Contacts of the strand formed by residues 289 - 294 (chain A) in PDB entry 2HVY


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 LEU 289 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  GLN*     3.5    31.2    -      -       -      +
    105A  ALA*     4.0    15.3    -      -       -      -
    108A  PRO*     4.9    11.0    -      -       +      -
    253A  LEU*     3.9    30.1    -      -       +      +
    254A  PRO*     3.4    24.4    -      -       -      +
    287A  GLY      3.7     2.6    +      -       -      -
    288A  ASP*     1.3    71.2    -      -       -      +
    290A  VAL*     1.3    60.0    +      -       -      +
    302A  LEU*     4.2    20.9    -      -       +      -
    303A  GLY      3.4    15.5    -      -       -      +
    304A  LYS*     4.9     0.9    -      -       -      +
    324A  GLU*     4.4    11.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 290 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253A  LEU*     4.6     2.5    -      -       -      -
    254A  PRO*     3.4    21.5    -      -       +      +
    256A  VAL*     4.5    11.0    -      -       +      -
    284A  ILE*     4.0    32.8    -      -       +      -
    288A  ASP      3.8     9.6    -      -       -      +
    289A  LEU*     1.3    79.8    -      -       -      +
    291A  ALA*     1.3    62.5    +      -       -      +
    292A  ILE*     4.9     0.7    -      -       +      -
    302A  LEU*     3.5     8.9    -      -       -      +
    303A  GLY      2.9    42.2    +      -       -      +
    305A  ALA*     4.2     4.3    -      -       +      +
    321A  VAL*     3.7    35.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 291 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250A  VAL*     3.7    41.5    -      -       +      -
    253A  LEU*     4.3     5.5    -      -       +      +
    254A  PRO      3.0     7.6    +      -       -      +
    255A  LYS*     3.3    12.3    -      -       +      +
    256A  VAL*     2.9    26.1    +      -       -      +
    290A  VAL*     1.3    73.8    -      -       -      +
    292A  ILE*     1.3    62.5    +      -       -      +
    293A  MET*     3.7     9.4    +      -       -      +
    299A  LEU*     4.1     3.6    -      -       +      -
    301A  ALA      3.7     3.6    -      -       -      -
    302A  LEU*     4.2     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 292 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256A  VAL*     3.5    20.2    -      -       +      -
    258A  ILE*     3.8    38.6    -      -       +      -
    266A  VAL*     4.6     4.5    -      -       +      -
    272A  LEU*     4.1    10.3    -      -       +      -
    290A  VAL*     4.9     2.5    -      -       +      +
    291A  ALA*     1.3    71.3    -      -       -      +
    293A  MET*     1.3    64.8    +      -       -      +
    299A  LEU*     3.9     0.3    -      -       -      +
    300A  VAL*     2.9    36.1    +      -       +      -
    301A  ALA*     2.8    30.8    +      -       +      +
    303A  GLY*     5.2     1.3    -      -       -      +
    321A  VAL*     3.8    31.0    -      -       +      -
    323A  VAL*     3.8    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 293 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247A  GLU*     4.1    10.5    -      -       +      -
    250A  VAL*     3.9    27.1    -      -       +      -
    255A  LYS*     3.8    38.1    -      -       +      +
    256A  VAL      2.8     8.5    +      -       -      +
    257A  TRP*     3.3    14.9    -      -       +      +
    258A  ILE*     2.8    29.8    +      -       -      +
    291A  ALA*     3.9     6.1    -      -       -      +
    292A  ILE*     1.3    82.0    -      -       -      +
    294A  THR*     1.3    68.1    +      -       -      +
    297A  ASP*     3.6    30.7    -      -       +      +
    298A  GLU      3.2    14.6    -      -       -      +
    299A  LEU*     4.0    11.2    -      -       -      +
    300A  VAL*     4.0     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 294 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  THR*     5.6     0.2    -      -       -      -
    257A  TRP*     3.2    13.4    -      -       -      -
    258A  ILE*     4.1     7.6    -      -       -      -
    260A  ASP*     5.4     1.6    -      -       -      -
    263A  VAL*     3.9    18.2    -      -       +      -
    293A  MET*     1.3    75.8    -      -       -      +
    295A  LEU*     1.3    59.9    +      -       -      +
    296A  LYS      3.2     5.6    +      -       -      -
    297A  ASP*     2.9    15.6    +      -       -      -
    298A  GLU*     2.8    48.0    +      -       -      +
    300A  VAL*     3.5    22.2    -      -       +      -
    328A  MET*     3.7    13.5    -      -       +      -
    333A  TYR*     3.8    12.1    -      -       +      +
----------------------------------------------------------
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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