Contacts of the strand formed by residues 20 - 27 (chain D) in PDB entry 3C5C


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 GLU 20 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141C  TYR*     5.4    10.5    -      -       -      +
     19D  LEU*     1.3    83.8    +      -       -      +
     21D  VAL*     1.3    64.5    +      -       -      +
     22D  ASN*     3.3    18.9    +      -       -      +
     69D  HIS*     3.2    20.6    -      -       +      +
     71D  ARG*     2.9    36.9    +      -       +      +
     90D  TRP*     5.5     1.2    +      -       -      -
     92D  HIS*     3.7    14.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 21 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19D  LEU*     4.0     6.5    -      -       -      +
     20D  GLU*     1.3    76.6    -      -       -      +
     22D  ASN*     1.3    63.4    +      -       -      +
     23D  LEU*     3.8    26.0    -      -       +      -
     68D  VAL*     3.5    28.5    -      -       +      -
     69D  HIS      3.0     7.1    +      -       -      +
     70D  LEU*     3.5     6.4    -      -       +      +
     71D  ARG*     2.9    28.2    +      -       -      -
     92D  HIS*     3.7     7.0    -      -       +      +
    180D  VAL*     4.2    20.6    -      -       +      -
    183D  ALA*     3.9    23.6    -      -       +      -
    184D  ARG*     6.4     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 22 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138C  MET*     5.2     4.0    -      -       -      +
     20D  GLU*     3.3    26.7    +      -       -      +
     21D  VAL*     1.3    73.9    -      -       -      +
     23D  LEU*     1.3    63.1    +      -       -      +
     71D  ARG*     3.5     6.0    -      -       -      +
     90D  TRP*     3.0    65.4    +      -       +      +
     91D  ALA*     3.5     1.6    -      -       -      -
     92D  HIS*     2.7    53.3    +      -       -      +
     93D  ALA      3.3     6.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 23 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21D  VAL*     3.8    19.7    -      -       +      -
     22D  ASN*     1.3    73.7    -      -       -      +
     24D  ALA*     1.3    59.7    +      -       -      +
     25D  ILE*     4.3    10.8    -      -       +      -
     70D  LEU*     3.7    25.4    -      -       +      -
     71D  ARG      2.7    13.0    +      -       -      +
     72D  VAL*     3.3     5.8    -      -       +      +
     73D  MET      2.8    26.2    +      -       -      -
     90D  TRP*     3.4     3.5    -      -       -      -
     93D  ALA*     3.4    32.3    -      -       +      +
     95D  LEU*     5.1     3.4    -      -       +      -
    176D  PHE*     3.8    34.3    -      -       +      +
    179D  ALA*     3.7    26.2    -      -       +      -
    180D  VAL*     4.5     0.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 24 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23D  LEU*     1.3    72.3    -      -       -      +
     25D  ILE*     1.3    63.7    +      -       -      +
     26D  LEU*     4.0     5.8    +      -       +      -
     73D  MET*     3.6     9.2    -      -       +      +
     87D  TYR*     3.9    17.3    -      -       +      -
     90D  TRP*     4.2     5.8    -      -       +      -
     91D  ALA*     3.8    12.0    -      -       +      +
     93D  ALA      3.1     7.9    +      -       -      -
     94D  PHE*     3.4    28.6    -      -       +      +
     95D  LEU      3.0    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 25 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23D  LEU*     4.3     4.7    -      -       +      -
     24D  ALA*     1.3    84.2    -      -       -      +
     26D  LEU*     1.3    56.1    +      -       -      +
     33D  LYS*     3.7    23.3    -      -       +      +
     36D  LEU*     6.0     1.6    -      -       +      -
     37D  THR*     4.0    10.8    -      -       -      +
     72D  VAL*     3.5    33.2    -      -       +      -
     73D  MET      2.8    13.8    +      -       -      +
     74D  ASP*     4.5     5.2    -      -       -      -
     75D  THR*     2.7    34.7    +      -       -      +
     95D  LEU*     3.4    36.1    -      -       +      +
     97D  VAL*     3.6    28.5    -      -       +      -
    176D  PHE*     4.2     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 26 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24D  ALA*     4.4     5.2    -      -       +      +
     25D  ILE*     1.3    80.2    -      -       -      +
     27D  GLY*     1.3    60.2    +      -       -      +
     33D  LYS*     3.3    14.6    -      -       -      +
     75D  THR*     3.7    14.1    -      -       +      +
     87D  TYR*     3.7    50.0    -      -       +      +
     94D  PHE*     3.9    24.9    -      -       +      -
     95D  LEU      2.8    12.6    +      -       -      +
     96D  VAL*     4.3    10.5    -      -       +      -
     97D  VAL*     2.9    24.3    +      -       -      +
    112D  TYR*     4.0    21.3    -      -       +      -
    115D  LEU*     5.7     0.2    -      -       +      -
    116D  LEU*     4.0    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 27 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26D  LEU*     1.3    79.2    -      -       -      +
     28D  ARG*     1.3    69.0    +      -       -      -
     29D  ARG      3.5     0.9    +      -       -      -
     33D  LYS*     3.1    16.3    +      -       -      -
     75D  THR*     4.8     0.9    +      -       -      -
     77D  ASP*     4.9     4.3    -      -       -      +
     96D  VAL*     5.0     2.0    -      -       -      -
     97D  VAL      3.5    13.9    -      -       -      -
    109D  SER*     5.6     1.1    -      -       -      -
    112D  TYR*     3.5    34.3    +      -       -      -
----------------------------------------------------------
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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