Contacts of the strand formed by residues 351 - 355 (chain D) 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 ILE 351 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122D  TRP*     4.5     2.2    -      -       +      -
    123D  TYR*     3.5    40.8    -      -       +      +
    201D  GLU*     3.5    32.8    -      -       +      +
    341D  TYR      4.1     8.1    -      -       -      +
    342D  SER*     4.0    25.4    -      -       -      +
    350D  GLN*     1.3    82.1    -      -       -      +
    352D  VAL*     1.3    65.4    +      -       -      +
    353D  THR*     4.8     0.2    -      -       +      -
    361D  THR      3.8     1.4    -      -       -      +
    362D  GLU      3.4     7.9    -      -       -      -
    364D  HIS*     3.1    44.5    +      -       +      +
    369D  ALA*     3.5    20.9    -      -       +      -
    373D  LEU*     4.5     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 352 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117D  LYS*     3.8    31.9    -      -       +      -
    120D  GLN*     3.9    31.6    -      -       +      +
    121D  GLN*     3.2    22.9    +      -       +      +
    123D  TYR*     3.0    23.4    +      -       -      +
    200D  GLY      5.7     0.2    -      -       -      +
    201D  GLU*     5.3     2.6    -      -       -      +
    211D  CYS*     4.3     8.3    -      -       -      -
    212D  GLY      4.8     0.7    -      -       -      +
    350D  GLN      3.8     5.1    +      -       -      +
    351D  ILE*     1.3    73.0    -      -       -      +
    353D  THR*     1.3    67.4    +      -       -      +
    360D  CYS*     4.4     0.2    -      -       -      -
    361D  THR      3.3    10.8    -      -       -      +
    362D  GLU*     3.9    24.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 353 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121D  GLN*     5.3     0.4    -      -       -      +
    197D  ARG*     2.8    36.2    +      -       -      +
    200D  GLY*     3.2    17.1    -      -       -      -
    201D  GLU*     3.2    11.5    +      -       +      -
    211D  CYS*     3.6    13.5    -      -       -      -
    212D  GLY*     6.4     0.4    -      -       -      -
    351D  ILE*     4.8     0.7    -      -       +      -
    352D  VAL*     1.3    78.4    -      -       -      +
    354D  THR*     1.3    66.0    +      -       -      +
    361D  THR*     2.9    49.3    +      -       +      +
    364D  HIS*     3.8    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 354 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160D  HIS*     3.5    22.4    -      -       +      +
    162D  ASP*     3.4    37.0    -      -       +      +
    163D  LEU*     3.9    14.7    -      -       +      +
    196D  THR*     2.9    26.9    +      -       -      +
    197D  ARG*     3.1    25.6    +      -       -      +
    200D  GLY*     3.3    17.1    +      -       -      -
    204D  ALA*     4.4     3.8    -      -       +      +
    211D  CYS*     4.6     4.3    -      -       -      -
    353D  THR*     1.3    79.7    +      -       -      +
    355D  ASP*     1.3    59.6    +      -       -      +
    359D  LYS      3.9     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 355 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160D  HIS*     3.1    11.8    -      -       -      -
    193D  ARG*     3.6    13.2    +      -       -      +
    196D  THR*     3.9     5.6    -      -       -      -
    197D  ARG*     2.8    42.4    +      -       -      +
    353D  THR      3.7     0.4    +      -       -      -
    354D  THR*     1.3    74.6    -      -       -      +
    356D  LEU*     1.3    86.7    +      -       -      +
    359D  LYS*     2.8    41.0    +      -       +      +
    360D  CYS      4.3     0.2    -      -       -      -
    361D  THR*     3.6    18.6    -      -       +      +
----------------------------------------------------------
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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