Contacts of the strand formed by residues 18 - 23 (chain A) in PDB entry 3KDM


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 ILE 18 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  VAL*     4.0    14.1    -      -       +      -
     11A  SER      3.5    26.5    -      -       -      +
     12A  GLY*     3.6    14.8    -      -       -      -
     16A  GLN*     5.0     2.0    -      -       +      +
     17A  SER*     1.3    78.2    -      -       -      +
     19A  THR*     1.3    65.9    +      -       -      +
     20A  ILE*     5.2     0.7    -      -       +      -
     75A  LEU      4.0     0.3    -      -       -      +
     76A  THR*     3.5     5.4    -      -       -      +
     77A  ILE*     2.9    51.8    +      -       +      +
     80A  LEU*     3.9    25.4    -      -       +      -
    108A  VAL*     3.9    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  PRO*     5.4     0.2    -      -       -      +
     10A  VAL*     3.8    17.8    -      -       -      +
     18A  ILE*     1.3    78.5    +      -       -      +
     20A  ILE*     1.3    71.7    +      -       -      +
     21A  SER*     4.2     2.4    +      -       -      +
     74A  SER*     3.8    29.6    -      -       -      +
     75A  LEU      3.6     5.2    -      -       -      +
     76A  THR*     3.8    15.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  GLN*     3.8    11.4    -      -       -      +
      7A  PRO*     4.1     4.7    -      -       +      -
     10A  VAL*     3.8    14.4    -      -       +      -
     18A  ILE*     5.2     1.3    -      -       +      -
     19A  THR*     1.3    82.8    -      -       -      +
     21A  SER*     1.3    64.2    +      -       -      +
     37A  TRP*     3.5    11.3    -      -       +      -
     74A  SER*     3.2     4.7    -      -       -      -
     75A  LEU*     2.9    44.6    +      -       +      +
     77A  ILE*     4.4     7.2    -      -       +      -
     88A  TYR*     3.8    29.2    -      -       +      -
    106A  THR*     3.1    34.3    -      -       +      +
    108A  VAL*     3.9    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  THR      4.2     3.6    +      -       -      -
      6A  GLN*     3.4    13.0    -      -       -      +
      7A  PRO*     3.4    32.0    -      -       -      +
     19A  THR*     4.2     2.6    +      -       -      +
     20A  ILE*     1.3    77.2    -      -       -      +
     22A  CYS*     1.3    63.0    +      -       -      +
     23A  THR*     4.9     3.6    +      -       -      -
     37A  TRP*     4.2     0.2    -      -       -      -
     72A  THR*     4.0    16.6    -      -       -      -
     73A  ALA      3.5     4.7    -      -       -      -
     74A  SER*     4.3     5.2    -      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
      4A  LEU*     3.9    17.3    -      -       -      -
      5A  THR      3.5     4.7    -      -       -      -
     21A  SER*     1.3    78.3    -      -       -      +
     23A  THR*     1.3    60.7    +      -       -      +
     24A  GLY      3.8     1.6    +      -       -      -
     29A  VAL*     4.1     9.7    -      -       -      +
     35A  VAL*     5.1     2.0    -      -       -      -
     37A  TRP*     3.5    13.2    -      -       +      -
     71A  ASN      3.8     0.3    -      -       -      +
     72A  THR*     3.3     1.1    -      -       -      +
     73A  ALA*     2.8    39.5    +      -       +      +
     90A  CYS*     2.1    54.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  ALA      4.3     0.9    -      -       -      +
      4A  LEU*     3.4     6.1    -      -       -      -
      5A  THR*     2.9    47.8    +      -       -      -
     21A  SER*     4.9     3.1    +      -       -      -
     22A  CYS*     1.3    72.9    +      -       -      +
     24A  GLY*     1.3    66.7    +      -       -      +
     71A  ASN*     3.6    20.9    -      -       -      +
     72A  THR*     2.7    24.0    +      -       -      +
----------------------------------------------------------
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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