Contacts of the strand formed by residues 654 - 662 (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 VAL 654 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    613L  GLU*     3.7    14.4    -      -       -      +
    645L  TYR*     3.2    36.1    -      -       +      +
    650L  ILE*     3.4    33.2    -      -       +      -
    652L  THR*     3.8     3.6    -      -       -      +
    653L  PRO*     1.3    75.1    -      -       -      +
    655L  LYS*     1.3    62.8    +      -       -      +
    656L  VAL*     3.7    11.6    +      -       +      +
    674L  THR*     3.3     6.7    -      -       -      -
    675L  TYR*     3.0    37.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 655 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    586L  ASP      5.3     1.6    +      -       -      -
    613L  GLU*     4.5     8.3    -      -       -      +
    653L  PRO      4.0     2.2    +      -       -      -
    654L  VAL*     1.3    76.3    -      -       -      +
    656L  VAL*     1.3    69.4    +      -       -      +
    657L  ASN*     4.7     5.6    +      -       -      +
    672L  HIS*     4.1    22.8    -      -       +      +
    673L  PHE*     3.4    18.8    +      -       -      +
    674L  THR*     3.1    22.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 656 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    611L  PHE*     4.3     7.2    -      -       +      -
    612L  THR      3.4    14.4    -      -       -      +
    613L  GLU*     4.1    15.3    -      -       +      +
    622L  TRP*     4.2     8.3    -      -       +      -
    645L  TYR*     4.4     1.3    -      -       +      -
    654L  VAL*     4.0    16.2    -      -       +      +
    655L  LYS*     1.3    79.9    -      -       -      +
    657L  ASN*     1.3    76.5    +      -       -      +
    673L  PHE*     2.8    51.2    +      -       +      +
    674L  THR*     4.7     0.2    -      -       -      -
    675L  TYR*     3.7    39.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 657 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    611L  PHE*     3.2     9.8    -      -       -      -
    612L  THR*     2.8    42.3    +      -       -      +
    613L  GLU*     5.0     1.3    -      -       -      +
    614L  LYS*     5.2     9.1    -      -       +      +
    655L  LYS*     4.7     6.7    +      -       -      +
    656L  VAL*     1.3    99.7    +      -       -      +
    658L  PHE*     1.3    68.1    +      -       -      +
    670L  PRO*     3.6    23.5    -      -       +      +
    671L  GLN      3.2    17.4    +      -       -      +
    672L  HIS*     3.5    19.7    +      -       -      +
    673L  PHE      4.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 658 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    580L  VAL*     5.2     0.9    -      -       +      -
    583L  GLN*     3.4    31.2    -      -       -      -
    596L  MET*     4.2     9.9    -      -       +      -
    598L  LEU*     3.7    34.8    -      -       +      -
    609L  VAL*     3.9    16.2    -      -       +      -
    610L  VAL      3.0    14.8    -      -       -      +
    611L  PHE*     3.5    33.9    -      +       +      +
    612L  THR      4.5     0.4    -      -       -      +
    657L  ASN*     1.3    78.8    -      -       -      +
    659L  TYR*     1.3    68.6    +      -       -      +
    660L  VAL*     5.1     1.6    -      -       +      -
    670L  PRO*     4.7     1.1    -      -       -      -
    671L  GLN*     2.8    60.2    +      -       +      +
    672L  HIS      3.9     6.7    -      -       -      -
    673L  PHE*     4.0    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 659 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    609L  VAL*     3.4     6.6    -      -       -      +
    610L  VAL*     2.7    76.8    +      -       +      +
    612L  THR*     4.0    17.7    -      -       +      -
    620L  GLN*     5.3     1.3    -      -       -      -
    623L  GLU*     4.8     6.2    +      -       -      -
    658L  PHE*     1.3    79.0    -      -       -      +
    660L  VAL*     1.3    75.5    +      -       -      +
    661L  ILE*     4.0    16.9    -      -       +      +
    667L  ARG*     3.7    49.2    +      -       -      -
    668L  SER*     3.8    21.8    -      -       -      +
    669L  GLN      4.2     3.6    -      -       -      +
    670L  PRO*     4.5    10.3    -      -       +      -
    671L  GLN*     5.2     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 660 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578L  PRO*     3.9    23.6    -      -       +      -
    580L  VAL*     3.3    33.0    -      -       +      -
    598L  LEU*     4.1    16.6    -      -       +      -
    603L  PHE*     4.4     5.2    -      -       +      -
    607L  SER*     4.3    10.3    -      -       -      -
    608L  LYS      3.4    11.4    -      -       -      +
    609L  VAL*     4.9     2.7    -      -       +      -
    638L  LEU*     3.7    22.4    -      -       +      -
    658L  PHE*     5.1     2.0    -      -       +      -
    659L  TYR*     1.3    77.1    -      -       -      +
    661L  ILE*     1.3    66.4    +      -       -      +
    667L  ARG*     3.2     5.4    -      -       -      +
    668L  SER*     2.9    33.6    +      -       -      +
    671L  GLN*     6.0     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 661 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578L  PRO*     4.1     0.9    -      -       -      -
    606L  GLU      4.2     0.9    -      -       -      +
    607L  SER*     3.5     2.4    -      -       -      -
    608L  LYS*     2.9    52.9    +      -       +      +
    610L  VAL*     4.8     5.8    -      -       +      -
    659L  TYR*     4.0    20.6    -      -       +      +
    660L  VAL*     1.3    79.6    -      -       -      +
    662L  ASN*     1.3    70.9    +      -       -      +
    663L  GLY      3.3    21.8    +      -       -      +
    664L  LYS      3.6    17.7    -      -       -      +
    665L  ARG      3.7     8.1    -      -       -      +
    666L  LYS      3.2    13.2    -      -       -      +
    667L  ARG*     3.8    15.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 662 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A    G      4.8     0.2    +      -       -      -
    575L  HIS*     3.6    28.8    -      -       +      +
    576L  GLU      3.0    23.1    +      -       -      +
    578L  PRO*     3.0    20.2    -      -       -      +
    602L  ASN      3.1    19.8    +      -       -      +
    604L  THR*     3.6    12.3    +      -       -      +
    606L  GLU      4.6     3.6    -      -       -      -
    607L  SER*     2.5    29.6    +      -       -      -
    661L  ILE*     1.3    73.8    -      -       -      +
    663L  GLY*     1.3    64.8    +      -       -      +
    665L  ARG      4.3     0.2    +      -       -      -
    666L  LYS*     2.8    31.0    +      -       +      +
----------------------------------------------------------
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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