Contacts of the strand formed by residues 287 - 293 (chain G) in PDB entry 1II4


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 HIS 287 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66C  ALA*     3.8    11.9    -      -       +      -
     67C  GLU      3.5     6.5    +      -       -      -
     68C  GLU*     3.4    33.6    -      -       +      -
     69C  ARG*     3.5    25.3    +      -       +      +
     70C  GLY      5.2     0.2    -      -       -      +
    285G  GLN      4.2     0.2    +      -       -      -
    286G  PRO*     1.3    73.2    -      -       -      +
    288G  ILE*     1.3    70.8    +      -       -      +
    289G  GLN*     3.9    25.3    +      -       +      -
    314G  ALA*     4.1    13.3    -      -       +      +
    315G  ALA*     3.0    37.1    +      -       +      -
    343G  LEU*     3.4     2.8    -      -       -      +
    344G  ALA*     3.3     3.1    -      -       -      -
    345G  GLY      2.8    31.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 288 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  PHE*     4.1    17.9    -      -       +      -
    278G  CYS*     4.9     0.7    -      -       -      -
    280G  VAL*     3.4    34.3    -      -       +      -
    286G  PRO*     4.1     6.3    +      -       +      +
    287G  HIS*     1.3    83.7    -      -       -      +
    289G  GLN*     1.3    66.6    +      -       -      +
    290G  TRP*     5.2     0.9    -      -       -      +
    315G  ALA*     2.8    32.3    +      -       -      +
    321G  ASP*     5.4     1.8    -      -       -      +
    324G  ILE*     3.6    30.9    -      -       +      +
    325G  GLU*     4.1    16.6    -      -       +      -
    342G  CYS*     3.7    28.5    -      -       -      -
    343G  LEU      3.3     5.4    -      -       -      +
    344G  ALA*     4.3     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 289 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287G  HIS*     3.9    20.5    +      -       +      +
    288G  ILE*     1.3    77.9    -      -       -      +
    290G  TRP*     1.3    65.0    +      -       -      +
    291G  ILE*     4.0     9.2    -      -       +      +
    311G  VAL*     3.2    30.1    -      -       +      +
    313G  LYS      3.0    17.0    -      -       -      +
    314G  ALA*     3.8    11.7    -      -       +      +
    324G  ILE*     4.9     0.2    -      -       -      -
    341G  THR      3.8     0.2    -      -       -      +
    342G  CYS*     3.8     2.3    -      -       -      -
    343G  LEU*     3.0    62.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 290 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263G  PRO*     4.0     9.4    -      -       +      -
    276G  PHE*     3.0    45.8    -      +       +      -
    277G  VAL      3.8     1.8    -      -       -      -
    278G  CYS*     3.6    21.5    -      -       +      -
    288G  ILE*     5.2     1.6    -      -       +      +
    289G  GLN*     1.3    74.8    -      -       -      +
    291G  ILE*     1.3    64.8    +      -       -      +
    311G  VAL*     3.6     2.6    -      -       -      +
    312G  LEU*     2.9    29.8    +      -       +      -
    313G  LYS*     2.7    39.4    +      -       +      +
    324G  ILE*     2.6    27.9    +      -       +      +
    325G  GLU      3.2    24.5    -      -       -      -
    326G  VAL      4.2     1.8    -      -       -      -
    327G  LEU*     3.6    36.6    -      -       +      +
    340G  TYR*     5.2     2.9    -      -       +      -
    341G  THR      3.4    21.8    -      -       -      -
    342G  CYS*     3.9    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 291 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289G  GLN*     4.0    21.3    -      -       +      +
    290G  TRP*     1.3    81.0    -      -       -      +
    292G  LYS*     1.3    65.2    +      -       -      +
    293G  HIS*     4.4     1.6    +      -       +      -
    309G  LEU*     3.6    44.4    -      -       +      -
    310G  LYS      3.3    14.6    -      -       -      +
    311G  VAL*     4.5     5.8    -      -       +      +
    312G  LEU*     4.7     3.4    -      -       -      -
    339G  GLU      3.9     0.3    -      -       -      +
    340G  TYR*     3.5     2.5    -      -       -      +
    341G  THR*     2.7    52.2    +      -       +      +
    343G  LEU*     3.6    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 292 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291G  ILE*     1.3    75.1    -      -       -      +
    293G  HIS*     1.3    67.4    +      -       -      +
    294G  VAL*     3.5     8.7    -      -       +      +
    309G  LEU*     3.6     1.6    -      -       -      -
    310G  LYS*     2.9    33.8    +      -       +      +
    312G  LEU*     3.9    28.0    -      -       +      +
    339G  GLU      3.6     6.3    -      -       -      +
    340G  TYR*     4.5    16.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 293 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291G  ILE*     4.4     2.2    +      -       +      -
    292G  LYS*     1.3    76.9    -      -       -      +
    294G  VAL*     1.3    60.2    +      -       -      +
    307G  PRO*     5.6     5.6    -      -       +      -
    308G  TYR      3.5     6.1    -      -       -      +
    309G  LEU*     3.6    23.3    -      -       +      +
    338G  GLY*     5.4     3.3    -      -       -      -
    339G  GLU*     3.0    58.5    +      -       +      +
    341G  THR*     3.0    32.5    -      -       +      -
    354G  SER*     4.5     1.5    +      -       -      -
----------------------------------------------------------
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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