Contacts of the strand formed by residues 33 - 38 (chain A) in PDB entry 1CD8


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 CYS 33 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  PHE*     3.7    13.5    -      -       -      -
     22A  CYS*     3.6    29.4    -      -       -      -
     24A  VAL*     4.0     3.6    -      -       -      -
     32A  GLY*     1.3    73.8    -      -       -      -
     34A  SER*     1.3    61.5    +      -       -      +
     35A  TRP*     5.2     2.0    -      -       +      -
     50A  LEU      3.7     0.7    -      -       -      +
     51A  TYR*     3.4     2.2    -      -       -      -
     52A  LEU*     2.7    41.2    +      -       +      +
     77A  PHE*     3.5    37.2    -      -       +      -
     94A  CYS*     3.6    11.0    -      -       -      -
     95A  SER      3.4    13.9    -      -       -      -
     96A  ALA*     4.6     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  GLY      4.8     0.5    +      -       -      -
     33A  CYS*     1.3    76.2    -      -       -      +
     35A  TRP*     1.3    63.0    +      -       -      +
     36A  LEU*     4.6     4.7    -      -       -      -
     48A  PHE*     3.6    20.6    -      -       -      -
     50A  LEU      3.0     8.5    -      -       -      -
     51A  TYR*     3.3    22.0    -      -       -      -
     94A  CYS*     3.2     9.0    -      -       -      +
     95A  SER*     2.9    44.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  VAL*     5.1     3.6    -      -       +      -
     20A  LEU*     3.9    27.1    -      -       +      -
     21A  LYS      4.2     2.5    -      -       -      -
     22A  CYS*     3.7    13.2    -      -       +      -
     33A  CYS*     5.2     0.9    -      -       +      -
     34A  SER*     1.3    77.3    -      -       -      +
     36A  LEU*     1.3    64.3    +      -       -      +
     48A  PHE*     4.4     0.5    -      -       -      -
     49A  LEU*     2.9    28.9    +      -       +      +
     50A  LEU*     2.9    15.8    +      -       +      +
     52A  LEU*     4.0    21.5    -      -       +      -
     77A  PHE*     3.7    29.4    +      -       +      +
     79A  LEU*     3.7    52.3    -      -       +      +
     92A  TYR*     4.0    13.5    -      -       +      -
     93A  PHE*     3.4    36.6    -      -       -      -
     94A  CYS*     3.2    28.2    -      -       -      -
    108A  VAL*     5.0     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  SER*     4.5     5.8    -      -       -      +
     35A  TRP*     1.3    79.7    -      -       -      +
     37A  PHE*     1.3    60.4    +      -       -      +
     46A  PRO*     4.7     8.1    -      -       +      -
     47A  THR      3.2    19.7    -      -       -      +
     48A  PHE*     3.6    28.3    -      -       +      -
     49A  LEU*     4.1     2.5    -      -       -      -
     92A  TYR*     3.3     7.8    -      -       -      +
     93A  PHE*     2.9    69.7    +      -       +      +
     95A  SER*     3.6    28.7    -      -       -      +
    104A  PHE*     3.9     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  LEU*     1.3    75.1    -      -       -      +
     38A  GLN*     1.3    61.4    +      -       -      +
     39A  PRO*     4.0    26.7    -      -       +      -
     46A  PRO*     3.6     0.5    -      -       -      +
     47A  THR*     2.9    48.8    +      -       +      -
     49A  LEU*     3.8    28.0    -      -       +      +
     87A  GLU      4.0    17.0    -      -       -      -
     88A  ASN*     3.5    20.9    -      -       -      -
     89A  GLU      3.4    21.5    -      -       -      -
     90A  GLY*     3.5    11.7    -      -       -      -
     91A  TYR      3.3     9.0    -      -       -      -
     92A  TYR*     3.4    23.6    -      +       +      +
     93A  PHE*     4.4     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  PHE*     1.3    76.4    -      -       -      +
     39A  PRO*     1.3    65.5    -      -       +      +
     40A  ARG      3.2     1.3    +      -       -      -
     41A  GLY*     3.4    31.6    +      -       -      +
     44A  ALA      2.9    24.4    +      -       -      +
     45A  SER*     3.8     1.0    -      -       -      +
     46A  PRO*     3.4    32.9    -      -       -      +
     91A  TYR*     2.8    40.1    +      -       +      +
     93A  PHE*     4.0    12.2    -      -       +      -
    107A  PHE*     3.6    22.9    -      -       +      -
----------------------------------------------------------
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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