Contacts of the strand formed by residues 325 - 331 (chain B) in PDB entry 2HA7


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 GLN 325 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223B  HIS      4.4     5.2    +      -       -      -
    224B  ARG*     3.1    50.4    -      -       +      +
    225B  ALA      3.3    21.8    +      -       -      -
    323B  ASP*     4.6     7.6    +      -       -      +
    324B  LEU*     1.3    81.1    +      -       -      +
    326B  VAL*     1.3    65.5    +      -       -      +
    424B  ARG*     3.4    25.8    -      -       +      +
    483B  PHE*     3.6    14.9    -      -       +      -
    486B  THR      4.4     3.4    +      -       -      -
    487B  GLY*     3.7    21.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 326 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213B  ILE*     4.9     3.4    -      -       +      -
    225B  ALA*     3.3     7.2    -      -       +      +
    227B  LEU*     3.5    31.9    -      -       +      -
    324B  LEU*     3.5    28.9    -      -       +      -
    325B  GLN*     1.3    79.4    -      -       -      +
    327B  LEU*     1.3    66.4    +      -       -      +
    328B  VAL*     4.1     7.0    -      -       +      -
    418B  LEU*     4.0    25.8    -      -       +      -
    423B  ALA*     4.8     4.7    -      -       +      -
    424B  ARG      2.7    15.0    +      -       -      +
    425B  VAL*     3.3     9.3    -      -       +      +
    426B  TYR*     2.9    27.7    +      -       -      +
    483B  PHE*     3.8     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 327 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225B  ALA      3.0     6.5    +      -       -      -
    226B  VAL*     3.1    27.0    -      -       +      +
    227B  LEU      2.9    24.8    +      -       -      -
    326B  VAL*     1.3    73.7    -      -       -      +
    328B  VAL*     1.3    62.7    +      -       -      +
    426B  TYR*     3.4    16.8    -      -       +      +
    428B  TYR*     4.0     9.0    -      -       +      -
    479B  TYR      5.3     1.1    -      -       -      +
    480B  TRP*     3.7    42.6    -      -       +      +
    483B  PHE*     3.5    25.6    -      -       +      -
    489B  PRO*     5.1     4.5    -      -       +      -
    500B  TRP*     3.4    39.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 328 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227B  LEU*     3.4    23.8    -      -       +      +
    230B  GLY      5.5     0.4    -      -       -      +
    326B  VAL*     4.7     8.3    -      -       +      -
    327B  LEU*     1.3    76.2    -      -       -      +
    329B  GLY*     1.3    62.8    +      -       -      +
    411B  VAL*     3.8    27.6    -      -       +      +
    414B  LEU*     4.7    14.1    -      -       +      -
    415B  ALA*     4.3    12.6    -      -       +      -
    418B  LEU*     6.4     1.6    -      -       +      -
    425B  VAL*     4.0    19.1    -      -       +      -
    426B  TYR      2.7    17.2    +      -       -      +
    427B  ALA*     3.0    19.2    -      -       +      -
    428B  TYR*     2.9    29.5    +      -       -      -
    524B  LEU*     6.4     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 329 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227B  LEU      3.3     5.5    +      -       -      +
    228B  GLN      3.9     0.2    -      -       -      -
    229B  SER*     2.9    26.2    +      -       -      -
    328B  VAL*     1.3    82.2    -      -       -      +
    330B  VAL*     1.3    68.9    +      -       -      +
    411B  VAL*     4.4     7.4    -      -       -      +
    427B  ALA*     5.6     0.7    -      -       -      -
    428B  TYR*     3.2    31.0    -      -       -      -
    524B  LEU*     6.1     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 330 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229B  SER*     3.9     1.6    -      -       -      -
    329B  GLY*     1.3    79.0    -      -       -      +
    331B  VAL*     1.3    65.0    +      -       -      +
    334B  GLU*     3.5     9.2    -      -       -      +
    407B  VAL*     3.9    13.0    -      -       +      -
    408B  VAL*     3.9    43.1    -      -       +      -
    411B  VAL*     4.0    14.8    -      -       +      -
    428B  TYR*     3.1    14.3    +      -       -      +
    429B  ILE*     3.3    21.2    -      -       +      -
    430B  PHE*     2.8    32.7    +      -       -      +
    524B  LEU*     4.7     9.6    -      -       +      -
    525B  ARG*     5.7     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 331 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229B  SER*     4.3     3.4    -      -       -      +
    330B  VAL*     1.3    83.4    -      -       -      +
    332B  LYS*     1.3    64.6    +      -       -      +
    333B  ASP      3.3     1.9    +      -       -      +
    334B  GLU*     2.8    43.7    +      -       +      +
    408B  VAL*     5.0     2.1    -      -       -      +
    428B  TYR*     5.7     0.7    -      -       +      -
    429B  ILE*     4.4     3.2    -      -       -      +
    430B  PHE*     3.4    26.0    -      -       +      +
    445B  VAL*     3.7    21.8    -      -       +      +
    446B  PRO      3.8    13.5    -      -       -      +
    447B  HIS*     3.9     8.5    -      -       -      +
    448B  GLY      5.0     0.4    -      -       -      +
    450B  GLU*     3.5    37.7    -      -       +      +
----------------------------------------------------------
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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