Contacts of the strand formed by residues 985 - 990 (chain A) in PDB entry 1B0P


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 ASN 985 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    956A  SER*     3.9     7.3    +      -       -      +
    957A  VAL      2.9    28.1    +      -       -      +
    958A  TRP*     3.2    49.3    -      -       +      +
    959A  ILE*     2.9    25.7    +      -       -      +
    983A  ASP*     4.5     4.0    +      -       -      -
    984A  VAL*     1.3    76.5    -      -       -      +
    986A  VAL*     1.3    62.1    +      -       -      +
   1056A  ALA      3.3    10.7    -      -       -      +
   1057A  GLU*     3.6    10.9    +      -       -      +
   1063A  SER*     3.6    11.0    +      -       -      -
   1238A   CA      2.7    27.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 986 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    958A  TRP*     4.7     1.5    -      -       -      -
    959A  ILE*     3.3    23.1    -      -       +      +
    965A  TRP*     4.0     9.0    -      -       +      -
    974A  LEU*     3.7    21.5    -      -       +      -
    977A  VAL*     6.0     0.2    -      -       +      -
    978A  LEU*     3.5    23.1    -      -       +      -
    984A  VAL*     5.0     1.8    -      -       +      -
    985A  ASN*     1.3    76.0    -      -       -      +
    987A  PHE*     1.3    60.1    +      -       -      +
    988A  VAL*     3.6    15.3    -      -       +      -
   1063A  SER*     3.0    20.3    +      -       -      +
   1064A  LEU*     3.5    21.5    +      -       +      -
   1065A  VAL*     3.0    29.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 987 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    820A  TYR*     3.3    37.2    -      +       +      -
    821A  VAL*     4.5     4.3    -      -       +      -
    824A  ILE*     3.8    25.1    -      -       +      -
    958A  TRP*     3.7    21.3    -      +       +      -
    959A  ILE      2.9     8.5    +      -       -      -
    960A  PHE*     3.5    15.8    -      +       +      +
    961A  GLY      3.1    24.1    +      -       -      +
    985A  ASN      3.9     0.4    +      -       -      -
    986A  VAL*     1.3    72.3    -      -       -      +
    988A  VAL*     1.3    62.2    +      -       -      +
    989A  MET*     3.5    32.9    +      -       +      +
   1049A  PHE*     4.3     9.0    -      +       -      -
   1053A  LEU*     5.0     1.1    -      -       +      -
   1065A  VAL*     3.6    31.2    -      -       +      -
   1067A  ALA*     3.8    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 988 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    961A  GLY      3.1     3.6    -      -       -      +
    962A  GLY      3.6    25.6    -      -       -      +
    963A  ASP*     4.1     6.5    -      -       -      +
    965A  TRP*     4.3     3.1    -      -       +      -
    966A  ALA*     3.7    24.7    -      -       +      -
    967A  TYR*     4.5     5.6    -      -       +      -
    986A  VAL*     3.6    24.5    -      -       +      -
    987A  PHE*     1.3    72.8    -      -       -      +
    989A  MET*     1.3    65.9    +      -       -      +
    990A  ASP*     3.4     1.1    +      -       +      +
   1025A  LEU*     4.9     0.9    -      -       +      -
   1064A  LEU*     3.7    17.0    -      -       +      -
   1065A  VAL      3.0     8.7    +      -       -      +
   1066A  ILE*     3.4    16.0    -      -       +      -
   1067A  ALA*     2.9    28.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 989 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    817A  GLU*     3.1    62.3    -      -       +      +
    820A  TYR*     5.1     2.7    -      -       +      -
    821A  VAL*     3.5    23.3    -      -       +      -
    841A  SER*     3.4    25.8    -      -       -      +
    844A  TRP*     3.6     4.5    -      -       +      -
    960A  PHE*     5.2     3.6    -      -       -      -
    961A  GLY      3.0    14.9    +      -       -      +
    962A  GLY*     3.4    20.1    -      -       -      -
    963A  ASP*     3.4     2.9    +      -       -      +
    987A  PHE*     3.5    35.6    +      -       +      +
    988A  VAL*     1.3    71.4    -      -       -      +
    990A  ASP*     1.3    59.7    +      -       -      +
    991A  THR*     3.5     4.2    +      -       -      +
   1067A  ALA*     3.9     4.9    -      -       -      +
   1069A  ALA*     4.2     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 990 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    963A  ASP*     3.5    16.8    -      -       +      +
    967A  TYR*     2.8    20.9    +      -       -      -
    988A  VAL*     3.4     2.0    +      -       +      -
    989A  MET*     1.3    70.7    -      -       -      +
    991A  THR*     1.3    57.7    +      -       -      +
    992A  GLU*     2.8    41.0    +      -       -      +
   1004A  ALA*     3.8     0.2    -      -       -      +
   1022A  LYS*     2.7    26.1    +      -       -      -
   1066A  ILE*     3.8    10.3    -      -       +      -
   1067A  ALA      2.7    18.5    +      -       -      +
   1068A  TYR*     3.8     5.4    -      -       -      -
   1069A  ALA*     2.9    24.8    +      -       -      +
   1096A  TRP*     3.4    16.4    -      -       +      -
----------------------------------------------------------
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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