Contacts of the strand formed by residues 671 - 676 (chain O) in PDB entry 2O93


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 671 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    580O  VAL*     3.2    47.1    +      -       +      +
    581O  GLU*     5.6     0.8    -      -       -      +
    583O  GLN*     3.2    16.2    -      -       -      +
    657O  ASN*     3.1    31.0    +      -       -      -
    658O  PHE*     2.8    51.4    +      -       +      +
    659O  TYR*     5.0     0.7    -      -       -      -
    669O  GLN*     3.4    17.1    -      -       -      +
    670O  PRO*     1.3    82.0    -      -       -      +
    672O  HIS*     1.3    65.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 672 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    583O  GLN*     3.2    27.4    -      -       -      +
    586O  ASP*     4.3     5.5    -      -       -      +
    655O  LYS*     4.9    14.5    -      -       +      +
    656O  VAL      3.9     2.0    -      -       -      +
    657O  ASN*     3.1    24.1    +      -       -      -
    658O  PHE*     3.7     1.8    -      -       -      -
    670O  PRO*     4.0    18.2    +      -       +      -
    671O  GLN*     1.3    77.8    -      -       -      +
    673O  PHE*     1.3    62.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 673 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    585O  THR*     3.7    19.3    -      -       +      -
    586O  ASP*     3.2    15.5    -      -       -      -
    587O  SER*     3.6    26.5    -      -       -      -
    588O  CYS*     3.8    11.4    -      -       -      -
    596O  MET*     4.3    10.1    -      -       -      -
    611O  PHE*     3.7    27.8    -      +       +      -
    642O  ILE*     3.2    37.9    -      -       +      -
    655O  LYS*     3.5     3.0    -      -       -      +
    656O  VAL*     2.8    38.7    +      -       +      +
    658O  PHE*     4.0     7.4    -      +       +      -
    672O  HIS*     1.3    76.5    -      -       -      +
    674O  THR*     1.3    78.3    +      -       -      +
    675O  TYR*     3.7    28.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with THR 674 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    586O  ASP      3.0     8.5    +      -       -      -
    587O  SER*     2.7    37.7    -      -       -      -
    588O  CYS      3.4     1.9    +      -       -      -
    653O  PRO*     3.7    26.7    -      -       +      -
    654O  VAL      3.5    12.3    -      -       -      +
    655O  LYS*     2.7    43.2    +      -       +      +
    673O  PHE*     1.3    74.8    -      -       -      +
    675O  TYR*     1.3    65.0    +      -       -      +
    676O  HIS*     3.8    10.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 675 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    588O  CYS*     3.3    17.3    -      -       -      -
    589O  LEU      4.0    11.2    -      -       -      -
    590O  VAL*     4.2     9.9    -      -       +      -
    592O  GLY*     4.9     0.2    -      -       -      -
    611O  PHE*     4.0     3.4    -      +       -      -
    622O  TRP*     3.5    26.1    -      +       -      -
    642O  ILE*     3.3    28.6    -      -       +      +
    643O  PRO*     2.6    40.7    +      -       -      +
    645O  TYR*     3.5    35.9    -      +       +      -
    650O  ILE*     3.9     6.3    -      -       +      +
    653O  PRO*     3.3     7.8    -      -       -      +
    654O  VAL*     2.9    34.3    +      -       +      +
    656O  VAL*     3.9    22.0    -      -       +      +
    673O  PHE*     3.7    11.2    -      +       -      -
    674O  THR*     1.3    73.1    -      -       -      +
    676O  HIS*     1.3    60.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 676 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    587O  SER*     3.4    32.1    +      -       -      -
    588O  CYS*     2.8    19.7    +      -       -      +
    589O  LEU*     3.2    16.0    -      -       +      +
    590O  VAL*     2.8    27.6    +      -       -      +
    653O  PRO*     3.4    30.2    -      -       +      +
    674O  THR*     4.2     9.0    -      -       +      -
    675O  TYR*     1.3    72.1    -      -       -      +
    677O  PRO*     1.3    72.8    -      -       +      +
----------------------------------------------------------
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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