Contacts of the strand formed by residues 4346 - 4351 (chain D) in PDB entry 2H7C


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 TYR4346 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4227D  VAL*     4.2     1.6    -      -       +      -
   4228D  SER*     3.4    25.4    +      -       -      -
   4231D  VAL*     4.5    14.1    -      -       +      -
   4243D  ALA*     3.4    25.4    -      -       +      -
   4245D  SER*     2.7    34.1    +      -       -      -
   4249D  VAL*     4.2     4.0    -      -       -      +
   4344D  VAL*     3.8     1.1    -      -       +      +
   4345D  PRO*     1.3    75.6    -      -       -      +
   4347D  MET*     1.3    70.0    +      -       -      +
   4348D  VAL*     3.8    19.7    -      -       +      -
   4433D  VAL*     3.8    21.3    -      -       +      -
   4437D  HIS*     3.4    46.7    -      +       +      +
   4443D  PRO      3.0     7.5    +      -       -      -
   4444D  THR*     3.4     7.4    -      -       +      +
   4445D  TYR      3.0    24.3    +      -       -      +
   4503D  PHE*     3.7     4.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET4347 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4243D  ALA      2.8     8.7    +      -       -      +
   4244D  ILE*     3.2    25.0    -      -       +      +
   4245D  SER      2.8    26.2    +      -       -      +
   4346D  TYR*     1.3    72.2    -      -       -      +
   4348D  VAL*     1.3    63.7    +      -       -      +
   4445D  TYR*     3.3    13.2    -      -       +      +
   4447D  TYR*     4.1    12.6    -      -       +      -
   4499D  PHE      4.6     0.2    -      -       -      +
   4500D  TRP*     3.9    24.0    -      -       +      -
   4503D  PHE*     3.6    47.0    -      -       +      -
   4509D  PRO*     4.2     7.4    -      -       +      -
   4517D  TRP*     3.6    37.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL4348 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4245D  SER*     3.5     5.6    -      -       -      +
   4249D  VAL*     4.0    14.6    -      -       +      -
   4346D  TYR*     3.8    38.1    -      -       +      +
   4347D  MET*     1.3    79.4    -      -       -      +
   4349D  GLY*     1.3    62.7    +      -       -      +
   4430D  SER*     3.7    38.6    -      -       -      +
   4433D  VAL*     4.8     3.1    -      -       +      -
   4434D  ALA*     4.6    13.7    -      -       +      -
   4444D  THR*     5.2     0.7    -      -       +      -
   4445D  TYR      2.7    12.5    +      -       -      +
   4446D  MET*     3.0    38.7    -      -       +      +
   4447D  TYR*     3.3     2.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY4349 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4245D  SER      3.0    10.8    +      -       -      +
   4247D  SER*     2.9    24.3    +      -       -      -
   4248D  GLY      4.7     0.2    +      -       -      -
   4348D  VAL*     1.3    77.7    -      -       -      +
   4350D  ILE*     1.3    69.4    +      -       -      +
   4430D  SER*     4.5     2.1    +      -       -      -
   4446D  MET*     5.1     1.1    -      -       -      -
   4447D  TYR*     3.2    35.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE4350 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4247D  SER*     4.1     2.7    -      -       -      -
   4349D  GLY*     1.3    79.5    -      -       -      +
   4351D  ASN*     1.3    73.0    +      -       -      +
   4354D  GLU*     3.4    14.8    -      -       +      +
   4426D  PHE*     3.9    14.1    -      -       +      +
   4427D  GLY*     4.0    11.7    -      -       -      +
   4430D  SER*     3.4    30.1    -      -       -      +
   4446D  MET*     5.5     1.6    -      -       +      -
   4447D  TYR*     3.0    11.1    +      -       -      +
   4448D  GLU*     3.2    23.4    -      -       +      +
   4449D  PHE      2.8    23.0    +      -       -      -
   4539D  LEU*     4.4    10.1    -      -       +      -
   4540D  LYS*     3.7    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN4351 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   4247D  SER*     3.9    10.2    +      -       -      -
   4350D  ILE*     1.3    86.6    -      -       -      +
   4352D  LYS*     1.3    65.3    +      -       -      +
   4353D  GLN      3.3     1.3    +      -       -      -
   4354D  GLU*     2.7    29.6    +      -       -      +
   4447D  TYR*     4.3     3.3    -      -       -      -
   4448D  GLU*     4.5     2.7    -      -       -      -
   4449D  PHE*     3.2    30.2    -      -       -      +
   4466D  GLY      3.1    17.9    -      -       -      +
   4467D  ASP      3.0    20.3    +      -       -      +
   4468D  HIS*     4.1     0.8    -      -       -      +
   4469D  GLY      3.5     7.3    -      -       -      +
   4470D  ASP*     3.7     3.0    -      -       -      +
   4471D  GLU*     2.8    32.6    +      -       -      +
----------------------------------------------------------
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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