Contacts of the strand formed by residues 18 - 24 (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 VAL 18 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  TRP*     3.6    26.7    -      -       +      +
     16A  GLU      3.9     4.0    -      -       -      +
     17A  THR*     1.3    71.0    -      -       -      +
     19A  GLU*     1.3    59.1    +      -       -      +
     20A  LEU*     3.8    28.9    -      -       +      -
     79A  LEU      3.8     0.5    -      -       -      +
     80A  THR*     3.4     4.0    -      -       -      +
     81A  LEU*     2.7    56.0    +      -       +      +
     84A  PHE*     3.7    34.5    -      -       +      -
     92A  TYR*     5.9     0.7    -      -       +      -
    110A  VAL*     3.9    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  PRO*     3.4    20.6    -      -       -      +
     12A  TRP*     4.6     3.5    -      -       -      +
     17A  THR*     3.7     8.9    +      -       +      +
     18A  VAL*     1.3    72.9    -      -       -      +
     20A  LEU*     1.3    62.8    +      -       -      +
     21A  LYS*     3.0    34.5    +      -       -      +
     71A  LYS*     5.2     7.2    -      -       -      -
     78A  VAL*     3.6    26.8    -      -       +      +
     79A  LEU      3.4     3.1    -      -       -      -
     80A  THR*     3.7    13.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  SER      3.6     2.9    -      -       -      +
      7A  PRO*     3.6    20.9    -      -       +      -
     12A  TRP*     4.0     7.9    -      -       +      -
     18A  VAL*     3.8    21.3    -      -       +      -
     19A  GLU*     1.3    78.6    -      -       -      +
     21A  LYS*     1.3    62.4    +      -       -      +
     35A  TRP*     3.9    16.3    -      -       +      -
     77A  PHE      3.8     0.7    -      -       -      +
     78A  VAL*     3.3     6.1    -      -       -      +
     79A  LEU*     2.9    48.8    +      -       +      +
     92A  TYR*     3.7    37.2    -      -       +      -
    108A  VAL*     3.7    20.9    -      -       +      -
    110A  VAL*     3.9     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  ARG      4.5     0.4    -      -       -      -
      5A  VAL*     3.3     4.5    -      -       -      +
      6A  SER*     2.8    50.4    +      -       -      +
      7A  PRO*     5.9     0.7    -      -       +      -
     19A  GLU*     3.0    35.7    +      -       -      +
     20A  LEU*     1.3    78.6    -      -       -      +
     22A  CYS*     1.3    60.2    +      -       -      +
     35A  TRP*     4.0     3.5    -      -       -      -
     73A  LEU*     5.9     4.2    -      -       +      +
     76A  THR*     3.8    23.8    -      -       +      -
     77A  PHE      3.5     4.3    -      -       -      -
     78A  VAL*     4.2    13.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  PHE*     4.1     9.2    -      -       +      -
      4A  ARG      3.2     5.8    -      -       -      +
      5A  VAL*     3.7    18.2    -      -       +      -
     21A  LYS*     1.3    74.0    -      -       -      +
     23A  GLN*     1.3    59.4    +      -       -      +
     24A  VAL*     4.8     0.2    -      -       -      -
     33A  CYS*     3.6    16.2    -      -       -      -
     35A  TRP*     3.7     3.5    -      -       +      -
     75A  ASP      3.8     1.2    -      -       -      +
     76A  THR*     3.3     2.2    -      -       -      -
     77A  PHE*     2.9    36.5    +      -       -      -
     94A  CYS*     2.0    50.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  PHE*     3.1     8.5    -      -       -      +
      4A  ARG*     2.8    51.4    +      -       +      +
     21A  LYS      4.2     0.4    -      -       -      -
     22A  CYS*     1.3    73.3    -      -       -      +
     24A  VAL*     1.3    60.6    +      -       -      +
     25A  LEU*     3.6    24.2    +      -       +      +
     75A  ASP*     3.3    34.4    +      -       -      +
     76A  THR*     3.5    14.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  GLN      3.6     6.5    -      -       -      +
      3A  PHE*     3.6    27.1    -      -       +      -
     22A  CYS      4.5     1.1    -      -       -      +
     23A  GLN*     1.3    72.5    -      -       -      +
     25A  LEU*     1.3    60.9    +      -       -      +
     26A  LEU*     3.3    35.5    +      -       +      +
     29A  PRO*     4.8    10.5    -      -       +      -
     33A  CYS*     4.0     4.9    -      -       -      -
     75A  ASP*     2.9    34.2    +      -       +      +
     77A  PHE*     3.4    34.1    -      -       +      -
     96A  ALA*     4.7     4.7    -      -       +      -
----------------------------------------------------------
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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