Contacts of the strand formed by residues 330 - 335 (chain A) in PDB entry 1OFD


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 ALA 330 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  HIS*     4.2     6.1    -      -       -      +
    227A  ASN      3.2     7.9    -      -       -      +
    230A  ILE*     5.5     5.6    -      -       +      -
    274A  LEU*     5.8     0.2    -      -       +      -
    296A  VAL*     5.2     6.1    -      -       +      -
    326A  TRP      6.1     0.7    -      -       -      +
    328A  GLY      4.1     2.5    -      -       -      +
    329A  PRO*     1.3    77.4    -      -       -      +
    331A  LEU*     1.3    59.6    +      -       -      +
    332A  LEU*     4.0    25.4    -      -       +      -
    344A  LEU*     3.3    10.8    -      -       -      +
    345A  ASP*     3.0    44.9    +      -       +      +
    350A  ARG*     3.8     7.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 331 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  VAL*     3.4    33.8    -      -       +      +
    225A  GLY      3.7     1.4    -      -       -      +
    226A  HIS*     3.7     2.6    -      -       -      -
    227A  ASN*     2.8    35.8    +      -       +      +
    330A  ALA*     1.3    72.5    -      -       -      +
    332A  LEU*     1.3    73.6    +      -       -      +
    333A  VAL*     4.1     9.1    +      -       +      -
    342A  ALA*     4.2    10.8    -      -       +      -
    343A  GLY      3.6    10.8    -      -       -      +
    344A  LEU*     3.8    17.9    -      -       +      -
    350A  ARG*     3.6    10.9    -      -       +      +
    351A  PRO      3.5    21.5    -      -       -      +
    352A  ALA*     4.0    14.6    -      -       +      -
    364A  LEU*     4.7     2.5    -      -       +      -
    365A  GLY      4.7     1.6    -      -       -      -
    366A  SER*     4.1    11.2    -      -       -      +
    384A  LEU*     4.5     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 332 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224A  LEU*     3.6    20.6    -      -       +      -
    225A  GLY      3.6     2.9    -      -       -      -
    226A  HIS*     3.5    31.4    -      -       +      -
    274A  LEU*     3.7    16.6    -      -       +      -
    278A  LEU*     5.1     6.5    -      -       +      -
    292A  ALA*     4.5    19.7    -      -       +      -
    296A  VAL*     4.2    28.0    -      -       +      -
    330A  ALA*     4.0    11.2    -      -       +      -
    331A  LEU*     1.3    73.6    -      -       -      +
    333A  VAL*     1.3    62.3    +      -       -      +
    334A  PHE*     3.7    11.5    -      -       +      -
    342A  ALA*     3.0     8.0    -      -       -      +
    343A  GLY*     2.9    40.3    +      -       -      +
    344A  LEU      6.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 333 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  VAL*     3.7    37.0    -      -       +      -
      4A  GLY*     3.8    15.7    -      -       -      +
      5A  PHE*     3.8    22.0    -      -       +      -
    202A  VAL*     3.6    24.7    -      -       +      +
    223A  LEU      4.0     0.2    -      -       -      +
    224A  LEU*     3.4     2.5    -      -       -      +
    225A  GLY      2.7    36.2    +      -       -      -
    331A  LEU*     4.1    11.4    -      -       +      -
    332A  LEU*     1.3    78.6    -      -       -      +
    334A  PHE*     1.3    66.5    +      -       -      +
    341A  GLY      3.4    11.2    -      -       -      +
    342A  ALA*     4.2     6.1    -      -       +      -
    364A  LEU*     4.5     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 334 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  VAL*     4.4     5.4    -      -       -      -
    223A  LEU*     3.1    26.7    -      -       +      +
    224A  LEU*     4.3     7.2    -      -       +      -
    278A  LEU*     5.3     5.8    -      -       +      -
    288A  PRO*     3.7    31.2    -      -       +      -
    289A  LEU*     3.6    32.3    -      -       +      -
    292A  ALA*     4.5    14.4    -      -       +      -
    332A  LEU*     3.7    33.4    -      -       +      -
    333A  VAL*     1.3    80.6    -      -       -      +
    335A  SER*     1.3    64.6    +      -       -      +
    339A  ILE*     4.9     2.0    -      -       +      -
    340A  VAL*     3.3     3.1    -      -       -      +
    341A  GLY*     2.9    39.8    +      -       -      -
    342A  ALA*     3.7    17.9    -      -       -      -
    343A  GLY*     4.1     3.8    -      -       -      -
    389A  MET*     5.3     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 335 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  MET*     4.0    16.5    -      -       -      +
    172A  THR*     5.1     2.6    +      -       -      +
    200A  PHE*     3.7    29.0    -      -       -      -
    202A  VAL*     4.3     1.1    -      -       -      -
    222A  ARG      4.5     1.6    -      -       -      +
    223A  LEU*     3.1    29.8    +      -       -      +
    283A  ARG*     5.9     0.2    +      -       -      -
    288A  PRO*     5.3     0.2    -      -       -      -
    334A  PHE*     1.3    80.8    -      -       -      +
    336A  ASP*     1.3    58.3    -      -       -      +
    337A  GLY*     2.8    18.1    +      -       -      -
    339A  ILE      2.7    21.2    +      -       -      -
    340A  VAL*     3.9     8.4    -      -       -      +
    394A  LEU*     5.1     0.2    -      -       -      +
----------------------------------------------------------
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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