Contacts of the strand formed by residues 76 - 92 (chain A) in PDB entry 1BND


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 TRP 76 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  ILE*     3.7    16.6    -      -       +      +
     72A  ASP*     3.0    27.9    +      -       +      +
     73A  LYS*     3.6    22.2    -      -       -      +
     74A  ARG      3.4     2.6    -      -       -      -
     75A  HIS*     1.3   100.6    -      -       +      +
     77A  ASN*     1.3    68.8    +      -       -      +
     78A  SER      4.3     0.2    +      -       -      -
    113A  LEU*     3.5    31.4    -      -       +      -
    114A  THR      3.3    17.9    -      -       -      -
    115A  ILE*     3.6    31.9    -      -       +      -
    116A  LYS*     4.3     5.4    -      -       -      +
     11B  VAL*     4.2    21.3    -      -       +      -
     68B  ARG*     4.5    11.4    -      -       +      -
     69B  GLY*     3.3    31.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  TRP*     1.3    78.0    -      -       -      +
     78A  SER*     1.3    63.4    +      -       -      +
    113A  LEU*     3.2     8.1    -      -       -      +
    114A  THR*     3.1    48.7    +      -       -      +
    115A  ILE      5.1     0.6    +      -       -      -
    116A  LYS*     3.7    36.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  GLU      3.9     5.4    -      -       -      +
     67A  GLY*     3.8    14.1    -      -       -      -
     68A  CYS*     3.2    30.0    +      -       -      -
     71A  ILE*     3.4    27.1    -      -       -      +
     76A  TRP      5.2     0.2    +      -       -      -
     77A  ASN*     1.3    77.1    -      -       -      +
     79A  GLN*     1.3    67.7    +      -       -      +
    111A  CYS*     3.9     2.5    -      -       -      -
    112A  THR      3.1    10.8    -      -       -      -
    113A  LEU*     4.0     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  LYS      5.5     2.3    -      -       -      +
     66A  GLU      5.1     4.4    -      -       -      +
     67A  GLY*     4.4     6.5    -      -       -      +
     68A  CYS*     3.4     9.0    -      -       -      -
     78A  SER*     1.3    80.5    -      -       -      +
     80A  CYS*     1.3    74.4    +      -       -      +
     81A  ARG*     2.8    39.7    -      -       +      +
    111A  CYS*     3.5     0.3    -      -       -      -
    112A  THR      2.9    35.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  CYS*     2.0    50.7    -      -       -      -
     58A  CYS*     3.7     8.6    -      -       +      +
     64A  THR*     3.7    32.5    +      -       -      +
     66A  GLU      6.0     0.2    -      -       -      -
     67A  GLY*     5.2     0.8    -      -       -      -
     68A  CYS*     3.8    12.5    -      -       -      +
     79A  GLN*     1.3    83.2    -      -       -      +
     81A  ARG*     1.3    61.6    +      -       -      +
    109A  CYS*     3.7    13.0    -      -       -      -
    110A  VAL      3.4     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  CYS*     3.1     5.8    -      -       -      -
     79A  GLN*     2.8    57.4    -      -       -      +
     80A  CYS*     1.3    75.2    -      -       -      +
     82A  THR*     1.3    65.6    +      -       -      +
     83A  THR*     3.7     4.2    +      -       +      -
    109A  CYS*     3.1     1.2    -      -       -      -
    110A  VAL*     2.7    48.7    +      -       +      +
    112A  THR*     3.3    29.5    +      -       -      +
     10B  GLU*     3.6    21.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  LYS*     3.7    10.5    -      -       +      +
     58A  CYS*     3.1    26.2    +      -       -      +
     81A  ARG*     1.3    75.9    -      -       -      +
     83A  THR*     1.3    65.1    +      -       -      +
     84A  GLN*     5.1     3.5    -      -       +      +
    106A  ASP*     3.6    41.3    -      -       +      +
    108A  SER      3.1    12.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  ARG*     4.1     5.6    -      -       +      +
     82A  THR*     1.3    78.3    -      -       -      +
     84A  GLN*     1.3    65.9    +      -       -      +
    106A  ASP*     3.7     2.4    -      -       -      -
    107A  THR*     3.1    22.4    +      -       -      -
    108A  SER*     2.8    31.3    +      -       -      +
    110A  VAL*     3.4    37.2    -      -       +      +
    107B  SER*     5.0     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  VAL*     5.5     1.3    -      -       -      +
     82A  THR*     5.1     3.6    -      -       +      +
     83A  THR*     1.3    80.6    -      -       -      +
     85A  SER*     1.3    62.1    +      -       -      +
    104A  ARG*     3.4    47.5    +      -       +      +
    105A  ILE      3.3    12.3    -      -       -      +
    106A  ASP*     3.0    31.6    +      -       -      +
    107A  THR*     4.2     1.5    +      -       -      -
     53B  TYR*     5.2     3.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  GLN*     1.3    74.2    -      -       -      +
     86A  TYR*     1.3    72.0    +      -       -      +
