Contacts of the strand formed by residues 1063 - 1068 (chain B) 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 SER1063 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    978B  LEU*     3.9     2.7    -      -       -      +
    984B  VAL      3.1     5.7    +      -       -      -
    985B  ASN*     3.7    14.1    -      -       -      -
    986B  VAL*     2.9    33.0    +      -       -      +
   1035B  VAL*     4.9     0.2    -      -       -      -
   1036B  TYR*     3.3    15.5    -      -       -      +
   1056B  ALA*     2.6    51.6    +      -       -      -
   1059B  PHE*     4.0     1.0    -      -       -      +
   1062B  PRO*     1.3    74.8    -      -       -      +
   1064B  LEU*     1.3    60.8    -      -       -      +
   1065B  VAL*     5.1     0.9    -      -       -      -
   1238B   CA      3.4     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU1064 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    974B  LEU*     4.8     5.2    -      -       +      -
    978B  LEU*     3.8    21.1    -      -       +      -
    986B  VAL*     3.7    13.7    -      -       +      -
    988B  VAL*     3.7    28.3    -      -       +      -
   1025B  LEU*     4.2    17.5    -      -       +      +
   1029B  VAL*     3.7    36.1    -      -       +      -
   1035B  VAL*     4.8     0.9    -      -       +      -
   1036B  TYR*     2.7    13.1    +      -       -      +
   1037B  VAL*     3.3    11.6    -      -       +      +
   1038B  ALA      2.9    26.9    +      -       -      +
   1063B  SER*     1.3    72.3    -      -       -      +
   1065B  VAL*     1.3    66.5    +      -       -      +
   1066B  ILE*     4.2    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1065 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    958B  TRP*     5.4     7.6    -      -       +      -
    986B  VAL      2.9    13.3    +      -       -      +
    987B  PHE*     3.5    28.0    -      -       +      -
    988B  VAL*     3.0    26.9    +      -       -      +
   1036B  TYR*     4.8     0.4    -      -       +      -
   1038B  ALA*     3.4     7.0    -      -       +      +
   1040B  VAL*     4.0    15.0    -      -       +      -
   1052B  VAL*     3.4    35.0    -      -       +      -
   1053B  LEU*     5.3     5.4    -      -       +      +
   1056B  ALA*     3.9    22.7    -      -       +      -
   1063B  SER*     5.1     0.9    -      -       -      -
   1064B  LEU*     1.3    78.6    -      -       -      +
   1066B  ILE*     1.3    62.6    +      -       -      +
   1067B  ALA      4.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE1066 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    967B  TYR*     4.0    15.3    -      -       -      +
    988B  VAL*     3.6    17.3    -      -       +      +
    990B  ASP*     3.9    23.1    -      -       +      -
   1025B  LEU*     4.1    21.8    -      -       +      -
   1026B  ALA*     4.0    29.8    -      -       +      +
   1037B  VAL*     5.5     0.4    -      -       +      -
   1038B  ALA      3.0    11.9    +      -       -      +
   1039B  THR*     3.3    14.2    -      -       +      -
   1040B  VAL*     3.0    24.7    +      -       -      +
   1064B  LEU*     4.2    20.0    -      -       +      -
   1065B  VAL*     1.3    75.7    -      -       -      +
   1067B  ALA*     1.3    62.2    +      -       -      +
   1096B  TRP*     4.0    11.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA1067 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    820B  TYR*     3.6    22.7    -      -       +      -
    987B  PHE*     3.6    20.9    -      -       +      -
    988B  VAL      2.9     9.5    +      -       -      +
    989B  MET*     3.9     2.4    -      -       -      -
    990B  ASP*     2.9    29.5    +      -       -      +
   1040B  VAL*     3.4    24.2    -      -       +      -
   1065B  VAL      4.1     0.2    -      -       -      -
   1066B  ILE*     1.3    75.2    -      -       -      +
   1068B  TYR*     1.3    61.0    +      -       -      +
   1069B  ALA*     5.9     0.2    -      -       +      -
   1096B  TRP*     3.8     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR1068 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    820B  TYR*     2.7    25.6    +      -       -      -
    990B  ASP      4.0     5.8    -      -       -      -
    992B  GLU*     4.1    11.4    -      -       +      -
   1040B  VAL      3.1     9.3    +      -       -      +
   1041B  SER*     4.0    13.2    -      -       -      +
   1067B  ALA*     1.3    70.2    -      -       -      +
   1069B  ALA*     1.3    60.8    +      -       -      +
   1070B  THR*     4.1    20.9    -      -       +      -
   1074B  GLN*     4.4     7.6    +      -       -      -
   1086B  VAL*     4.3     7.9    -      -       +      +
   1087B  MET*     3.8    26.6    -      -       +      +
   1090B  ALA*     4.1    15.9    -      -       +      -
   1095B  TYR*     3.8    20.6    -      +       -      -
   1096B  TRP*     3.4    45.6    -      +       +      +
   1127B  PHE*     3.5    14.0    -      -       -      -
   1131B  GLN*     4.0     2.9    +      -       -      -
   1133B  ARG*     2.9    25.6    +      -       -      -
----------------------------------------------------------
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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