     3.9    23.1    -      -       -      +
     14I  VAL*     4.3    10.1    -      -       +      +
     43I  LEU      3.6     1.0    -      -       -      +
     44I  ALA*     3.1     3.5    -      -       -      -
     45I  GLY      2.6    41.7    +      -       -      +
     95I  LEU*     1.3    78.1    -      -       -      +
     97I  VAL*     1.3    63.4    +      -       -      +
     98I  ALA*     5.4     1.1    -      -       +      -
    103I  SER*     5.4     0.2    -      -       -      +
    104I  LEU      3.5    12.6    -      -       -      +
    105I  ILE*     4.5     1.8    -      -       +      -
    121I  LEU*     3.8    28.0    -      -       +      +
    122I  ALA*     3.8     1.3    -      -       -      -
    123I  ILE*     3.6    32.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 97 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43I  LEU      2.9     9.9    -      -       -      +
     44I  ALA*     4.1     9.4    -      -       +      -
     60I  PHE*     3.3    48.2    -      -       +      -
     71I  LEU*     3.9    10.3    -      -       +      +
     95I  LEU*     4.3    15.5    -      -       +      -
     96I  ILE*     1.3    79.8    -      -       -      +
     98I  ALA*     1.3    60.3    -      -       -      +
    103I  SER*     4.4     0.3    +      -       -      -
    104I  LEU*     2.6    59.3    +      -       +      +
    106I  ILE*     4.1    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 98 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5I  SER*     4.9     0.7    -      -       -      +
     12I  VAL*     3.7    18.8    -      -       +      -
     14I  VAL*     4.5    11.7    -      -       +      -
     42I  VAL*     3.5     0.8    -      -       -      -
     43I  LEU*     2.6    44.0    +      -       -      +
     71I  LEU*     4.3     5.7    -      -       -      +
     96I  ILE*     5.4     1.3    -      -       +      -
     97I  VAL*     1.3    79.2    -      -       -      +
     99I  ASP*     1.3    56.9    +      -       -      +
    102I  GLU      3.2    17.9    -      -       -      +
    103I  SER*     3.5    16.2    -      -       -      +
    172I  LEU*     4.5     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 99 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7I  ARG*     2.9     7.4    +      -       -      -
     12I  VAL*     3.8     2.0    -      -       -      +
     41I  LYS      3.3    16.6    -      -       -      +
     42I  VAL*     3.5    13.2    -      -       +      +
     69I  GLY      4.4     5.9    -      -       -      +
     71I  LEU*     3.5    26.0    +      -       +      +
     98I  ALA*     1.3    74.0    -      -       -      +
    100I  GLU*     1.3    68.3    +      -       -      +
    101I  LYS*     3.1     8.5    +      -       -      +
    102I  GLU*     2.7    40.0    +      -       -      +
    172I  LEU*     3.3    14.1    -      -       -      -
----------------------------------------------------------
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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