Contacts of the strand formed by residues 429 - 434 (chain B) in PDB entry 1F6A


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 LEU 429 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330B  ASP      5.3     0.2    -      -       -      +
    331B  SER*     3.1    18.6    -      -       -      +
    333B  PRO*     3.3    18.8    -      -       +      +
    336B  VAL*     3.0    35.9    -      -       +      +
    337B  SER      4.3     0.9    -      -       -      -
    338B  ALA*     4.0    20.0    -      -       +      -
    418B  CYS      3.8     0.2    -      -       -      +
    419B  ARG*     3.4     0.7    -      -       -      +
    420B  VAL*     2.8    60.7    +      -       +      +
    425B  LEU*     5.3     2.6    -      -       +      +
    428B  ALA*     1.3    72.6    -      -       -      +
    430B  MET*     1.3    73.0    +      -       -      +
    431B  ARG*     2.9    33.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 430 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330B  ASP      5.9     0.2    +      -       -      -
    331B  SER*     5.2     2.6    -      -       -      -
    417B  GLN*     3.8    31.6    -      -       -      +
    418B  CYS      3.3     6.7    -      -       -      +
    419B  ARG*     3.8    30.3    -      -       +      +
    428B  ALA*     4.1    11.7    +      -       +      +
    429B  LEU*     1.3    84.8    -      -       -      +
    431B  ARG*     1.3    83.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 431 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331B  SER*     2.9    50.2    +      -       -      -
    332B  ASN*     4.3     3.7    +      -       -      -
    338B  ALA*     2.9    46.2    +      -       +      +
    339B  TYR*     4.3     5.6    -      -       -      +
    340B  LEU*     3.7    19.3    -      -       +      +
    358B  CYS*     5.8     1.1    -      -       -      -
    417B  GLN*     3.3     4.6    -      -       -      +
    418B  CYS*     2.8    35.7    +      -       +      +
    429B  LEU*     2.9    21.2    -      -       +      +
    430B  MET*     1.3    90.2    +      -       -      +
    432B  SER*     1.3    62.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 432 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340B  LEU*     3.6     8.4    -      -       -      +
    415B  THR*     4.8     7.8    +      -       -      -
    416B  TYR      3.2    15.5    -      -       -      -
    417B  GLN*     3.9    18.7    +      -       -      -
    431B  ARG*     1.3    78.5    -      -       -      +
    433B  THR*     1.3    65.3    +      -       -      +
    434B  THR*     6.0     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 433 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340B  LEU*     3.6    31.5    +      -       +      +
    341B  SER      4.8     3.6    -      -       -      +
    342B  ARG*     3.7    28.5    +      -       -      +
    356B  ILE*     4.7    15.9    -      -       +      -
    410B  TRP*     4.2    16.8    -      -       +      -
    416B  TYR*     3.0    21.9    +      -       -      +
    432B  SER*     1.3    79.6    -      -       -      +
    434B  THR*     1.3    73.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 434 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342B  ARG*     3.6    15.9    +      -       -      -
    410B  TRP*     3.8    13.5    -      -       -      -
    413B  GLY*     4.2     5.7    +      -       -      +
    414B  GLU      3.1    14.6    -      -       -      +
    415B  THR*     2.9    40.8    -      -       -      +
    432B  SER*     6.0     0.4    -      -       -      +
    433B  THR*     1.3    80.4    +      -       -      +
    435B  LYS*     1.3    73.8    +      -       -      +
    436B  THR*     3.3     2.4    +      -       -      -
----------------------------------------------------------
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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