Contacts of the strand formed by residues 263 - 268 (chain A) in PDB entry 4HYY


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 263 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  PHE*     4.4     1.6    -      -       +      -
    101A  ILE*     4.2    10.8    -      -       +      -
    116A  ILE*     3.9    20.4    -      -       +      +
    117A  GLU      3.6    28.5    -      -       -      +
    118A  SER*     3.8     4.9    +      -       -      +
    218A  LYS      2.9    14.1    +      -       -      +
    219A  LEU*     3.3     9.4    -      -       +      +
    220A  LEU      3.0    23.4    +      -       -      -
    262A  VAL*     1.3    75.8    -      -       -      +
    264A  VAL*     1.3    61.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 264 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  ILE*     4.7     1.3    -      -       -      +
    117A  GLU      5.2     0.2    -      -       -      +
    120A  ALA      3.1     9.7    +      -       -      +
    121A  ILE*     3.3    21.6    -      -       +      -
    122A  THR*     2.8    28.1    +      -       -      -
    220A  LEU*     3.3    20.2    -      -       +      +
    222A  ILE*     4.8     0.2    -      -       +      -
    253A  LEU*     4.2    24.5    -      -       +      +
    256A  ILE*     5.1     0.2    -      -       +      -
    257A  SER*     3.7    34.8    -      -       -      +
    262A  VAL*     4.1     6.1    -      -       +      -
    263A  ALA*     1.3    77.9    -      -       -      +
    265A  PHE*     1.3    61.7    +      -       -      +
    266A  VAL*     3.9    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 265 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  ILE*     4.1    22.0    -      -       +      -
    122A  THR*     3.4    13.2    -      -       +      -
    124A  ALA*     3.9    20.2    -      -       +      -
    132A  LYS      4.3     0.7    -      -       -      -
    135A  LEU*     3.6    36.3    -      -       +      -
    136A  SER*     3.4    24.9    -      -       -      -
    139A  LEU*     3.7    22.9    -      -       +      -
    219A  LEU*     4.0    19.3    -      -       +      -
    220A  LEU      2.8     8.1    +      -       -      +
    221A  ILE*     3.2    18.1    -      -       +      +
    222A  ILE      3.1    23.0    +      -       -      -
    264A  VAL*     1.3    73.6    -      -       -      +
    266A  VAL*     1.3    64.8    +      -       -      +
    267A  THR*     4.0    20.0    -      -       +      -
    301A  ILE*     5.7     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 266 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  ILE*     4.3    11.2    -      -       +      -
    122A  THR      2.9    14.8    +      -       -      +
    123A  GLU*     3.3    16.8    -      -       +      -
    124A  ALA*     2.8    27.0    +      -       -      +
    222A  ILE*     3.2    32.5    -      -       +      +
    225A  ILE*     3.8    32.1    -      -       +      -
    250A  LEU*     6.3     0.4    -      -       +      -
    253A  LEU*     4.7     0.9    -      -       +      -
    264A  VAL*     3.9    19.5    -      -       +      -
    265A  PHE*     1.3    83.8    -      -       -      +
    267A  THR*     1.3    65.0    +      -       -      +
    293A  LEU*     5.4     2.0    -      -       +      -
    297A  SER*     5.2     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 267 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  ALA      3.1     8.1    -      -       -      +
    132A  LYS*     3.8    29.8    -      -       +      +
    136A  SER*     3.7    20.4    -      -       -      +
    222A  ILE      3.2     4.2    +      -       -      +
    223A  ASP*     2.5    33.2    +      -       +      +
    224A  SER*     3.0    15.7    -      -       -      -
    225A  ILE*     2.9    31.9    +      -       -      +
    265A  PHE*     4.0    11.7    -      -       +      -
    266A  VAL*     1.3    76.0    -      -       -      +
    268A  ASN*     1.3    60.8    +      -       -      +
    269A  GLN*     4.9     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 268 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  GLU*     3.2    28.7    -      -       -      +
    124A  ALA      3.0     5.3    +      -       -      -
    125A  PHE*     3.2    24.5    -      -       +      +
    126A  GLY      3.8     0.9    +      -       -      -
    132A  LYS*     3.6    11.6    -      -       -      +
    225A  ILE*     3.6    20.0    -      -       +      +
    226A  MET*     3.9     6.9    -      -       -      +
    267A  THR*     1.3    80.0    -      -       -      +
    269A  GLN*     1.3    82.4    +      -       -      +
    287A  PRO*     4.1     2.1    -      -       -      +
    288A  ILE*     3.1    48.0    +      -       -      +
    293A  LEU*     3.5     4.1    -      -       -      +
----------------------------------------------------------
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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