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


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 E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274E  PHE*     3.7    31.6    -      -       +      -
    289E  PHE*     3.1    12.3    -      -       +      -
    291E  TRP*     3.9    22.4    -      -       +      +
    308E  TYR      2.7    27.4    +      -       -      +
    309E  THR*     3.5     3.1    +      -       -      -
    311E  SER*     3.4     6.9    +      -       -      +
    312E  ILE*     3.3     4.7    -      -       -      +
    313E  TYR*     1.3    82.0    -      -       -      +
    315E  LEU*     1.3    59.4    +      -       -      +
    316E  SER      3.5     0.9    +      -       -      -
    337E  LEU*     5.9     0.2    -      -       -      +
    394E  GLN*     4.1     5.4    +      -       -      +
    534E  MET*     5.5     0.7    -      -       -      +
    608E   NA      2.4    47.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 315 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288E  ILE*     3.5    29.8    -      -       +      -
    289E  PHE      2.8    23.3    +      -       -      +
    290E  VAL*     3.7     4.7    -      -       +      -
    291E  TRP      3.0    21.7    +      -       -      +
    313E  TYR      5.2     1.1    -      -       -      +
    314E  THR*     1.3    72.3    -      -       -      +
    316E  SER*     1.3    63.3    +      -       -      +
    317E  ILE*     3.5    16.0    +      -       +      +
    337E  LEU*     3.8    21.8    -      -       +      -
    378E  ILE*     4.1    16.8    -      -       +      -
    390E  TRP      5.7     0.7    -      -       -      +
    393E  MET*     4.3     9.4    -      -       +      -
    394E  GLN*     3.8    32.5    -      -       +      +
    397E  VAL*     4.0    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 316 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291E  TRP*     3.5     7.2    -      -       -      -
    293E  SER*     3.4    19.2    -      -       -      -
    303E  CYS*     5.4     0.2    -      -       -      +
    309E  THR*     3.4    45.1    -      -       -      +
    314E  THR      3.5     4.6    +      -       -      -
    315E  LEU*     1.3    73.2    -      -       -      +
    317E  ILE*     1.3    63.8    +      -       -      +
    335E  SER*     4.2     2.6    +      -       -      -
    336E  THR*     3.7    19.0    +      -       -      +
    337E  LEU*     3.0    28.9    +      -       -      +
    338E  ALA      3.6     1.4    +      -       -      -
    608E   NA      3.8     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 317 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290E  VAL*     4.0     9.0    -      -       +      -
    291E  TRP      2.8    13.2    +      -       -      +
    292E  ALA*     3.9     3.1    -      -       -      -
    293E  SER*     3.0    21.9    +      -       -      -
    315E  LEU*     3.7    22.9    -      -       +      +
    316E  SER*     1.3    82.9    +      -       -      +
    318E  SER*     1.3    75.0    +      -       -      +
    337E  LEU*     5.2     0.9    -      -       +      -
    338E  ALA*     3.4    25.6    -      -       +      +
    339E  THR*     4.2     0.7    -      -       -      +
    340E  THR*     3.8    28.5    -      -       +      +
    367E  THR*     4.3     3.1    +      -       -      -
    370E  SER*     4.1    10.5    -      -       -      +
    371E  ALA*     4.4     6.1    -      -       -      -
    374E  ALA*     3.6    24.2    -      -       +      -
    378E  ILE*     6.1     0.7    -      -       +      -
    397E  VAL*     5.8     2.0    -      -       +      -
    429E  LEU*     4.9     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 318 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293E  SER*     2.9    19.1    +      -       -      -
    317E  ILE*     1.3    76.7    -      -       -      +
    319E  SER*     1.3    65.8    +      -       -      +
    330E  SER*     5.1     4.0    -      -       -      -
    331E  GLU      4.2     6.8    +      -       -      -
    336E  THR*     3.2    25.2    +      -       -      +
    338E  ALA      2.9     9.5    +      -       -      -
    339E  THR*     3.2     6.9    -      -       -      +
    340E  THR      3.1    24.8    +      -       -      +
    367E  THR*     5.6     0.4    -      -       -      -
    370E  SER*     3.5     2.0    +      -       -      -
    423E  SER      3.3    24.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 319 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318E  SER*     1.3    77.2    -      -       -      +
    320E  ALA*     1.3    62.2    +      -       -      +
    327E  PRO*     3.2    17.3    -      -       -      +
    329E  TYR*     3.7    31.1    -      -       -      -
    330E  SER*     4.8     6.0    +      -       -      -
    339E  THR*     3.5     4.2    -      -       -      +
    340E  THR      3.3     4.5    -      -       -      -
    342E  SER*     3.8     4.6    -      -       -      -
    367E  THR*     3.7    20.1    -      -       -      -
    370E  SER*     2.8    21.8    +      -       -      -
    423E  SER      4.6     0.9    -      -       -      +
    424E  TYR*     3.7    12.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 320 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319E  SER*     1.3    77.0    -      -       -      +
    321E  THR*     1.3    65.1    +      -       -      +
    324E  GLY*     5.1     0.2    -      -       -      -
    325E  ASN      3.5     7.9    -      -       -      +
    327E  PRO*     4.0     3.1    -      -       -      -
    339E  THR*     3.8    14.8    -      -       +      -
    340E  THR      3.3     6.2    +      -       -      +
    341E  TYR*     3.4    16.2    -      -       +      -
    342E  SER      2.9    23.0    +      -       -      -
    406E  LEU*     3.9    27.1    -      -       +      -
    424E  TYR*     4.1     6.3    -      -       +      -
    428E  LEU*     4.6     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