Contacts of the strand formed by residues 595 - 601 (chain M) 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 595 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    584M  ASP*     4.7     3.3    -      -       -      +
    585M  THR*     4.4     5.8    +      -       -      -
    594M  GLN*     1.3    76.6    -      -       -      +
    596M  MET*     1.3    63.5    +      -       -      +
    597M  ILE*     3.7    17.1    +      -       -      +
    629M  ASP*     5.0     4.6    +      -       +      +
    632M  LYS*     4.4    13.9    -      -       -      +
    639M  PHE*     3.3    32.4    -      -       +      +
    640M  VAL      3.1    19.1    -      -       -      +
    641M  GLU*     4.5     2.2    -      -       +      +
    642M  ILE*     5.0     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 596 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    583M  GLN*     4.4     1.3    -      -       -      +
    584M  ASP*     3.5    12.1    -      -       -      +
    585M  THR*     3.7    33.2    -      -       -      +
    594M  GLN      4.1     1.6    +      -       -      -
    595M  GLN*     1.3    73.9    -      -       -      +
    597M  ILE*     1.3    66.7    +      -       -      +
    598M  LEU*     3.7    35.7    -      -       +      -
    609M  VAL*     5.6     0.4    -      -       +      -
    611M  PHE*     4.2    22.2    -      -       +      -
    638M  LEU      3.4     2.3    -      -       -      +
    639M  PHE*     3.6     1.4    -      -       -      -
    640M  VAL*     2.8    46.3    +      -       +      +
    642M  ILE*     3.9    15.5    -      -       +      +
    658M  PHE*     3.8    22.9    -      -       +      -
    673M  PHE*     4.1    10.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 597 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    582M  ARG      4.0     0.2    -      -       -      +
    583M  GLN*     3.7     1.7    -      -       -      -
    584M  ASP*     2.8    52.2    +      -       +      +
    595M  GLN*     3.7    16.6    -      -       -      +
    596M  MET*     1.3    75.2    -      -       -      +
    598M  LEU*     1.3    68.3    +      -       -      +
    599M  THR*     4.6     3.1    +      -       -      +
    637M  MET*     3.4    33.2    -      -       +      -
    638M  LEU      3.1     7.6    -      -       -      +
    639M  PHE*     3.3    37.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 598 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    580M  VAL*     4.3    11.7    -      -       +      -
    582M  ARG      3.4     2.9    -      -       -      +
    583M  GLN*     3.9    16.8    -      -       +      -
    596M  MET*     3.7    28.7    -      -       +      -
    597M  ILE*     1.3    76.1    -      -       -      +
    599M  THR*     1.3    61.8    +      -       -      +
    603M  PHE*     4.1     6.7    -      -       +      -
    609M  VAL*     4.7     4.9    -      -       +      -
    637M  MET*     3.2     6.6    -      -       -      +
    638M  LEU*     2.8    47.0    +      -       +      +
    640M  VAL*     4.2    21.3    -      -       +      -
    658M  PHE*     3.7    29.2    -      -       +      -
    660M  VAL*     4.2    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 599 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    580M  VAL*     4.8     0.4    -      -       -      -
    581M  GLU*     2.8    28.7    +      -       +      +
    582M  ARG*     2.8    36.1    +      -       +      +
    597M  ILE*     4.6     3.3    +      -       -      +
    598M  LEU*     1.3    76.4    +      -       -      +
    600M  GLY*     1.3    63.7    +      -       -      +
    603M  PHE*     3.9     1.6    -      -       -      -
    636M  ASN*     3.2    14.4    -      -       +      +
    637M  MET*     4.2    19.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 600 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    579M  MET      2.9    16.8    -      -       -      -
    581M  GLU*     3.7     8.8    -      -       -      +
    599M  THR*     1.3    75.8    -      -       -      +
    601M  GLN*     1.3    71.6    +      -       -      +
    603M  PHE*     3.2    12.4    -      -       -      -
    636M  ASN*     2.8    32.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 601 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578M  PRO*     3.4     1.7    -      -       -      +
    579M  MET*     3.1    50.6    +      -       +      +
    581M  GLU*     3.4    18.2    +      -       -      +
    600M  GLY*     1.3    78.3    -      -       -      +
    602M  ASN*     1.3    82.6    +      -       -      +
    603M  PHE*     3.3     8.1    +      -       -      -
    635M  PRO      3.9     3.8    -      -       -      -
    636M  ASN*     4.8     1.1    -      -       +      +
----------------------------------------------------------
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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