Contacts of the strand formed by residues 626 - 633 (chain N) in PDB entry 2O5J


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 SER 626 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1006M  HIS      4.4     0.2    -      -       -      +
   1008M  ARG*     3.3    15.9    +      -       -      +
   1028M  GLY      4.9     1.6    +      -       -      -
   1029M  GLY*     3.9     4.0    -      -       -      -
   1030M  GLN*     2.9    36.4    +      -       -      +
    623N  VAL*     4.0     9.0    -      -       -      -
    624N  ASP      3.6     3.4    +      -       -      -
    625N  TYR*     1.3    74.6    -      -       -      +
    627N  GLY*     1.3    59.6    +      -       -      +
    652N  LEU*     3.3    20.1    -      -       -      +
    747N  VAL      3.2     7.4    -      -       -      -
    748N  HIS*     3.2    27.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 627 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1006M  HIS      3.4    11.7    -      -       -      -
   1007M  ALA*     4.4     3.8    -      -       -      -
   1030M  GLN*     3.3     8.2    -      -       -      +
    626N  SER*     1.3    77.9    -      -       -      +
    628N  ARG*     1.3    60.4    +      -       -      +
    648N  MET*     4.5     2.5    -      -       -      -
    652N  LEU*     4.5     2.7    -      -       -      -
    746N  ALA*     3.1     5.2    -      -       -      +
    747N  VAL*     2.6    50.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 628 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1001M  VAL      5.1     3.2    +      -       -      -
   1002M  GLU*     3.9    14.5    +      -       -      +
   1005M  MET*     3.7     3.4    -      -       -      +
   1006M  HIS*     3.4    40.4    +      -       +      +
   1030M  GLN*     2.9    39.0    +      -       -      +
    627N  GLY*     1.3    72.3    -      -       -      +
    629N  SER*     1.3    61.5    +      -       -      +
    648N  MET*     3.0    15.6    -      -       -      +
    744N  GLN*     3.9    23.5    -      -       +      +
    745N  MET      3.7     7.6    -      -       -      +
    746N  ALA*     3.9    11.2    -      -       +      +
    747N  VAL*     4.8     1.3    -      -       -      -
     17X    C      2.5    30.6    +      -       -      -
     18X    G      2.8    42.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 629 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1002M  GLU      5.4     0.7    -      -       -      -
   1003M  ASP      5.2     2.0    +      -       -      -
   1005M  MET*     3.7     9.8    -      -       -      +
    628N  ARG*     1.3    78.5    -      -       -      +
    630N  VAL*     1.3    81.4    +      -       -      +
    631N  ILE*     4.1     1.2    -      -       -      +
    648N  MET*     3.6    19.5    -      -       -      -
    724N  GLN*     2.7    29.5    +      -       -      +
    725N  SER*     3.7     0.7    -      -       -      -
    726N  ILE*     3.8    11.4    -      -       -      +
    744N  GLN*     3.3    24.5    -      -       -      +
    745N  MET      3.5    14.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 630 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    836M  GLY      4.7    13.9    -      -       -      +
    838M  LYS*     6.5     0.9    -      -       -      -
    848M  VAL*     4.7    15.7    -      -       +      -
   1003M  ASP*     4.1    26.2    -      -       +      +
    629N  SER*     1.3    81.2    +      -       -      +
    631N  ILE*     1.3    71.2    +      -       -      +
    632N  VAL*     5.2     0.2    -      -       +      -
    724N  GLN*     4.4    12.1    -      -       -      +
    725N  SER*     3.2    14.1    -      -       -      -
    726N  ILE*     2.9    24.8    +      -       -      -
    742N  GLY*     5.3     6.3    -      -       -      +
    743N  ASP      4.1    11.4    -      -       -      +
    744N  GLN*     3.8    22.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 631 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    848M  VAL*     5.1     1.9    -      -       -      +
    629N  SER      4.1     1.6    -      -       -      +
    630N  VAL*     1.3    81.4    -      -       -      +
    632N  VAL*     1.3    71.9    +      -       -      +
    726N  ILE*     3.5    16.4    -      -       +      +
    728N  LEU*     4.7     7.4    -      -       +      -
    738N  ALA*     4.0    20.6    -      -       +      -
    739N  ASP      4.7     0.9    -      -       -      +
    740N  PHE*     3.6    26.6    -      -       +      +
    743N  ASP*     3.2    41.3    -      -       +      +
    745N  MET*     3.4    55.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 632 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    687M  ALA*     5.5     0.7    -      -       +      -
    835M  VAL*     4.7     3.1    -      -       +      +
    848M  VAL*     4.2    21.8    -      -       +      -
    849M  VAL      3.8     5.2    -      -       -      +
    850M  ALA*     3.5    39.9    -      -       +      +
    630N  VAL*     4.6     1.6    -      -       +      +
    631N  ILE*     1.3    81.8    -      -       -      +
    633N  VAL*     1.3    72.3    +      -       +      +
    725N  SER*     3.3    31.6    -      -       -      +
    726N  ILE      2.9     7.4    +      -       -      +
    727N  GLN*     3.1    10.6    -      -       +      +
    728N  LEU      3.1    19.6    +      -       -      +
    740N  PHE*     3.3    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 633 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681M  GLY*     3.3    25.1    -      -       -      +
    682M  TYR*     3.4    19.7    -      -       +      +
    684M  PHE*     4.6     3.8    -      -       +      -
    687M  ALA*     4.4     3.4    -      -       +      -
    850M  ALA*     3.8    15.8    -      -       +      +
    632N  VAL*     1.3    78.3    -      -       +      +
    634N  GLY*     1.3    62.7    +      -       -      +
    635N  PRO*     3.2    22.0    -      -       +      +
    727N  GLN*     4.0     7.3    +      -       -      +
    728N  LEU      4.0     1.3    -      -       -      -
    730N  PRO*     4.6    17.3    -      -       +      -
    740N  PHE*     3.0    37.8    -      -       +      -
----------------------------------------------------------
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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