Contacts of the strand formed by residues 314 - 320 (chain A) in PDB entry 4OMD


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 THR 314 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A  PHE*     3.6    33.0    -      -       +      -
    289A  PHE*     3.1    14.8    -      -       +      -
    291A  TRP*     3.9    17.0    -      -       +      +
    308A  TYR      2.7    25.5    +      -       -      +
    309A  THR*     3.6     3.6    +      -       -      -
    311A  SER*     3.4     7.2    +      -       -      +
    312A  ILE*     3.2     3.7    -      -       -      +
    313A  TYR*     1.3    83.6    -      -       -      +
    315A  LEU*     1.3    61.0    +      -       -      +
    316A  SER      3.5     0.7    +      -       -      -
    337A  LEU*     5.9     0.3    -      -       -      +
    394A  GLN*     4.4     5.6    +      -       -      +
    534A  MET*     5.3     1.0    -      -       -      +
    606A   NA      2.4    44.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 315 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288A  ILE*     3.7    25.6    -      -       +      -
    289A  PHE      2.8    24.4    +      -       -      +
    290A  VAL*     3.7     6.8    -      -       +      -
    291A  TRP      3.0    22.3    +      -       -      +
    313A  TYR      5.0     1.3    -      -       -      +
    314A  THR*     1.3    71.2    -      -       -      +
    316A  SER*     1.3    63.7    +      -       -      +
    317A  ILE*     3.5    16.3    +      -       +      +
    337A  LEU*     4.2    14.6    -      -       +      -
    378A  ILE*     3.7    21.8    -      -       +      -
    390A  TRP      5.6     0.9    -      -       -      +
    393A  MET*     4.3     8.1    -      -       +      -
    394A  GLN*     3.9    30.3    -      -       +      +
    397A  VAL*     4.0    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291A  TRP*     3.5     7.6    -      -       -      -
    293A  SER*     3.5    15.2    -      -       -      -
    309A  THR*     3.2    49.1    -      -       -      +
    314A  THR      3.5     4.4    +      -       -      -
    315A  LEU*     1.3    70.8    -      -       -      +
    317A  ILE*     1.3    66.1    +      -       -      +
    335A  SER*     4.1     3.0    +      -       -      -
    336A  THR*     3.6    21.9    +      -       -      +
    337A  LEU*     3.0    26.7    +      -       -      +
    338A  ALA      3.6     0.7    +      -       -      -
    606A   NA      4.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 317 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290A  VAL*     4.0     6.5    -      -       +      -
    291A  TRP      2.8    15.2    +      -       -      +
    292A  ALA*     3.9     4.0    -      -       -      -
    293A  SER*     3.2    21.3    +      -       -      -
    315A  LEU*     3.5    26.2    -      -       +      +
    316A  SER*     1.3    81.3    +      -       -      +
    318A  SER*     1.3    73.5    +      -       -      +
    337A  LEU*     5.2     1.3    -      -       +      -
    338A  ALA*     3.4    24.7    -      -       +      +
    339A  THR*     4.2     0.4    -      -       -      -
    340A  THR*     3.9    28.7    -      -       +      +
    367A  THR*     4.2     3.3    +      -       -      -
    370A  SER*     4.1    11.4    -      -       -      +
    371A  ALA*     4.4     5.4    -      -       -      -
    374A  ALA*     3.6    23.8    -      -       +      -
    378A  ILE*     6.0     0.4    -      -       +      -
    397A  VAL*     5.8     1.3    -      -       +      -
    429A  LEU*     5.0     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 318 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293A  SER*     2.9    18.9    +      -       -      -
    317A  ILE*     1.3    77.5    -      -       -      +
    319A  SER*     1.3    64.4    +      -       -      +
    330A  SER*     5.0     4.0    -      -       -      -
    331A  GLU      4.1     7.4    +      -       -      -
    336A  THR*     3.3    25.2    +      -       -      +
    338A  ALA      2.9     8.3    +      -       -      -
    339A  THR*     3.3     9.0    -      -       -      +
    340A  THR      3.1    23.6    +      -       -      +
    367A  THR*     5.4     0.7    -      -       -      -
    370A  SER*     3.5     2.0    +      -       -      -
    423A  SER      3.2    25.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 319 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318A  SER*     1.3    75.7    -      -       -      +
    320A  ALA*     1.3    62.1    +      -       -      +
    327A  PRO*     3.3    16.8    -      -       -      +
    329A  TYR*     3.7    29.8    -      -       -      -
    330A  SER*     4.7     6.9    +      -       -      -
    339A  THR*     3.5     4.4    -      -       -      +
    340A  THR      3.4     4.0    -      -       -      -
    342A  SER*     3.7     4.4    -      -       -      -
    367A  THR*     3.7    19.9    -      -       -      -
    370A  SER*     2.7    23.1    +      -       -      -
    423A  SER      4.5     2.3    -      -       -      +
    424A  TYR*     3.5    15.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 320 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  SER*     1.3    76.6    -      -       -      +
    321A  THR*     1.3    69.1    +      -       -      +
    324A  GLY*     5.1     0.7    -      -       -      -
    325A  ASN      3.5     7.2    -      -       -      +
    327A  PRO*     4.0     3.6    -      -       -      -
    339A  THR*     3.7    15.9    -      -       +      -
    340A  THR      3.3     4.8    +      -       -      +
    341A  TYR*     3.4    12.5    -      -       +      -
    342A  SER      3.0    23.2    +      -       -      -
    406A  LEU*     4.0    20.2    -      -       +      -
    424A  TYR*     3.9    12.3    -      -       +      +
    428A  LEU*     4.3     2.0    -      -       +      -
----------------------------------------------------------
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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