Contacts of the strand formed by residues 331 - 335 (chain J) in PDB entry 1F1H


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 MET 331 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330J  VAL*     1.3    85.5    -      -       +      +
    332J  LEU*     1.3    56.1    +      -       -      +
    333J  ALA*     2.9    11.3    +      -       +      +
    338J  ASN*     6.2     0.2    -      -       -      +
    340J  SER*     3.4    30.8    +      -       -      +
    341J  ALA*     3.9     2.5    -      -       -      -
    342J  SER*     2.5    30.4    +      -       -      -
    392J  MET*     5.8     7.2    -      -       +      -
    396J  LEU*     4.8     4.0    -      -       -      -
    397J  TYR*     3.9    43.5    -      -       +      +
    405J  LYS*     5.1     4.9    -      -       +      +
    407J  ILE*     4.0    31.9    -      -       +      -
    408J  PRO      3.9     3.4    -      -       -      -
    409J  GLN*     3.9    25.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 332 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302J  ILE*     3.6    43.2    -      -       +      +
    305J  ALA*     3.6    29.2    -      -       +      -
    306J  LYS*     5.3     3.4    -      -       +      +
    331J  MET*     1.3    66.6    -      -       -      +
    333J  ALA*     1.3    61.0    +      -       -      +
    342J  SER*     3.7     9.4    -      -       -      +
    343J  ILE*     6.0     0.7    -      -       -      -
    360J  PHE*     5.0     4.0    -      -       +      -
    407J  ILE*     4.4     5.5    -      -       -      +
    408J  PRO*     2.8    35.4    +      -       +      +
    409J  GLN      3.4    21.8    -      -       -      +
    410J  VAL*     3.5    35.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 333 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302J  ILE*     4.1     8.5    -      -       -      +
    331J  MET*     2.9    10.8    +      -       +      +
    332J  LEU*     1.3    75.9    -      -       -      +
    334J  TYR*     1.3    62.5    +      -       -      +
    341J  ALA*     3.5    12.1    -      -       +      +
    342J  SER*     3.7     1.1    +      -       -      -
    343J  ILE*     3.4    25.5    +      -       -      +
    390J  GLU      5.5     1.3    -      -       -      +
    392J  MET*     3.6    43.1    -      -       +      +
    407J  ILE*     4.7     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 334 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287J  TYR*     4.4    16.9    -      +       -      +
    290J  LEU*     5.0     0.2    -      -       +      -
    295J  LEU*     4.0    20.1    -      -       +      +
    298J  ILE*     4.1    36.1    -      -       +      -
    302J  ILE*     4.7     2.0    -      -       +      -
    333J  ALA*     1.3    78.1    -      -       -      +
    335J  SER*     1.3    60.9    +      -       -      +
    341J  ALA*     4.4     0.4    -      -       -      -
    343J  ILE*     3.3    15.9    -      -       +      +
    345J  ILE*     4.4     6.7    -      -       +      -
    387J  HIS*     4.7     2.3    -      -       -      -
    388J  PRO*     3.3    42.3    -      -       +      +
    389J  GLY      2.6    21.0    +      -       -      -
    390J  GLU*     3.9     8.0    -      -       -      -
    391J  PRO*     3.2    37.3    -      -       +      +
    392J  MET      2.9    25.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 335 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287J  TYR*     3.9     8.7    -      -       -      -
    334J  TYR*     1.3    77.9    -      -       -      +
    336J  ALA*     1.3    63.4    +      -       -      +
    337J  ARG*     3.1     5.1    +      -       -      +
    338J  ASN*     2.9    32.6    +      -       -      +
    341J  ALA*     4.0     7.4    -      -       -      +
    343J  ILE      3.1     6.3    +      -       -      +
    344J  ARG*     3.2    11.1    -      -       -      +
    345J  ILE*     2.9    24.9    +      -       -      +
    392J  MET      3.7    17.0    -      -       -      -
    393J  ASP*     3.6    12.0    +      -       -      -
----------------------------------------------------------
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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