Contacts of the strand formed by residues 296 - 299 (chain D) 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 GLY 296 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245D  ILE*     4.7     4.7    -      -       -      -
    292D  SER*     5.1     0.7    -      -       -      -
    293D  THR*     2.5    42.6    +      -       -      -
    294D  LYS      3.6     0.4    -      -       -      -
    295D  HIS*     1.3    81.7    -      -       -      +
    297D  MET*     1.3    65.3    +      -       -      -
    298D  VAL*     4.8     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 297 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105C  ASP*     4.3    31.2    -      -       +      +
    106C  SER*     5.8     1.3    -      -       -      +
    109C  LYS*     5.5    15.0    -      -       +      +
    294C  LYS*     5.7     2.7    -      -       -      -
    245D  ILE*     3.5    14.8    -      -       -      +
    249D  GLU*     3.5     9.5    -      -       -      +
    290D  THR*     3.4    30.7    -      -       +      -
    291D  VAL      4.0     0.7    -      -       -      +
    292D  SER*     3.7    34.5    -      -       -      +
    296D  GLY*     1.3    74.3    -      -       -      -
    298D  VAL*     1.3    61.7    +      -       -      +
    299D  LYS*     5.1     1.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 298 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100D  ILE*     3.2    34.5    -      -       +      -
    104D  THR*     3.4    27.4    -      -       +      +
    245D  ILE*     3.9    21.3    -      -       +      +
    248D  VAL*     4.6     7.4    -      -       +      -
    249D  GLU*     3.4    11.0    -      -       +      -
    290D  THR*     3.2     3.6    -      -       -      +
    291D  VAL*     3.0    39.3    +      -       +      +
    293D  THR*     3.9    13.2    -      -       +      +
    297D  MET*     1.3    79.1    -      -       -      +
    299D  LYS*     1.3    62.5    +      -       -      +
    300D  THR      4.0     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 299 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  LYS*     3.8    24.3    -      -       +      +
     46D  HIS*     3.8    27.8    +      -       -      -
    249D  GLU*     3.0    45.5    +      -       -      +
    289D  SER      3.4     8.3    -      -       -      +
    290D  THR*     4.2    13.0    -      -       +      +
    297D  MET*     5.1     1.1    -      -       +      +
    298D  VAL*     1.3    78.0    -      -       -      +
    300D  THR*     1.3    60.4    +      -       -      +
    301D  ASP*     2.9    31.5    +      -       +      +
    302D  HIS*     3.9     6.4    +      -       -      -
    303D  ILE*     4.1     4.1    -      -       -      +
----------------------------------------------------------
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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