Contacts of the strand formed by residues 120 - 126 (chain B) in PDB entry 6DBU


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 VAL 120 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  GLU*     6.6     0.4    -      -       +      -
     27B  ASP*     6.0     3.8    -      -       +      +
     29B  TYR*     3.2    33.7    -      -       +      +
     58B  ARG*     6.1     2.0    -      -       -      +
     60B  ILE*     4.9    14.7    -      -       +      +
     61B  SER*     3.7    17.0    +      -       -      -
    111B  VAL*     3.8    24.5    -      -       +      -
    113B  SER      3.7     6.3    -      -       -      +
    114B  ARG*     5.0    10.5    -      -       +      +
    118B  ARG      4.9     4.5    -      -       -      +
    119B  LYS*     1.3    87.5    -      -       -      +
    121B  THR*     1.3    79.1    +      -       -      +
    122B  LEU*     4.0     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61B  SER*     4.7     9.6    -      -       -      +
     62B  PHE      4.9     8.7    -      -       -      +
     63B  SER*     5.5     2.0    -      -       -      -
    111B  VAL*     3.3     9.7    -      -       -      +
    112B  ASP*     2.9    26.8    +      -       -      +
    113B  SER*     2.5    56.5    +      -       -      +
    115B  GLY      5.1     4.7    -      -       -      +
    119B  LYS*     5.1     8.1    -      -       -      -
    120B  VAL*     1.3    81.1    -      -       -      +
    122B  LEU*     1.3    64.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  LEU*     5.2     0.2    -      -       +      -
     29B  TYR*     3.9    37.0    -      -       +      -
     45B  ILE*     4.3    22.4    -      -       +      -
     60B  ILE*     3.6    27.4    -      -       +      -
     61B  SER      3.9    10.7    +      -       -      +
     62B  PHE*     3.5    13.1    -      -       +      +
     63B  SER*     2.8    30.2    +      -       -      -
    109B  LEU*     4.4    11.9    -      -       +      -
    110B  SER      3.4    11.7    -      -       -      +
    111B  VAL*     3.8    19.5    -      -       +      +
    112B  ASP*     4.9     2.5    -      -       -      -
    120B  VAL*     4.0     4.9    -      -       +      -
    121B  THR*     1.3    84.8    -      -       -      +
    123B  ARG*     1.3    62.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62B  PHE*     5.2     0.9    -      -       -      -
     63B  SER*     4.0     7.0    -      -       -      -
     65B  ASN*     2.8    45.0    +      -       -      +
     66B  SER*     3.7    14.8    -      -       -      +
     86B  LYS*     5.1    18.4    -      -       -      +
    108B  MET      3.7     1.1    -      -       -      +
    109B  LEU*     3.4     4.0    -      -       -      +
    110B  SER*     2.9    57.4    +      -       -      +
    111B  VAL      4.8     3.6    -      -       -      +
    112B  ASP*     4.9    18.6    +      -       +      +
    122B  LEU*     1.3    77.9    -      -       -      +
    124B  CYS*     1.3    65.2    +      -       -      +
    125B  GLU*     2.3    43.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  ILE*     4.2     0.4    -      -       -      -
     62B  PHE*     3.5    24.6    -      -       +      -
     66B  SER*     3.2     8.3    -      -       -      -
     67B  SER*     2.5    48.8    +      -       -      +
     69B  LEU*     3.5    42.8    -      -       +      -
    107B  TYR*     5.4     1.1    -      -       +      -
    108B  MET      3.4     7.0    -      -       -      +
    109B  LEU*     3.5    31.0    -      -       -      -
    123B  ARG*     1.3    71.0    -      -       -      +
    125B  GLU*     1.3    57.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 125 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65B  ASN      5.6     1.3    -      -       -      +
     66B  SER*     5.2     4.7    -      -       -      -
     67B  SER      4.9     1.6    -      -       -      +
     86B  LYS*     6.0     1.7    -      -       -      -
    107B  TYR*     3.8     1.3    -      -       -      -
    108B  MET*     2.9    62.8    +      -       +      +
    123B  ARG*     2.3    52.7    +      -       +      +
    124B  CYS*     1.3    72.9    -      -       -      +
    126B  GLU*     1.3    67.2    +      -       -      +
    127B  LYS*     3.2     9.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    783A  ARG*     3.6    28.8    +      -       -      -
    784A  LYS*     3.6    33.6    +      -       -      +
     67B  SER*     3.7    12.7    +      -       -      +
    105B  SER*     4.8    10.7    -      -       -      -
    106B  LEU      4.5     1.8    -      -       -      +
    107B  TYR*     3.9    25.4    -      -       +      -
    124B  CYS      3.6     4.8    +      -       -      -
    125B  GLU*     1.3    72.2    -      -       -      +
    127B  LYS*     1.3    70.1    +      -       -      +
    128B  GLU*     3.9     6.8    +      -       -      +
----------------------------------------------------------
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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