Contacts of the strand formed by residues 115 - 123 (chain A) in PDB entry 1BMZ


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 115 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  HIS*     3.9     4.5    -      -       -      -
    112A  SER*     2.9    42.8    +      -       -      +
    114A  TYR*     1.3    82.0    -      -       -      +
    116A  TYR*     1.3    68.7    +      -       -      +
    117B  SER*     5.2     2.1    -      -       -      -
    118B  THR      3.0    14.9    +      -       -      -
    119B  THR*     3.1    23.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  THR*     5.7     2.5    -      -       +      -
     88A  HIS*     3.8    35.7    -      +       +      -
     90A  HIS      4.4     2.0    +      -       -      -
     91A  ALA*     3.6    39.3    -      -       +      -
     92A  GLU      3.9     4.3    +      -       -      -
     93A  VAL*     6.1     0.2    -      -       +      -
    109A  ALA*     5.9     1.3    -      -       +      -
    110A  LEU      3.3    13.9    -      -       -      +
    111A  LEU*     4.0    16.8    -      -       +      -
    112A  SER      5.3     0.2    -      -       -      +
    115A  SER*     1.3    79.4    +      -       -      +
    117A  SER*     1.3    70.5    +      -       -      +
    118A  THR*     4.7     8.3    -      -       +      -
     92B  GLU      3.0    25.6    +      -       -      -
     93B  VAL*     4.5     1.0    -      -       -      -
    116B  TYR*     4.2    19.9    +      +       -      -
    117B  SER*     3.2     2.9    -      -       -      -
    118B  THR*     2.9    51.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  ALA*     3.3     5.0    -      -       -      +
    110A  LEU*     2.9    53.6    +      -       -      +
    116A  TYR*     1.3    78.6    -      -       -      +
    118A  THR*     1.3    62.9    +      -       -      +
    119A  THR*     5.1     5.4    -      -       -      +
    115B  SER*     5.2     3.6    -      -       -      -
    116B  TYR      3.2     7.2    -      -       -      -
    117B  SER*     3.5    20.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  VAL*     3.5    29.5    -      -       +      +
    107A  ILE*     3.7     8.7    -      -       -      +
    108A  ALA      3.1    14.2    +      -       -      -
    109A  ALA*     4.6     5.9    -      -       -      +
    116A  TYR*     4.7     7.9    -      -       +      -
    117A  SER*     1.3    77.5    -      -       -      +
    119A  THR*     1.3    65.5    +      -       -      +
     88B  HIS*     4.2     6.1    +      -       -      +
    115B  SER*     2.9    16.8    +      -       -      -
    116B  TYR*     2.9    58.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  THR      3.8     0.7    -      -       -      +
    107A  ILE*     3.6     3.0    -      -       -      -
    108A  ALA*     2.8    42.1    +      -       +      +
    117A  SER*     5.1     5.8    -      -       -      +
    118A  THR*     1.3    80.4    +      -       -      +
    120A  ALA*     1.3    63.7    +      -       -      +
    121A  VAL*     4.2    10.3    -      -       -      +
     88B  HIS*     5.4     2.2    -      -       -      -
    114B  TYR      3.4     5.2    -      -       -      -
    115B  SER*     3.1    28.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  TYR*     5.7     0.2    -      -       +      -
    106A  THR      3.4     5.2    -      -       -      +
    107A  ILE*     4.2     5.4    -      -       +      -
    119A  THR*     1.3    75.7    +      -       -      +
    121A  VAL*     1.3    63.2    +      -       -      +
    122A  VAL*     3.9     2.6    +      -       +      -
     87B  PHE*     3.3    55.0    -      -       +      -
     88B  HIS*     5.0     0.2    -      -       -      +
    114B  TYR*     3.0    31.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  ARG      3.6     3.8    -      -       -      +
    105A  TYR*     3.7     0.3    -      -       -      -
    106A  THR*     2.9    48.7    +      -       +      +
    108A  ALA*     6.0     2.9    -      -       +      -
    119A  THR*     4.5    11.2    -      -       -      +
    120A  ALA*     1.3    75.5    -      -       -      +
    122A  VAL*     1.3    62.8    +      -       -      +
    123A  THR*     4.0    19.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  ARG*     3.6    33.7    -      -       +      -
    104A  ARG      3.4     4.0    -      -       -      +
    105A  TYR*     3.7    27.8    -      -       +      +
    120A  ALA*     3.9     3.0    +      -       +      -
    121A  VAL*     1.3    78.5    -      -       -      +
    123A  THR*     1.3    68.6    +      -       -      +
     87B  PHE*     4.0    15.3    -      -       +      -
    114B  TYR*     4.0    22.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  ARG*     3.6    16.0    -      -       -      -
    104A  ARG*     2.6    57.3    +      -       -      +
    121A  VAL*     4.0    18.2    +      -       +      -
    122A  VAL*     1.3    80.6    -      -       -      +
----------------------------------------------------------
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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