Contacts of the strand formed by residues 78 - 87 (chain A) in PDB entry 1DGB


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 GLY 78 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  ALA      3.4     6.1    +      -       -      -
     77A  LYS*     1.3    80.3    -      -       -      +
     79A  ALA*     1.3    59.4    +      -       -      +
    112A  ARG*     3.6    14.0    -      -       -      +
    113A  PHE      2.9    14.1    -      -       -      -
    114A  SER*     3.9     1.3    -      -       -      -
    124A  ASP*     5.5     2.0    -      -       -      -
    209A  HIS*     5.2     2.0    -      -       -      -
    262A  ILE*     3.8    13.3    -      -       -      +
    325A  TYR*     2.7    30.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  GLY*     1.3    75.1    -      -       -      +
     80A  GLY*     1.3    59.3    +      -       -      +
    112A  ARG*     3.2     3.1    -      -       -      +
    113A  PHE*     2.7    33.3    +      -       -      +
    209A  HIS*     4.0    23.9    +      -       +      +
    262A  ILE*     3.9    31.2    -      -       +      -
    265A  LEU*     4.1    12.1    -      -       +      -
    325A  TYR*     4.6     3.4    -      -       -      -
    329A  VAL*     4.2     6.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  ALA*     1.3    77.4    -      -       -      +
     81A  ALA*     1.3    62.7    +      -       -      +
     82A  PHE*     5.0     0.7    -      -       -      -
    111A  VAL      3.2    11.9    -      -       -      -
    112A  ARG*     4.3     0.2    -      -       -      -
    113A  PHE*     5.4     0.2    -      -       -      -
    265A  LEU*     4.1     7.5    -      -       -      +
    321A  ASN*     4.8     1.6    -      -       -      +
    322A  PRO*     3.2    26.6    -      -       -      +
    325A  TYR*     4.9     1.4    -      -       -      -
    329A  VAL*     3.8    23.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  GLY*     1.3    75.7    -      -       -      +
     82A  PHE*     1.3    75.0    +      -       -      +
    111A  VAL*     3.0    31.0    +      -       +      +
    113A  PHE*     5.5     1.1    -      -       +      -
    265A  LEU*     4.1    12.8    -      -       +      +
    269A  ILE*     3.5    29.8    -      -       +      -
    318A  LEU*     4.3    18.2    -      -       +      -
    320A  ARG      3.5     5.6    -      -       -      +
    321A  ASN*     4.9     0.9    -      -       -      +
    322A  PRO*     4.7     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  GLY*     5.0     0.9    -      -       -      -
     81A  ALA*     1.3    84.1    -      -       -      +
     83A  GLY*     1.3    57.7    +      -       -      +
    109A  ILE      3.6     7.2    -      -       -      +
    110A  ALA*     3.9    27.6    -      -       +      -
    111A  VAL      6.0     0.4    -      -       -      -
    137A  TYR*     4.8     4.3    -      +       -      -
    318A  LEU*     3.5     7.4    -      -       -      +
    319A  ASN      2.9     6.1    +      -       -      -
    320A  ARG*     2.6    90.3    +      -       +      +
    321A  ASN      4.2     4.9    -      -       -      -
    322A  PRO*     3.9    20.9    -      -       +      -
    328A  GLU*     3.5    47.8    -      -       +      -
    329A  VAL*     5.3     1.1    -      -       +      -
    332A  ILE*     5.6     0.4    -      -       +      -
    375A  VAL*     4.0    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  PHE*     1.3    77.1    -      -       -      +
     84A  TYR*     1.3    65.4    +      -       -      +
    108A  PRO*     3.7     5.2    -      -       -      +
    109A  ILE*     3.0    26.5    +      -       -      +
    317A  VAL      3.1    12.6    -      -       -      -
    318A  LEU*     4.0     2.0    -      -       -      +
    319A  ASN*     3.5    17.0    -      -       -      -
    320A  ARG*     4.7     5.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  GLY*     1.3    75.1    -      -       -      +
     85A  PHE*     1.3    71.6    +      -       -      +
     86A  GLU*     3.7    28.0    +      -       +      -
    106A  LYS*     4.2    24.1    +      -       +      -
    107A  THR      3.3    17.0    -      -       -      +
    108A  PRO*     4.5     1.6    -      -       +      -
    109A  ILE*     3.5    11.5    -      -       -      +
    315A  LYS      3.7     0.3    -      -       -      +
    317A  VAL*     2.8    67.0    +      -       +      +
    319A  ASN*     3.7    27.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  TYR*     1.3    74.5    -      -       -      +
     86A  GLU*     1.3    63.0    +      -       -      +
     87A  VAL*     3.5    30.7    -      -       +      -
     99A  VAL*     3.7    30.3    -      -       +      -
    100A  PHE*     4.2    18.6    -      +       -      -
    105A  LYS      3.6     1.7    -      -       -      +
    106A  LYS*     3.0     5.7    -      -       -      +
    107A  THR*     2.7    39.5    +      -       -      +
    109A  ILE*     3.9     5.1    -      -       +      +
    136A  PHE*     3.8    23.1    -      +       +      -
    279A  PHE*     4.0    29.4    -      +       +      -
    313A  VAL*     4.3     6.5    -      -       +      -
    314A  GLY*     4.0    13.7    -      -       -      -
    315A  LYS      3.2    16.6    -      -       -      -
    316A  LEU*     3.7    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  TYR*     3.7    24.8    +      -       +      -
     85A  PHE*     1.3    78.4    -      -       -      +
     87A  VAL*     1.3    74.9    +      -       -      +
     88A  THR*     3.9     9.1    -      -       +      +
    104A  GLY*     4.4    11.0    -      -       -      +
    105A  LYS      3.4     4.7    -      -       -      +
    106A  LYS*     3.3    33.0    +      -       +      -
    314A  GLY*     3.0     2.9    -      -       -      -
    315A  LYS*     2.7    45.2    +      -       +      +
    317A  VAL*     5.8     0.2    -      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
     85A  PHE*     3.5    14.6    -      -       +      -
     86A  GLU*     1.3    77.3    -      -       -      +
     88A  THR*     1.3    63.8    +      -       -      +
     89A  HIS      3.2    23.1    -      -       -      +
     99A  VAL      3.3    27.1    -      -       -      +
    100A  PHE*     4.1    14.1    -      -       +      +
    102A  HIS      3.4    27.1    -      -       -      +
    103A  ILE*     3.7     9.1    -      -       +      +
    104A  GLY*     2.9    24.0    +      -       -      +
    105A  LYS*     3.0    13.7    +      -       +      +
    313A  VAL*     3.7     9.0    -      -       +      +
    314A  GLY*     4.1     1.3    -      -       -      -
----------------------------------------------------------
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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