     87A  VAL*     4.0     2.4    +      -       -      +
    103A  ILE      3.5     0.5    -      -       -      +
    104A  ARG*     3.2     7.5    -      -       -      -
    105A  ILE*     2.8    31.5    +      -       -      +
    107A  THR*     3.3    31.0    -      -       -      -
     53B  TYR*     3.6    27.7    +      -       -      -
     55B  THR*     4.6     4.8    -      -       -      +
    104B  ILE*     5.8     1.6    -      -       -      +
    106B  THR*     3.9    12.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  ASP      4.4     0.4    -      -       -      -
     31A  MET*     3.6    37.9    +      -       +      +
     85A  SER*     1.3    77.9    +      -       -      +
     87A  VAL*     1.3    64.8    +      -       -      +
    102A  PHE*     3.9    28.4    -      -       +      -
    103A  ILE      3.4    12.6    -      -       -      -
    104A  ARG*     3.0    49.6    +      -       +      -
    500A  IPA      3.7     7.0    +      -       +      +
     20B  TRP*     4.1     7.9    -      +       +      -
     53B  TYR*     3.6    63.5    +      +       +      +
    104B  ILE*     5.9     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  PHE*     3.7    35.9    -      -       +      -
     85A  SER*     4.0     2.7    +      -       -      +
     86A  TYR*     1.3    78.1    -      -       -      +
     88A  ARG*     1.3    64.5    +      -       -      +
    101A  ARG      3.4     0.2    -      -       -      +
    102A  PHE*     3.3     4.6    -      -       -      -
    103A  ILE*     2.9    34.1    +      -       +      +
    105A  ILE*     3.7    39.0    -      -       +      -
    107A  THR*     5.4     3.4    -      -       +      -
     84B  THR*     6.1     0.2    -      -       +      -
     86B  VAL*     4.3    26.0    -      -       +      -
    104B  ILE*     6.0     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  GLN*     4.8     0.3    -      -       -      +
     53A  PHE*     4.3     4.5    -      -       -      -
     87A  VAL*     1.3    81.1    -      -       -      +
     89A  ALA*     1.3    64.1    +      -       -      +
    100A  TRP*     3.9    45.8    +      -       +      +
    101A  ARG*     3.2    15.0    -      -       -      +
    102A  PHE*     3.7    26.6    -      -       +      -
     41B  ILE*     5.0    13.1    -      -       -      +
     48B  VAL*     3.8    17.4    -      -       -      +
     49B  LYS      3.4    15.5    +      -       -      -
     50B  GLN*     5.3     1.2    -      -       -      +
     51B  TYR*     2.7    56.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  VAL*     4.7     1.3    -      -       +      -
     51A  GLN*     3.4    12.8    -      -       -      +
     53A  PHE*     3.9    11.0    -      -       +      -
     88A  ARG*     1.3    77.5    -      -       -      +
     90A  LEU*     1.3    64.6    +      -       -      +
     91A  THR*     3.4    13.6    +      -       +      +
    100A  TRP*     3.3     9.0    -      -       -      -
    101A  ARG      2.9    28.7    +      -       -      +
    103A  ILE*     3.8    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  VAL*     4.1     0.5    -      -       -      -
     39A  LEU*     3.4    31.2    +      -       +      -
     41A  LYS      4.7     2.5    -      -       -      +
     42A  VAL*     3.8    27.1    -      -       +      -
     43A  PRO*     4.1    15.5    -      -       +      -
     51A  GLN*     2.8    32.6    +      -       -      +
     89A  ALA*     1.3    70.4    -      -       -      +
     91A  THR*     1.3    62.6    +      -       -      +
     98A  ILE*     3.7    16.6    -      -       +      -
     99A  GLY*     3.7    24.5    -      -       -      +
    100A  TRP*     3.7    31.6    -      -       +      +
     44B  GLN*     4.6    10.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  VAL*     3.4    27.1    -      -       +      -
     37A  THR      3.2    12.6    -      -       -      +
     38A  VAL*     4.4     5.2    -      -       +      -
     39A  LEU*     4.2     7.4    -      -       -      +
     89A  ALA*     3.6    22.4    -      -       +      +
     90A  LEU*     1.3    81.4    -      -       -      +
     92A  MET*     1.3    61.0    +      -       -      +
     98A  ILE*     3.2     4.7    -      -       -      +
     99A  GLY      2.7    38.2    +      -       -      +
    101A  ARG*     2.7    35.7    +      -       +      +
    103A  ILE*     4.0     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  VAL*     3.7     2.8    -      -       -      -
     37A  THR*     2.9    53.1    +      -       +      +
     39A  LEU*     3.9    14.1    -      -       +      -
     91A  THR*     1.3    77.6    -      -       -      +
     93A  ASP*     1.3    69.2    +      -       -      +
     96A  LYS*     3.7    52.7    -      -       +      +
     97A  ARG      3.0     7.6    -      -       -      +
     98A  ILE*     4.0    15.5    -      -       +      -
    101A  ARG*     4.2     1.8    -      -       -      -
----------------------------------------------------------
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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