Contacts of the strand formed by residues 219 - 227 (chain A) in PDB entry 1GIA


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 THR 219 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  VAL*     3.8    22.1    -      -       +      -
     35A  LYS*     2.8    36.9    +      -       -      +
    217A  GLY      3.3     4.4    +      -       -      -
    218A  VAL*     1.3    72.4    -      -       -      +
    220A  ALA*     1.3    61.2    +      -       +      +
    261A  ASP      4.7     1.9    -      -       -      +
    262A  THR*     3.6     4.7    -      -       -      +
    263A  SER*     3.4    19.9    +      -       -      -
    343A  ILE*     4.3    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LYS      3.2     1.4    +      -       -      -
     36A  LEU*     3.4    24.9    -      -       +      +
     37A  LEU      3.1    22.0    +      -       -      -
    218A  VAL*     3.4     4.1    -      -       -      +
    219A  THR*     1.3    84.7    -      -       +      +
    221A  ILE*     1.3    63.7    +      -       -      +
    262A  THR*     3.7     2.0    -      -       -      -
    263A  SER*     3.4    13.9    -      -       -      +
    265A  ILE*     3.6    22.7    -      -       +      -
    343A  ILE*     4.5     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  LEU*     3.3    15.3    -      -       +      +
     39A  LEU*     4.2    19.5    -      -       +      -
    218A  VAL*     3.9    14.8    -      -       +      -
    220A  ALA*     1.3    75.7    -      -       -      +
    222A  ILE*     1.3    71.8    +      -       -      +
    223A  PHE*     4.0    11.9    -      -       +      +
    253A  ILE*     3.9    20.6    -      -       +      -
    259A  PHE*     3.8    41.7    -      -       +      -
    262A  THR*     4.0     3.4    -      -       +      -
    263A  SER      2.9    10.1    +      -       -      +
    264A  ILE*     4.1    14.8    -      -       +      -
    265A  ILE*     2.8    31.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 222 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  LEU*     4.3    29.2    -      -       +      -
     37A  LEU      2.9     8.0    +      -       -      +
     38A  LEU*     3.4    32.2    -      -       +      +
     39A  LEU      3.1    21.3    +      -       -      +
     49A  ILE*     5.5     1.8    -      -       +      -
    198A  MET*     4.8     4.5    -      -       +      -
    221A  ILE*     1.3    77.0    -      -       -      +
    223A  PHE*     1.3    58.8    +      -       -      +
    224A  CYS*     3.6     6.9    +      -       -      -
    265A  ILE*     3.4    21.5    -      -       +      -
    267A  PHE*     3.8    46.4    -      -       +      -
    336A  PHE*     4.7    12.8    -      -       +      -
    339A  VAL*     5.1     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 223 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  LEU*     3.4    18.4    -      -       +      -
     40A  GLY*     3.9    18.2    -      -       -      -
     41A  ALA      5.0     0.7    -      -       -      -
    211A  TRP*     5.2     1.6    -      +       -      -
    221A  ILE*     3.7     7.5    -      -       +      -
    222A  ILE*     1.3    72.7    -      -       -      +
    224A  CYS*     1.3    67.2    +      -       -      +
    225A  VAL*     3.7    25.6    -      -       +      -
    246A  SER*     4.1     6.7    -      -       -      -
    249A  LEU*     3.8    15.3    -      -       +      -
    250A  PHE*     3.6    63.5    -      +       +      -
    253A  ILE*     4.1    25.8    -      -       +      -
    264A  ILE*     5.0     1.8    -      -       +      -
    265A  ILE      2.8    14.5    +      -       -      +
    266A  LEU*     3.6     6.7    -      -       +      +
    267A  PHE      2.9    26.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 224 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  LEU*     4.7     4.9    -      -       -      -
     39A  LEU      2.8    11.7    +      -       -      +
     40A  GLY*     3.6    13.0    -      -       -      -
     41A  ALA      4.4     1.0    +      -       -      -
     44A  SER*     3.5    36.9    -      -       -      +
     45A  GLY      4.5     2.9    -      -       -      -
     46A  LYS*     4.0    28.0    -      -       +      -
     49A  ILE*     4.7     4.0    -      -       -      -
    222A  ILE*     4.2    21.1    -      -       -      -
    223A  PHE*     1.3    75.7    -      -       -      +
    225A  VAL*     1.3    65.8    +      -       -      +
    246A  SER*     5.2     0.9    +      -       -      -
    267A  PHE*     3.6    17.7    -      -       +      +
    269A  ASN*     5.1     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 225 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  SER*     4.5     2.5    -      -       -      -
    223A  PHE*     3.7    18.4    -      -       +      -
    224A  CYS*     1.3    79.4    -      -       -      +
    226A  ALA*     1.3    63.9    +      -       -      +
    227A  LEU*     3.5     3.0    +      -       +      +
    243A  MET*     3.9    18.4    -      -       +      -
    246A  SER*     4.3    11.7    -      -       -      +
    266A  LEU*     3.9    10.3    -      -       +      -
    267A  PHE      2.9     5.7    +      -       -      -
    268A  LEU*     3.6    16.6    -      -       +      -
    269A  ASN*     2.7    35.8    +      -       -      +
    307A  PHE*     3.7    43.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 226 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  GLU      4.4     0.4    -      -       -      +
     44A  SER*     4.2    17.0    -      -       -      -
    225A  VAL*     1.3    75.9    -      -       -      +
    227A  LEU*     1.3    66.0    +      -       -      +
    228A  SER      3.2     0.7    -      -       -      -
    229A  ASP*     3.1    43.4    +      -       -      +
    243A  MET*     3.7     6.9    -      -       -      +
    246A  SER*     5.2     1.8    +      -       -      -
    269A  ASN      3.8     6.1    -      -       -      -
    270A  LYS*     3.8    31.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 227 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  VAL*     3.5     2.9    +      -       +      -
    226A  ALA*     1.3    71.0    -      -       -      +
    228A  SER*     1.3    57.2    -      -       -      +
    229A  ASP      3.2     4.5    +      -       -      -
    230A  TYR*     3.3    18.5    -      -       -      -
    243A  MET*     3.5    13.0    -      -       +      +
    268A  LEU*     3.7    37.7    -      -       +      +
    269A  ASN      2.8    22.9    +      -       -      +
    271A  LYS*     3.9    19.1    -      -       +      -
    274A  PHE*     3.6    33.6    -      -       +      -
    296A  TYR*     5.0     0.9    -      -       +      +
    300A  ALA*     5.3     0.9    -      -       -      -
    303A  ILE*     3.9    35.9    -      -       +      -
    323A  PHE*     4.0    20.4    -      -       +      -
----------------------------------------------------------
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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