Contacts of the strand formed by residues 80 - 87 (chain D) in PDB entry 5CYP


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 ARG 80 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19D  LYS*     4.8     4.5    -      -       +      +
     20D  GLN      2.9    18.9    +      -       -      +
     21D  GLY*     3.3    28.9    +      -       -      +
     22D  PHE*     2.8    25.8    +      -       -      +
     23D  GLU*     6.3     1.0    -      -       -      +
     73D  ASP*     3.4    41.3    +      -       +      -
     74D  ILE      3.7     7.4    -      -       -      +
     75D  GLU*     4.7     5.2    -      -       +      +
     79D  VAL*     1.3    74.4    -      -       -      +
     81D  MET*     1.3    66.0    +      -       -      +
     82D  LYS*     4.1    14.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 81 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22D  PHE*     3.2    11.0    -      -       +      +
     24D  PHE*     5.8     5.2    -      -       +      -
     73D  ASP*     3.5     3.6    -      -       -      -
     74D  ILE*     2.8    42.3    +      -       +      +
     79D  VAL      3.7     2.4    +      -       -      +
     80D  ARG*     1.3    80.2    -      -       -      +
     82D  LYS*     1.3    60.9    +      -       -      +
     83D  LEU*     3.4     8.8    +      -       +      +
    266D  ILE*     5.7    10.1    -      -       +      -
    270D  MET*     6.4     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 82 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22D  PHE      2.9    14.4    +      -       -      +
     23D  GLU*     4.0    19.4    -      -       +      +
     24D  PHE*     3.4    16.9    +      -       -      +
     25D  ASN*     4.8     0.5    -      -       -      +
     71D  THR*     4.9     7.6    -      -       +      -
     72D  HIS      3.9     0.4    -      -       -      -
     73D  ASP*     3.9    18.2    -      -       -      +
     80D  ARG*     4.1    13.2    -      -       -      +
     81D  MET*     1.3    70.0    -      -       -      +
     83D  LEU*     1.3    63.9    +      -       -      +
     84D  THR*     3.3     8.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 83 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24D  PHE*     3.6    24.2    -      -       +      +
     26D  ILE*     3.9    26.9    -      -       +      -
     43D  LEU*     4.5    18.6    -      -       +      -
     44D  PHE*     3.7    28.4    -      -       +      -
     70D  ILE      3.7     1.0    -      -       -      +
     71D  THR*     3.4     1.7    -      -       -      -
     72D  HIS      2.9    41.9    +      -       -      +
     74D  ILE*     4.7    13.5    -      -       +      -
     81D  MET*     3.4     7.1    +      -       +      +
     82D  LYS*     1.3    73.2    -      -       -      +
     84D  THR*     1.3    64.5    +      -       -      +
     85D  VAL*     4.4     2.9    -      -       +      -
    262D  ARG*     4.8     8.7    -      -       -      +
    266D  ILE*     4.0    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 84 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24D  PHE      2.9     7.5    +      -       -      +
     25D  ASN*     3.3    23.1    +      -       -      +
     26D  ILE*     2.8    27.5    +      -       -      +
     69D  SER*     4.2    18.8    -      -       -      +
     70D  ILE      3.2     7.6    -      -       -      +
     71D  THR*     3.0    30.0    +      -       -      +
     82D  LYS*     3.3     4.9    +      -       -      +
     83D  LEU*     1.3    74.1    -      -       -      +
     85D  VAL*     1.3    64.8    +      -       -      +
     86D  ILE*     4.1    12.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 85 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26D  ILE*     3.2    13.7    -      -       +      +
     28D  VAL*     4.6    10.1    -      -       +      -
     40D  ILE*     3.6    43.5    -      -       +      -
     43D  LEU*     4.1    25.4    -      -       +      -
     44D  PHE*     3.6    26.0    -      -       +      -
     68D  LYS      3.7     2.1    -      -       -      +
     70D  ILE*     2.8    39.3    +      -       -      +
     83D  LEU*     4.4     7.6    -      -       +      -
     84D  THR*     1.3    76.9    -      -       -      +
     86D  ILE*     1.3    65.3    +      -       -      +
     87D  ASP      3.7     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 86 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25D  ASN*     4.4    18.8    -      -       +      -
     26D  ILE      2.9    18.1    +      -       -      +
     27D  MET*     3.6    23.2    -      -       +      +
     28D  VAL*     3.2    25.2    +      -       -      +
     67D  ILE*     3.6    30.3    -      -       +      -
     68D  LYS      3.5     6.1    -      -       -      +
     69D  SER*     3.7    16.8    -      -       -      +
     84D  THR*     4.3     9.6    -      -       +      -
     85D  VAL*     1.3    72.9    -      -       -      +
     87D  ASP*     1.3    62.0    +      -       -      +
     88D  THR      3.8     0.5    +      -       -      -
    107D  PHE*     3.8    15.0    -      -       +      -
    131D  THR      5.2     2.5    -      -       -      +
    133D  VAL*     3.7    29.8    -      -       +      -
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Residues in contact with ASP 87 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28D  VAL*     3.3    17.1    -      -       -      +
     36D  LYS*     4.3     1.7    -      -       -      +
     37D  SER*     2.9    25.2    +      -       -      -
     40D  ILE*     3.5    20.9    -      -       +      +
     64D  THR*     3.3    14.6    +      -       +      +
     66D  GLU      4.1     0.3    -      -       -      +
     67D  ILE*     3.3     7.3    -      -       -      +
     68D  LYS*     2.8    42.7    +      -       +      +
     70D  ILE*     5.2     6.2    -      -       +      +
     85D  VAL      3.7     2.2    +      -       -      -
     86D  ILE*     1.3    73.4    -      -       -      +
     88D  THR*     1.3    70.6    +      -       -      +
    302D   MG      3.1    14.9    -      -       -      -
----------------------------------------------------------
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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