Contacts of the strand formed by residues 620 - 628 (chain L) 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 620 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    612L  THR*     3.3    21.6    -      -       -      +
    613L  GLU      3.3     5.4    -      -       -      +
    614L  LYS*     3.5    26.1    +      -       -      +
    618L  GLY      3.0     6.2    +      -       -      +
    619L  GLN*     1.3    69.3    -      -       -      +
    621L  ILE*     1.3    56.9    -      -       -      +
    622L  TRP      3.0    23.0    +      -       -      +
    623L  GLU*     3.1    47.1    +      -       -      +
    659L  TYR*     5.3     1.9    -      -       -      -
    667L  ARG*     5.7     2.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 621 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    613L  GLU*     2.5    37.9    +      -       +      +
    614L  LYS*     4.6     1.6    -      -       -      +
    615L  THR*     3.5    26.5    -      -       +      -
    619L  GLN*     2.8    23.3    +      -       +      +
    620L  GLN*     1.3    71.2    -      -       -      +
    622L  TRP*     1.3    59.0    +      -       -      +
    646L  ARG*     3.4    34.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 622 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    611L  PHE*     4.1    17.3    -      -       +      -
    612L  THR*     3.5    29.1    -      -       -      -
    613L  GLU*     3.5    11.9    +      -       +      -
    620L  GLN*     3.0    25.7    +      -       -      +
    621L  ILE*     1.3    79.2    -      -       -      +
    623L  GLU*     1.3    70.2    +      -       -      +
    624L  MET*     3.5    40.6    -      -       +      +
    643L  PRO*     4.8     1.1    -      -       +      -
    644L  GLU      3.7    16.2    -      -       -      -
    645L  TYR*     3.8    25.6    -      +       -      -
    646L  ARG*     3.5    43.7    -      -       +      +
    656L  VAL*     4.2     6.5    -      -       +      -
    675L  TYR*     3.8    28.0    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLU 623 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    610L  VAL*     3.8    22.4    -      -       +      -
    611L  PHE      3.2     6.7    -      -       -      +
    620L  GLN*     3.1    24.0    +      -       -      +
    622L  TRP*     1.3    88.1    -      -       -      +
    624L  MET*     1.3    60.5    -      -       -      +
    625L  GLU      4.3     0.9    +      -       -      -
    659L  TYR*     4.8     6.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 624 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    610L  VAL*     3.6     3.4    -      -       -      -
    611L  PHE*     2.7    39.3    +      -       +      +
    622L  TRP*     3.5    39.4    -      -       +      +
    623L  GLU*     1.3    77.8    -      -       -      +
    625L  GLU*     1.3    68.3    +      -       -      +
    626L  ALA      3.8     0.2    +      -       -      -
    643L  PRO*     3.5    29.4    -      -       +      -
    644L  GLU      4.8     5.4    -      -       -      +
    646L  ARG*     6.2     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 625 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    608L  LYS*     3.3    37.0    +      -       -      +
    609L  VAL      3.5    15.9    -      -       -      +
    610L  VAL*     4.3    12.7    -      -       +      +
    623L  GLU      4.3     0.4    +      -       -      -
    624L  MET*     1.3    88.4    -      -       -      +
    626L  ALA*     1.3    72.5    +      -       -      +
    627L  THR*     4.1     0.7    +      -       -      -
    643L  PRO*     4.4     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 626 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    608L  LYS*     5.5     0.3    -      -       -      -
    609L  VAL*     2.8    21.9    +      -       +      +
    611L  PHE*     3.9     9.0    -      -       +      -
    624L  MET      3.8     1.8    +      -       -      -
    625L  GLU*     1.3    87.9    -      -       -      +
    627L  THR*     1.3    63.5    +      -       -      +
    628L  VAL*     3.7     3.5    +      -       -      +
    640L  VAL*     3.3    26.9    -      -       +      -
    641L  GLU      3.3    12.6    -      -       -      +
    643L  PRO*     3.5    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 627 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    625L  GLU      4.1     1.3    +      -       -      -
    626L  ALA*     1.3    72.4    -      -       -      +
    628L  VAL*     1.3    74.4    +      -       -      +
    629L  ASP*     4.2     0.4    +      -       -      -
    640L  VAL*     3.4     2.1    -      -       -      +
    641L  GLU*     2.6    65.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 628 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    605L  SER      5.1     2.5    -      -       -      +
    607L  SER      4.1    19.3    -      -       -      +
    608L  LYS*     4.5     0.9    -      -       -      -
    609L  VAL*     3.6    35.2    -      -       +      +
    626L  ALA      3.7     2.8    +      -       -      +
    627L  THR*     1.3    86.5    -      -       -      +
    629L  ASP*     1.3    66.3    +      -       -      +
    630L  LYS*     3.0    27.5    +      -       +      +
    633L  SER*     3.5    17.9    -      -       -      +
    638L  LEU*     3.8    13.0    -      -       +      -
    639L  PHE      3.4    13.7    -      -       -      +
    640L  VAL*     4.1     1.8    -      -       +      -
----------------------------------------------------------
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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