Contacts of the strand formed by residues 370 - 375 (chain A) in PDB entry 3H8E


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 370 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261A  PRO      3.8     0.6    +      -       -      -
    262A  PHE*     3.6    12.6    -      -       +      -
    263A  VAL      2.8    30.2    +      -       -      -
    368A  PRO*     3.4     3.0    -      -       -      +
    369A  GLN*     1.4    82.5    -      -       -      +
    371A  VAL*     1.4    60.7    +      -       -      +
    372A  ILE*     4.3     4.5    -      -       +      -
    399A  LEU*     4.1    16.2    -      -       +      -
    458A  TYR*     5.8     0.4    -      -       -      +
    459A  ASN*     3.4     9.9    -      -       +      -
    490A  TYR*     3.3    26.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 371 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263A  VAL*     3.3    14.6    -      -       +      +
    265A  VAL*     4.0    16.6    -      -       +      -
    360A  LEU*     3.8    29.6    -      -       +      -
    363A  ALA*     4.5     3.1    -      -       +      -
    368A  PRO*     3.3    34.3    -      -       +      -
    370A  ALA*     1.4    72.8    -      -       -      +
    372A  ILE*     1.3    64.4    +      -       -      +
    373A  ASP      4.1     0.2    -      -       -      -
    399A  LEU*     4.2     0.2    -      -       -      +
    458A  TYR*     3.4    33.4    -      -       +      +
    459A  ASN      2.9     6.3    +      -       -      -
    460A  TRP*     3.1     3.4    -      -       +      -
    461A  ALA      2.9    23.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 372 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262A  PHE*     6.3     0.9    -      -       +      -
    263A  VAL      2.9     7.4    +      -       -      +
    264A  LEU*     3.4    21.8    -      -       +      -
    265A  VAL*     2.8    25.6    +      -       -      -
    370A  ALA*     4.9     2.5    -      -       +      -
    371A  VAL*     1.3    81.4    -      -       -      +
    373A  ASP*     1.3    69.8    +      -       -      +
    374A  ILE*     3.5    10.4    -      -       +      +
    399A  LEU*     4.3    10.1    -      -       +      -
    403A  LEU*     3.8    28.0    -      -       +      -
    461A  ALA*     3.2    10.8    -      -       +      +
    463A  MET*     3.9    26.5    -      -       +      -
    487A  LEU*     4.5     2.9    -      -       +      -
    490A  TYR*     3.7    35.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 373 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265A  VAL*     3.1    25.1    -      -       +      +
    356A  LEU*     4.3    12.4    -      -       +      +
    360A  LEU*     4.1    11.6    -      -       +      +
    371A  VAL      4.1     0.6    -      -       -      -
    372A  ILE*     1.3    76.4    -      -       -      +
    374A  ILE*     1.3    64.0    +      -       -      +
    451A  LEU*     3.2    27.5    -      -       -      +
    460A  TRP*     3.5    18.0    +      -       -      +
    461A  ALA      2.9     3.2    +      -       -      +
    462A  HIS*     2.5    41.8    -      -       -      -
    463A  MET*     2.9    19.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 374 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264A  LEU*     4.3     6.3    -      -       +      -
    265A  VAL      2.8    14.3    +      -       -      +
    266A  GLY*     3.6     0.7    -      -       -      -
    267A  LYS      3.0    24.1    +      -       -      -
    293A  GLY*     3.4     8.7    -      -       -      +
    296A  SER*     3.5    21.1    -      -       -      +
    297A  VAL*     3.9    15.0    -      -       +      -
    356A  LEU*     5.0     0.2    -      -       -      +
    372A  ILE*     3.5    20.4    -      -       +      +
    373A  ASP*     1.3    78.4    -      -       -      +
    375A  ALA*     1.3    64.1    +      -       -      +
    463A  MET*     3.5    18.4    -      -       +      +
    465A  ILE*     3.5    25.8    -      -       +      -
    483A  PRO*     3.8    11.4    -      -       +      -
    487A  LEU*     3.9    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 375 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  LYS*     3.7    21.8    -      -       +      -
    293A  GLY*     4.6     2.0    -      -       -      -
    356A  LEU*     3.7    20.9    -      -       +      -
    374A  ILE*     1.3    78.8    -      -       -      +
    376A  THR*     1.3    54.3    +      -       -      +
    377A  LEU*     3.0    23.0    +      -       +      -
    462A  HIS*     4.5     4.9    -      -       +      -
    463A  MET      3.0     9.1    +      -       -      +
    464A  ASP*     3.2     5.4    -      -       -      -
    465A  ILE*     2.9    32.1    +      -       -      -
----------------------------------------------------------
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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