Contacts of the strand formed by residues 100 - 106 (chain B) in PDB entry 1BWN


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 TYR 100 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79B  ILE*     3.2    49.8    -      -       +      +
     98B  PHE      3.6     0.6    -      -       -      -
     99B  PRO*     1.3    92.7    -      -       +      +
    101B  PRO*     1.4    63.1    -      -       +      +
    102B  PHE*     3.8     1.0    +      -       -      -
    113B  VAL      3.6     0.9    -      -       -      +
    114B  PHE*     3.5     1.6    -      -       -      +
    115B  SER*     2.8    39.3    +      -       -      +
    116B  PRO      3.4     9.4    -      -       -      -
    117B  THR*     2.9    45.3    -      -       +      +
    118B  GLU*     2.9    33.8    +      -       +      +
    121B  ARG*     3.4    21.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66B  THR*     3.8     1.0    -      -       -      -
     67B  VAL*     3.4    30.7    +      -       +      +
     69B  PRO*     4.3    17.7    -      -       +      -
     70B  GLU      5.2     0.4    -      -       -      +
     99B  PRO      3.0    14.1    -      -       -      +
    100B  TYR*     1.4    85.8    -      -       +      +
    102B  PHE*     1.3    61.9    +      -       -      +
    113B  VAL      3.1     8.1    -      -       -      +
    114B  PHE*     3.6    25.8    -      -       +      -
    121B  ARG*     3.1    22.1    +      -       -      +
    146B  PHE*     3.8    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  PHE*     4.2    22.0    -      +       -      -
     30B  PHE*     6.3     0.9    -      +       -      -
     37B  LEU*     6.0     1.6    -      -       +      -
     64B  VAL*     4.5     4.0    -      -       +      -
     65B  GLU      3.2    13.2    -      -       -      +
     66B  THR*     4.1     0.2    -      -       -      +
     67B  VAL*     3.5     7.0    -      -       -      +
    100B  TYR      4.2     6.3    -      -       -      -
    101B  PRO*     1.3    76.1    -      -       -      +
    103B  GLN*     1.3    67.8    +      -       -      +
    104B  VAL*     4.1    13.2    -      -       +      -
    111B  LEU      3.8     0.3    -      -       -      +
    112B  TYR*     3.9     2.4    -      -       -      -
    113B  VAL*     2.9    70.2    +      -       +      +
    115B  SER*     5.0     1.8    -      -       -      -
    121B  ARG*     4.3    12.8    -      -       +      -
    124B  TRP*     4.1    22.9    -      +       +      -
    125B  ILE*     3.8    21.3    -      -       +      -
    128B  LEU*     3.6    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 103 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63B  CYS*     4.6     0.9    -      -       -      +
     64B  VAL*     3.0     8.5    -      -       -      +
     65B  GLU*     2.5    46.1    +      -       +      +
     66B  THR      2.9    21.5    -      -       -      +
     67B  VAL*     3.4    13.6    -      -       +      +
    102B  PHE*     1.3    76.8    -      -       -      +
    104B  VAL*     1.3    64.4    +      -       -      +
    105B  VAL*     3.8    24.7    -      -       +      +
    110B  PRO*     4.4     3.5    -      -       +      +
    111B  LEU      3.3     3.8    -      -       -      +
    112B  TYR*     3.9    27.8    +      -       +      -
    142B  TYR*     3.9     9.0    -      -       -      +
    143B  HIS*     3.1    29.7    +      -       -      +
    144B  PRO      4.5     0.2    -      -       -      +
    145B  CYS      4.3     1.6    +      -       -      -
    152B  TYR*     5.6     1.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 104 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  LEU*     4.2    24.0    -      -       +      -
     56B  ILE*     4.4     9.0    -      -       +      -
     61B  ILE*     3.7    35.0    -      -       +      -
     63B  CYS      3.6     1.6    -      -       -      -
     64B  VAL*     4.6     4.5    -      -       +      +
    102B  PHE*     4.1    23.3    -      -       +      -
    103B  GLN*     1.3    77.4    -      -       -      +
    105B  VAL*     1.3    62.6    +      -       -      +
    106B  TYR*     3.7     2.1    -      -       -      -
    109B  GLY      3.4     3.5    -      -       -      +
    111B  LEU*     2.7    48.6    +      -       +      +
    113B  VAL*     4.6     6.7    -      -       +      -
    128B  LEU*     4.3     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 105 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61B  ILE*     3.0    11.1    -      -       -      +
     62B  THR*     2.7    43.8    +      -       -      +
     63B  CYS*     2.6    29.9    +      -       +      +
    103B  GLN*     3.8    30.5    -      -       +      +
    104B  VAL*     1.3    75.8    -      -       -      +
    106B  TYR*     1.3    62.0    +      -       -      +
    109B  GLY*     3.6    15.5    -      -       -      +
    110B  PRO*     4.0    10.5    -      -       +      -
    142B  TYR*     6.5     0.4    -      -       +      -
    152B  TYR*     5.8     2.2    -      -       -      +
    160B  LYS      6.1     0.2    -      -       -      +
    161B  ASN*     5.7     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  GLN*     2.2    36.2    +      -       -      -
     17B  LYS*     3.0    22.2    +      -       -      -
     55B  SER      5.0     2.2    -      -       -      -
     56B  ILE*     3.8    49.7    -      -       +      +
     60B  LYS*     3.0    28.0    -      -       -      +
     61B  ILE*     4.0     1.6    -      -       +      -
     62B  THR*     4.2     7.4    -      -       -      +
    104B  VAL      3.7    10.8    -      -       -      -
    105B  VAL*     1.3    78.7    -      -       -      +
    107B  ASP*     1.4    85.8    +      -       -      +
    108B  GLU*     3.1    28.8    -      -       +      +
    109B  GLY*     2.8    44.4    +      -       -      +
    111B  LEU*     4.4     2.7    -      -       +      -
    161B  ASN*     4.3     1.2    -      -       -      +
----------------------------------------------------------
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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