Contacts of the strand formed by residues 65 - 72 (chain B) in PDB entry 4DOH


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 65 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62B  GLU*     5.6     2.2    -      -       +      -
     63B  THR*     3.2    45.7    +      -       -      -
     64B  VAL*     1.3    74.9    -      -       -      +
     66B  TYR*     1.3    60.8    +      -       -      +
     91B  LEU*     4.3    29.4    -      -       +      -
     92B  THR      3.6    10.8    -      -       -      +
     93B  GLU*     3.3    40.8    +      -       +      -
    115B  ALA*     3.4     2.1    -      -       -      -
    116B  THR*     2.6    49.7    +      -       -      +
    118B  GLY      5.8     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  PRO*     4.1     7.6    -      -       +      -
     54B  TRP*     3.2    43.7    -      +       +      -
     56B  PRO*     3.4     8.5    -      -       -      +
     57B  VAL*     2.8    31.3    +      -       -      -
     64B  VAL*     3.7    18.2    -      -       +      +
     65B  TYR*     1.3    75.8    -      -       -      +
     67B  SER*     1.3    56.2    +      -       -      +
     68B  VAL*     4.3     1.8    -      -       +      -
     89B  CYS*     4.0     2.8    -      -       +      +
     91B  LEU*     2.7    31.8    +      -       -      -
     92B  THR*     3.0    18.3    +      -       -      +
     93B  GLU      3.2    27.8    -      -       -      -
     94B  GLY      3.5    12.3    -      -       -      -
     95B  PRO*     3.9     5.2    -      -       +      -
    113B  VAL*     4.2     3.6    -      -       +      -
    114B  ARG      3.3     4.5    -      -       -      +
    115B  ALA*     3.5    33.7    -      -       +      -
    116B  THR*     5.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 67 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66B  TYR*     1.3    72.0    +      -       -      +
     68B  VAL*     1.3    62.5    +      -       -      +
     69B  GLU*     5.8     0.9    -      -       -      -
     89B  CYS      3.5     5.6    -      -       -      -
     90B  SER*     4.7     1.6    -      -       -      -
     91B  LEU*     3.1    38.0    +      -       -      +
    113B  VAL*     3.3     1.0    -      -       -      -
    114B  ARG*     2.7    55.4    +      -       -      -
    116B  THR*     4.8     1.1    -      -       -      +
    124B  TRP*     3.0    18.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 68 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  LEU*     3.3    24.0    -      -       +      -
     54B  TRP*     3.7    29.8    -      -       +      -
     66B  TYR*     5.2     1.1    -      -       +      -
     67B  SER*     1.3    75.1    -      -       -      +
     69B  GLU*     1.3    74.2    +      -       -      +
     85B  PRO*     4.2     0.9    -      -       -      +
     86B  SER*     2.9    30.3    +      -       -      +
     89B  CYS*     2.9    33.1    +      -       +      +
     90B  SER*     5.3     0.5    +      -       -      -
     97B  CYS*     4.0    10.8    -      -       +      -
     99B  VAL*     4.6     6.5    -      -       +      -
    111B  LEU*     4.9     3.6    -      -       +      -
    112B  ARG      3.2     8.5    -      -       -      +
    113B  VAL*     3.7     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 69 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  SER*     4.2     1.1    +      -       -      -
     68B  VAL*     1.3    82.0    -      -       -      +
     70B  TYR*     1.3    64.7    +      -       -      +
     83B  TRP*     3.6    18.3    -      -       +      +
     84B  ILE      3.6     8.5    -      -       -      +
     85B  PRO*     3.8    23.5    -      -       +      +
     86B  SER      4.1     1.6    -      -       -      +
    111B  LEU*     3.4     5.9    -      -       -      +
    112B  ARG*     2.7    72.7    +      -       +      +
    124B  TRP*     3.3    25.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 70 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  ARG*     3.3    24.0    +      -       +      +
    110A  SER*     4.3    14.3    -      -       -      -
     69B  GLU*     1.3    73.3    -      -       -      +
     71B  GLN*     1.3    67.8    +      -       -      +
     72B  GLY      4.8     0.4    -      -       -      -
     83B  TRP*     3.6     5.8    -      -       -      -
     84B  ILE*     2.8    88.5    +      -       +      +
     85B  PRO      4.0     5.2    -      -       -      -
     86B  SER*     4.1     8.1    -      -       -      -
     99B  VAL*     6.4     0.2    -      -       +      -
    102B  ASP*     3.5    44.6    +      -       +      -
    109B  TYR*     3.9    29.2    -      +       +      -
    110B  ASN      3.1     6.1    -      -       -      +
    111B  LEU*     3.2    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 71 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70B  TYR*     1.3    79.8    -      -       -      +
     72B  GLY*     1.3    60.5    +      -       -      +
     75B  GLU*     3.6    18.4    -      -       +      +
     76B  SER*     3.2    32.7    +      -       -      +
     80B  SER*     3.4    20.8    +      -       -      +
     82B  ILE      2.9    22.6    -      -       -      +
     83B  TRP*     3.7    25.7    -      -       +      -
     84B  ILE*     4.7     0.4    -      -       -      -
    109B  TYR*     3.5     4.0    -      -       -      -
    110B  ASN*     2.7    60.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 72 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  ASN*     3.5     8.9    -      -       -      +
     70B  TYR*     4.3     1.8    -      -       -      -
     71B  GLN*     1.3    76.1    -      -       -      +
     73B  GLU*     1.3    57.1    +      -       -      -
     74B  TYR      3.1     3.1    -      -       -      -
     75B  GLU*     2.8    38.6    +      -       -      -
     76B  SER*     2.9    11.0    +      -       -      -
    108B  PRO      4.1     2.0    -      -       -      -
    109B  TYR*     3.8    25.5    -      -       -      -
----------------------------------------------------------
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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