Contacts of the strand formed by residues 284 - 291 (chain B) in PDB entry 1HYH


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 284 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146B  ASP*     3.7     9.6    -      -       -      -
    196B  GLY      4.1     4.0    -      -       -      +
    273B  VAL      3.6     0.5    -      -       -      +
    274B  SER*     3.9     6.0    +      -       -      -
    275B  ASN*     3.0    28.3    +      -       -      +
    277B  ARG*     4.6     4.7    -      -       -      +
    280B  MET*     4.0    21.5    -      -       +      -
    282B  MET      3.3     7.8    +      -       -      +
    283B  TYR*     1.3    76.4    -      -       -      +
    285B  SER*     1.3    76.9    +      -       -      +
    286B  TYR*     3.6    13.0    +      -       +      -
    311B  LEU*     3.6    42.8    -      -       +      +
    314B  SER*     4.7     2.2    -      -       -      -
    315B  ARG*     3.9    24.0    -      -       +      +
    318B  ILE*     3.9    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 285 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146B  ASP*     4.0     1.4    +      -       -      -
    167B  GLY*     3.2    13.2    -      -       -      -
    168B  THR*     2.8    46.7    +      -       -      +
    195B  LEU*     3.7     8.8    -      -       -      +
    196B  GLY      3.2    31.9    +      -       -      -
    272B  VAL*     4.1     5.4    -      -       -      -
    273B  VAL      3.3     7.6    -      -       -      -
    274B  SER*     3.7     7.6    +      -       -      -
    284B  LEU*     1.3    76.1    -      -       -      +
    286B  TYR*     1.3    64.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 286 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195B  LEU*     3.9     8.1    -      -       +      -
    272B  VAL*     3.8     5.3    -      -       -      +
    273B  VAL      3.3     9.0    +      -       -      +
    275B  ASN*     3.0    19.2    +      -       -      +
    277B  ARG*     3.1    57.5    +      -       -      -
    280B  MET*     6.0     0.9    -      -       +      -
    284B  LEU*     3.6     6.0    +      -       +      -
    285B  SER*     1.3    77.5    -      -       -      +
    287B  PRO*     1.3    86.5    -      -       +      +
    288B  ALA      3.5     0.7    +      -       -      -
    299B  THR*     3.4    18.4    -      -       -      -
    300B  THR*     3.8     2.9    -      -       -      -
    301B  LEU*     2.8    44.0    +      -       +      +
    303B  LEU*     4.5     8.9    -      -       +      +
    311B  LEU*     3.8    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 287 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193B  TYR*     4.1    28.7    -      -       +      +
    195B  LEU*     3.8    17.0    -      -       +      -
    270B  GLU*     4.1    15.7    -      -       +      +
    271B  LEU      3.5    10.5    -      -       -      +
    272B  VAL*     3.8     7.8    -      -       +      -
    275B  ASN*     5.0     0.9    +      -       -      +
    277B  ARG*     4.5     1.6    +      -       -      -
    286B  TYR*     1.3   100.2    -      -       +      +
    288B  ALA*     1.3    56.9    +      -       -      +
    298B  GLU*     4.6     0.3    -      -       -      -
    299B  THR*     2.7    42.8    +      -       -      +
    301B  LEU*     3.7    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 288 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269B  ALA      3.5     0.7    -      -       -      +
    270B  GLU*     3.3     4.0    -      -       -      -
    271B  LEU      3.0    30.4    +      -       -      +
    273B  VAL*     4.4     1.8    -      -       +      -
    275B  ASN*     4.0    20.4    -      -       -      +
    287B  PRO*     1.3    73.7    -      -       -      +
    289B  ILE*     1.3    66.9    +      -       -      +
    290B  ILE*     3.8    13.6    +      -       +      +
    295B  VAL*     3.6    25.8    -      -       +      -
    297B  ALA      3.6     6.5    -      -       -      +
    298B  GLU*     4.7     0.9    -      -       -      +
    299B  THR*     4.2     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 289 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184A  ASP      5.0     0.9    -      -       -      +
    185A  LEU*     3.6    26.0    -      -       +      -
    212A  MET*     3.7    33.9    -      -       +      -
    268B  HIS*     3.5    36.8    -      -       +      +
    269B  ALA      3.5     1.3    -      -       -      -
    270B  GLU*     3.8    23.8    -      -       +      -
    288B  ALA*     1.3    71.2    -      -       -      +
    290B  ILE*     1.3    56.1    +      -       -      +
    295B  VAL*     3.5     3.3    -      -       -      -
    296B  LEU*     2.7    38.9    +      -       +      -
    297B  ALA*     2.9    26.3    +      -       +      +
    298B  GLU      5.1     0.2    -      -       -      +
    299B  THR*     3.8     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 290 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164B  ILE*     4.2    10.1    -      -       +      -
    259B  ILE*     4.5     9.2    -      -       +      +
    262B  ALA*     4.2    17.2    -      -       +      +
    263B  VAL*     3.9    26.0    -      -       +      -
    267B  ALA      3.8     0.2    -      -       -      -
    268B  HIS*     2.7    31.0    +      -       -      -
    269B  ALA      2.9    22.7    +      -       -      +
    271B  LEU*     4.2    26.2    -      -       +      -
    273B  VAL*     4.0    26.0    -      -       +      -
    288B  ALA*     4.2     7.0    -      -       +      +
    289B  ILE*     1.3    78.6    -      -       -      +
    291B  GLY*     1.3    58.0    +      -       -      +
    294B  GLY      3.6     4.9    -      -       -      +
    295B  VAL*     4.1    21.3    -      -       +      +
    296B  LEU*     4.5     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 291 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262B  ALA      3.9     7.4    -      -       -      -
    263B  VAL*     3.6    19.4    -      -       -      +
    266B  ASP*     3.5    13.0    -      -       -      -
    268B  HIS      4.1     0.9    -      -       -      -
    290B  ILE*     1.3    75.1    -      -       -      +
    292B  ARG*     1.3    60.5    +      -       -      -
    293B  ASP      3.2     3.1    -      -       -      -
    294B  GLY*     2.9    28.3    +      -       -      +
    296B  LEU*     3.9    11.3    -      -       -      +
----------------------------------------------------------
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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