Contacts of the strand formed by residues 84 - 90 (chain B) in PDB entry 1CD0


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 ALA 84 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  GLN*     3.9    20.4    -      -       +      -
     38B  GLN      3.5    12.6    -      -       -      +
     39B  ARG*     3.9    18.6    -      -       +      +
     40B  PRO*     5.1     4.0    -      -       -      -
     82B  ASP      3.1     9.6    +      -       -      +
     83B  GLU*     1.3    80.2    -      -       -      +
     85B  ASP*     1.3    65.6    +      -       -      +
     86B  TYR*     3.5    10.3    -      -       +      -
    104B  LEU*     2.9    29.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  TYR      3.5     2.1    -      -       -      +
     37B  GLN*     3.7     1.2    -      -       -      -
     38B  GLN*     2.9    42.4    +      -       +      +
     40B  PRO*     3.7    12.6    -      -       -      +
     84B  ALA*     1.3    75.4    -      -       -      +
     86B  TYR*     1.3    60.9    +      -       -      +
     87B  TYR*     3.9    27.9    +      -       +      +
    101B  GLY      5.7     0.7    -      -       -      -
    102B  THR      3.5     7.2    -      -       -      +
    103B  ARG*     2.7    57.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  GLN*     3.3     7.1    +      -       -      -
     21B  ILE*     3.9    28.5    -      -       +      -
     35B  TRP*     4.6     6.1    -      -       +      -
     36B  TYR      3.2    13.2    -      -       -      -
     37B  GLN*     2.9    37.6    +      -       +      -
     47B  VAL*     4.9     1.8    -      -       +      -
     62B  PHE*     3.8     9.6    -      +       -      -
     73B  LEU*     3.4    24.5    -      -       +      -
     75B  ILE*     3.7    22.6    -      -       +      +
     82B  ASP*     2.6    31.7    +      -       -      -
     84B  ALA*     3.5    20.0    -      -       +      -
     85B  ASP*     1.3    73.4    -      -       -      +
     87B  TYR*     1.3    62.1    +      -       -      +
    101B  GLY*     3.1     1.9    -      -       -      -
    102B  THR      2.8    37.5    +      -       -      +
    104B  LEU*     3.8    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  GLN*     3.4    19.7    +      -       -      -
     41A  GLY      5.7     0.3    -      -       -      -
     42A  SER      3.5     9.5    +      -       -      -
     43A  ALA*     3.5    23.3    -      -       +      -
     44A  PRO*     3.6    13.7    -      -       +      -
      6B  GLN*     3.7     3.1    -      -       -      +
     34B  GLN      3.8     0.2    -      -       -      +
     35B  TRP*     3.5     4.2    -      -       -      -
     36B  TYR*     2.8    49.4    +      -       +      +
     38B  GLN*     3.6    25.1    +      -       +      -
     44B  PRO*     6.0     2.2    -      -       +      -
     85B  ASP*     3.9    33.9    +      -       +      +
     86B  TYR*     1.3    75.2    -      -       -      +
     88B  CYS*     1.3    66.7    +      -       -      +
     98B  PHE*     4.6    12.1    -      -       +      -
     99B  GLY      3.6    12.3    -      -       -      -
    100B  GLY      3.6     3.3    +      -       -      -
    101B  GLY*     3.3    25.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 88 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  LEU*     3.8    13.2    -      -       -      -
      6B  GLN*     3.5     8.9    +      -       -      -
     23B  CYS*     2.0    55.2    -      -       +      -
     33B  VAL*     4.4     3.8    -      -       +      -
     34B  GLN      3.1     9.6    -      -       -      +
     35B  TRP*     3.8    20.9    -      -       +      -
     87B  TYR*     1.3    74.0    -      -       -      +
     89B  GLN*     1.3    63.1    +      -       -      +
     98B  PHE*     3.5     2.9    -      -       -      +
     99B  GLY*     2.8    32.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  TYR*     5.3     1.5    +      -       -      -
      4B  LEU*     3.9     2.9    -      -       -      -
     33B  VAL*     3.2     5.0    -      -       -      -
     34B  GLN*     2.7    56.6    +      -       -      +
     36B  TYR*     2.8    45.2    +      -       +      -
     88B  CYS*     1.3    78.4    -      -       -      +
     90B  SER*     1.3    93.9    +      -       -      +
     91B  TYR*     3.7    12.2    +      -       -      -
     96B  VAL*     3.1    27.5    -      -       +      +
     97B  VAL      3.3    15.5    -      -       -      +
     98B  PHE*     4.0    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 90 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  PHE*     4.2    13.9    -      -       -      -
      4B  LEU*     3.8     9.7    -      -       -      +
     25B  ARG*     4.3     6.0    +      -       -      -
     28B  ILE*     5.1     1.7    +      -       -      -
     31B  ASN*     3.6    17.2    +      -       -      +
     32B  TYR      2.8    19.5    +      -       -      -
     33B  VAL*     4.2    11.5    -      -       -      +
     89B  GLN*     1.3    92.3    +      -       -      +
     91B  TYR*     1.3    67.8    +      -       -      +
     96B  VAL*     3.8     0.5    -      -       -      -
     97B  VAL*     3.1    30.8    +      -       -      +
----------------------------------------------------------
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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