Contacts of the strand formed by residues 488 - 494 (chain B) in PDB entry 1OGS


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 488 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  SER      3.3    13.0    -      -       -      -
     43B  THR*     3.9    14.8    -      -       -      -
    357B  TRP*     4.1     4.7    -      -       -      +
    460B  VAL      5.3     0.3    +      -       -      -
    461B  LEU*     3.6     4.1    -      -       -      +
    462B  ASN      2.9    29.5    +      -       -      +
    484B  SER*     4.0     5.5    +      -       -      -
    485B  PRO*     2.7    43.9    +      -       -      +
    487B  TYR*     1.3    77.8    -      -       -      +
    489B  ILE*     1.3    63.6    +      -       -      +
    490B  HIS*     4.1     7.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 489 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  SER*     2.9    39.6    +      -       -      +
    364B  SER*     3.6    31.4    -      -       -      -
    419B  HIS*     3.9    22.4    -      -       +      +
    422B  HIS*     3.2    48.1    -      -       +      +
    423B  PHE*     4.0     1.3    -      -       +      -
    459B  VAL*     4.0    16.8    -      -       +      -
    460B  VAL      3.3    11.7    -      -       -      +
    461B  LEU*     4.0    12.1    -      -       +      -
    488B  SER*     1.3    76.0    -      -       -      +
    490B  HIS*     1.3    67.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 490 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  ARG*     3.9    16.2    -      -       +      -
     40B  TYR      3.2     7.2    -      -       -      +
     41B  GLU*     2.6    43.7    +      -       +      +
    422B  HIS*     3.9     1.3    -      -       -      -
    458B  VAL      3.8     0.4    -      -       -      +
    459B  VAL*     3.3     5.4    -      -       -      +
    460B  VAL*     2.8    41.6    +      -       +      +
    483B  ILE      3.3    25.2    +      -       -      -
    484B  SER*     4.9     3.7    -      -       -      -
    485B  PRO*     3.6    10.4    -      -       +      +
    488B  SER*     4.1     8.7    +      -       -      -
    489B  ILE*     1.3    86.4    -      -       -      +
    491B  THR*     1.3    62.4    +      -       -      +
    492B  TYR*     2.7    41.0    +      +       +      -
----------------------------------------------------------
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Residues in contact with THR 491 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  SER      3.8     0.5    -      -       -      +
     39B  ARG*     3.5     3.6    -      -       -      -
     40B  TYR*     3.0    33.0    +      -       -      +
    422B  HIS*     2.8    44.5    +      -       -      +
    426B  PHE*     3.6    31.2    -      -       +      -
    457B  VAL*     3.8    24.9    -      -       +      -
    458B  VAL      3.4     4.9    -      -       -      +
    459B  VAL*     3.9     5.9    -      -       +      +
    490B  HIS*     1.3    75.0    +      -       -      +
    492B  TYR*     1.3    63.3    +      -       -      +
    493B  LEU*     4.1     6.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 492 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  PHE*     3.9    25.6    -      +       -      -
     38B  SER      3.3     6.1    -      -       -      +
     39B  ARG*     3.4    23.1    +      -       +      -
    457B  VAL*     3.1     6.1    -      -       -      +
    458B  VAL*     2.7    44.9    +      -       +      +
    460B  VAL*     4.1    16.6    -      -       +      -
    470B  LEU*     5.6     0.6    -      -       +      +
    472B  ILE*     4.1    14.8    -      -       +      -
    480B  LEU*     4.3     7.2    -      -       +      -
    482B  THR*     2.6    42.0    +      -       +      +
    483B  ILE      4.0     1.2    +      -       -      -
    484B  SER*     5.6     0.2    -      -       -      -
    490B  HIS*     2.7    42.0    +      -       +      -
    491B  THR*     1.3    73.5    -      -       -      +
    493B  LEU*     1.3    64.1    +      -       -      +
    494B  TRP*     4.0    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 493 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  PHE*     4.0    17.9    -      -       +      -
     32B  PRO*     3.8     3.3    -      -       -      +
     37B  PHE*     3.4     1.0    -      -       -      +
     38B  SER*     2.8    46.8    +      -       -      -
     40B  TYR*     3.7    36.1    -      -       +      -
    426B  PHE*     3.8    34.3    -      -       +      -
    451B  HIS*     4.1    19.1    -      -       +      -
    456B  ALA      3.3     7.6    -      -       -      +
    457B  VAL*     4.0    11.9    -      -       +      -
    491B  THR*     4.1     7.2    -      -       +      +
    492B  TYR*     1.3    80.7    -      -       -      +
    494B  TRP*     1.3    67.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 494 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  PHE*     4.6     3.0    -      -       -      -
     32B  PRO*     4.3     5.4    -      -       -      -
     36B  THR      3.7    19.1    -      -       -      +
     37B  PHE*     4.0     2.9    -      -       +      -
     56B  ILE*     3.9    10.1    -      -       +      -
     69B  LEU*     4.3     7.4    -      -       +      -
    455B  SER*     3.7     2.4    -      -       -      -
    456B  ALA*     2.9    50.9    +      -       +      +
    458B  VAL*     3.6    31.6    -      -       +      -
    472B  ILE*     3.9    18.6    -      -       +      -
    474B  ASP*     2.7    42.5    +      -       +      -
    477B  VAL*     3.7    13.2    -      -       +      +
    480B  LEU*     3.5    31.4    -      -       +      -
    492B  TYR*     4.0    12.3    -      -       +      -
    493B  LEU*     1.3    85.0    -      -       -      +
    495B  HIS*     1.3    86.6    +      -       -      +
    496B  ARG*     4.2     0.9    -      -       +      +
----------------------------------------------------------
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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