Contacts of the strand formed by residues 78 - 82 (chain U) 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 PHE 78 (chain U).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64U  THR*     4.7     1.8    -      -       +      -
     67U  ALA*     2.9    40.4    -      -       +      -
     68U  ARG*     3.2    53.8    -      -       +      -
     71U  ALA*     3.5    24.0    -      -       +      -
     76U  ALA      3.2     1.2    +      -       -      +
     77U  PRO*     1.3    74.4    -      -       -      +
     79U  ILE*     1.3    79.3    +      -       -      +
     80U  LYS*     4.8     5.6    -      -       +      -
    103U  LEU*     3.9     2.4    -      -       -      +
    106U  SER*     3.9    21.4    +      -       -      +
    253U  ILE*     3.5    30.7    -      -       +      -
    255U  PHE*     4.0    26.5    -      +       +      -
----------------------------------------------------------
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Residues in contact with ILE 79 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289T  SER*     5.6     5.8    -      -       -      +
     78U  PHE*     1.3    86.4    -      -       -      +
     80U  LYS*     1.3    71.7    +      -       -      +
     81U  VAL*     4.1    10.7    +      -       +      -
     99U  ILE*     3.9    22.0    -      -       +      +
    102U  ASP*     4.3    25.8    -      -       +      +
    103U  LEU*     3.4    26.7    -      -       +      -
    106U  SER*     6.0     1.3    -      -       -      -
    253U  ILE      3.4     6.5    +      -       -      +
    254U  VAL*     4.0    14.8    -      -       +      +
    255U  PHE*     2.9    25.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 80 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284T  PRO*     6.1     0.9    -      -       -      +
    287T  GLU*     2.9    40.1    +      -       -      -
     64U  THR*     3.4    33.1    +      -       +      +
     68U  ARG*     4.5    17.0    -      -       -      +
     78U  PHE*     4.8     3.4    -      -       +      -
     79U  ILE*     1.3    82.6    -      -       -      +
     81U  VAL*     1.3    68.4    +      -       -      +
    255U  PHE*     3.3    37.5    -      -       +      +
    257U  ASP*     4.1    19.5    +      -       +      -
    458U  ATP      4.2     2.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 81 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79U  ILE*     4.5    10.1    -      -       +      -
     80U  LYS*     1.3    82.5    -      -       -      +
     82U  GLU*     1.3    60.4    +      -       -      +
     83U  ALA      4.0     1.2    +      -       -      +
     99U  ILE*     3.9    47.1    -      -       +      -
    254U  VAL*     4.7     1.1    -      -       +      -
    255U  PHE      2.7    23.7    +      -       -      +
    256U  ILE*     3.5    23.4    -      -       +      -
    257U  ASP*     2.9    27.7    +      -       -      +
    282U  LEU*     6.1     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 82 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280T  ARG*     3.9    44.0    +      -       +      +
    281T  ASP*     5.2     8.3    -      -       -      +
    283T  LEU*     4.1    15.9    -      -       +      +
    284T  PRO*     5.4    11.6    -      -       +      +
    322T  GLU*     5.3     0.2    -      -       -      +
     81U  VAL*     1.3    73.9    -      -       -      +
     83U  ALA*     1.3    74.3    +      -       -      +
    257U  ASP*     3.5    24.2    -      -       -      +
    258U  GLU*     3.1    34.9    -      -       -      +
    261U  LYS*     5.2     1.4    -      -       -      +
----------------------------------------------------------
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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