Contacts of the strand formed by residues 291 - 295 (chain G) in PDB entry 1F9E


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 GLN 291 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322F  PRO*     3.5    25.0    -      -       +      +
    323F  ASP*     3.2    10.6    -      -       -      +
    324F  GLU*     2.5    64.0    -      -       -      +
    289G  ASN      3.9     3.0    +      -       -      -
    290G  TYR*     1.3    69.8    -      -       -      +
    292G  LYS*     1.3    60.5    +      -       -      +
    334H  VAL*     4.0     2.8    -      -       +      +
    337H  CYS*     3.7    24.8    -      -       +      +
    338H  VAL*     5.4     0.6    -      -       -      +
    383H  GLY*     3.6     3.6    -      -       -      -
    384H  LYS*     2.8    51.0    +      -       -      +
    385H  GLN*     4.4     2.5    -      -       -      +
    386H  MET*     4.3    12.4    -      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
    268E  LEU*     4.1    27.3    -      -       +      +
    322F  PRO*     3.6     2.4    -      -       -      +
    323F  ASP*     2.7    47.2    +      -       +      +
    290G  TYR*     3.1    13.8    +      -       +      +
    291G  GLN*     1.3    77.9    -      -       -      +
    293G  GLY*     1.3    57.9    -      -       -      +
    382H  MET      4.6     7.0    -      -       -      +
    384H  LYS*     4.5     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 293 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268E  LEU*     4.5     4.9    -      -       -      +
    320F  TYR*     4.4    16.0    -      -       -      -
    321F  ILE      3.5     1.1    -      -       -      -
    291G  GLN      4.0     0.4    +      -       -      -
    292G  LYS*     1.3    76.7    -      -       -      +
    294G  ILE*     1.3    68.2    +      -       -      +
    295G  PRO*     4.6     1.6    -      -       -      +
    382H  MET      4.5     5.9    +      -       -      -
    384H  LYS*     3.4    28.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 294 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267E  GLY*     3.2    28.9    -      -       -      +
    268E  LEU*     3.5    27.1    -      -       +      -
    274E  ALA*     3.5    28.0    -      -       +      -
    275E  GLY      4.8     0.2    -      -       -      +
    320F  TYR*     3.3     4.6    -      -       -      -
    321F  ILE*     2.9    52.8    +      -       +      +
    322F  PRO      4.3     6.3    -      -       -      +
    323F  ASP*     3.8    20.0    -      -       +      +
    293G  GLY*     1.3    80.8    -      -       -      +
    295G  PRO*     1.3    70.4    -      -       +      +
    296G  VAL*     4.5     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 295 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268E  LEU*     6.2     0.7    -      -       +      -
    274E  ALA*     4.3     6.6    -      -       -      +
    318F  THR*     4.5     8.1    -      -       -      +
    319F  ARG      4.4     0.4    -      -       -      +
    320F  TYR*     3.4    35.8    -      -       +      +
    293G  GLY      4.6     2.0    -      -       -      +
    294G  ILE*     1.3    83.6    -      -       +      +
    296G  VAL*     1.3    73.1    +      -       -      +
----------------------------------------------------------
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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