Contacts of the strand formed by residues 17 - 24 (chain B) in PDB entry 7KAC


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 TYR 17 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  PRO      3.1    12.8    +      -       -      +
     14B  ARG*     3.4    26.9    -      -       -      +
     15B  ASP      3.7     0.4    -      -       -      -
     16B  HIS*     1.3    85.1    -      -       +      +
     18B  ASP*     1.3    60.7    +      -       -      +
     19B  LEU*     4.0     3.7    +      -       +      +
     34B  ALA*     4.2    12.8    -      -       +      -
     35B  ARG      3.3     5.8    -      -       -      +
     36B  ASP*     3.4    44.6    +      -       +      -
     37B  LYS*     3.7     7.2    -      -       -      -
     43B  VAL*     3.6    31.3    -      -       +      +
     45B  LEU*     4.4    14.4    -      -       +      -
     78B  HIS*     4.3     8.7    -      -       -      +
     81B  TYR*     3.4    30.7    +      +       -      -
     90B  CYS*     3.4    26.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 18 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  TYR*     1.3    71.0    -      -       -      +
     19B  LEU*     1.3    64.9    +      -       -      +
     20B  LEU*     3.6    13.2    +      -       +      +
     34B  ALA*     3.3     3.5    -      -       -      -
     35B  ARG*     2.9    38.7    +      -       +      +
     37B  LYS*     3.3    39.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 19 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  PRO*     6.4     0.4    -      -       +      -
     14B  ARG*     4.5    21.9    -      -       +      +
     17B  TYR*     4.0     3.4    +      -       +      +
     18B  ASP*     1.3    71.2    -      -       -      +
     20B  LEU*     1.4    65.2    +      -       -      +
     32B  PHE*     3.9    34.1    -      -       +      -
     33B  LYS      3.8     2.0    -      -       -      +
     34B  ALA*     4.2     3.1    -      -       +      -
     45B  LEU*     3.7    28.9    -      -       +      -
     88B  TRP*     4.2    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 20 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  ASP*     3.8    23.8    -      -       +      +
     19B  LEU*     1.4    77.7    -      -       -      +
     21B  GLN*     1.3    63.9    +      -       +      +
     33B  LYS*     2.9    36.1    +      -       +      +
     34B  ALA*     4.3     1.1    -      -       -      -
     35B  ARG*     4.3    20.0    -      -       +      +
     42B  LEU*     3.8    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 21 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  LEU*     5.4     0.8    -      -       -      +
     20B  LEU*     1.3    80.6    -      -       +      +
     22B  ARG*     1.3    71.6    +      -       -      +
     23B  LEU*     4.6    11.8    -      -       +      +
     32B  PHE*     3.4     9.2    -      -       -      +
     33B  LYS*     2.9    57.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 22 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  GLN*     1.3    82.4    +      -       -      +
     23B  LEU*     1.3    64.5    +      -       -      +
     24B  GLY*     3.3    25.6    +      -       -      +
     25B  GLY*     3.6    24.7    -      -       -      +
     26B  GLY      4.5     1.4    -      -       -      +
     30B  GLU*     4.4    10.2    -      -       +      +
     31B  VAL      3.7     6.7    -      -       -      +
     32B  PHE*     3.8    25.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 23 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  GLN*     3.6    14.6    +      -       -      +
     22B  ARG*     1.3    75.9    -      -       -      +
     24B  GLY*     1.3    59.2    +      -       -      +
     31B  VAL*     2.9    19.0    +      -       +      +
     32B  PHE      3.8     6.7    -      -       -      +
     33B  LYS*     3.7    39.0    -      -       +      +
     44B  ALA*     4.8     1.3    -      -       +      -
     93B  PHE*     4.1     5.2    -      -       +      -
    401B  W9D      3.7    73.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  ARG*     3.3    25.3    +      -       -      -
     23B  LEU*     1.3    80.5    -      -       -      +
     25B  GLY*     1.3    57.9    +      -       -      -
     30B  GLU*     3.5     0.5    -      -       -      -
     31B  VAL      2.9    24.5    +      -       -      +
    401B  W9D      3.6    15.6    -      -       -      -
----------------------------------------------------------
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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