Contacts of the strand formed by residues 278 - 284 (chain D) in PDB entry 6KQH


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 PRO 278 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271D  VAL*     3.9    22.2    -      -       +      -
    272D  LEU      3.4     5.8    -      -       -      +
    273D  ARG*     4.0     6.0    -      -       +      -
    276D  ASP      4.4     2.5    -      -       -      +
    277D  GLU*     1.4    91.0    -      -       +      +
    279D  VAL*     1.3    61.7    +      -       -      +
    280D  ALA      4.7     2.2    -      -       -      +
    281D  THR*     4.8     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 279 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255D  GLU*     3.5    38.9    -      -       +      +
    256D  GLU      3.5    18.8    -      -       -      +
    272D  LEU*     2.4    39.8    +      -       +      +
    273D  ARG      4.2     0.4    -      -       -      +
    274D  ARG*     4.2    18.8    -      -       +      +
    277D  GLU      3.2     1.9    +      -       -      +
    278D  PRO*     1.3    74.7    -      -       -      +
    280D  ALA*     1.3    63.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 280 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255D  GLU*     4.1    10.5    -      -       +      -
    270D  LEU      4.6     0.4    -      -       -      -
    271D  VAL*     3.3     4.3    -      -       -      +
    272D  LEU*     2.7    29.0    +      -       +      +
    278D  PRO*     3.6     1.5    -      -       -      -
    279D  VAL*     1.3    93.5    -      -       +      +
    281D  THR*     1.3    64.5    +      -       -      +
    282D  TYR*     3.8    34.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 281 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219D  GLU*     5.7     5.6    -      -       +      +
    220D  ARG      3.4    23.6    -      -       -      +
    221D  ALA*     3.3    12.1    -      -       +      -
    222D  GLY*     2.9    22.7    +      -       -      -
    269D  PHE*     4.5     9.6    -      -       +      -
    270D  LEU      3.7     3.6    -      -       -      -
    271D  VAL*     3.6    23.1    -      -       +      +
    278D  PRO*     4.8     5.7    -      -       -      +
    280D  ALA*     1.3    76.2    +      -       -      +
    282D  TYR*     1.3    66.7    +      -       -      +
    332D  TYR*     5.0     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 282 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221D  ALA*     4.1     2.5    -      -       -      -
    222D  GLY      3.2    14.4    -      -       -      +
    251D  PHE*     3.3    33.9    -      +       +      -
    253D  ALA*     4.6     1.3    -      -       -      -
    254D  GLU*     2.8    43.5    +      -       +      +
    255D  GLU*     3.3     7.4    +      -       -      +
    269D  PHE*     3.6     8.3    -      -       -      -
    270D  LEU*     2.8    47.4    +      -       +      +
    272D  LEU*     3.8    22.9    -      -       +      -
    280D  ALA*     3.8    17.8    -      -       +      +
    281D  THR*     1.3    76.8    -      -       -      +
    283D  PHE*     1.3    60.4    +      -       -      +
    284D  LEU*     4.8     2.5    -      -       +      -
    304D  LEU*     3.5    28.5    -      -       +      -
    332D  TYR*     3.8    22.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with PHE 283 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221D  ALA*     3.7    19.7    -      -       +      -
    222D  GLY      3.2     8.2    +      -       -      +
    223D  LEU*     3.7    21.3    -      -       +      +
    242D  LEU*     5.0     1.1    -      -       +      -
    264D  LEU*     5.9     0.7    -      -       +      -
    268D  ALA      3.8     9.9    -      -       -      -
    269D  PHE*     3.7    20.4    -      +       +      -
    282D  TYR*     1.3    74.8    -      -       -      +
    284D  LEU*     1.3    67.7    +      -       -      +
    285D  PRO*     3.3    36.9    -      -       +      +
    313D  MET*     4.3    18.8    -      -       +      -
    314D  PRO*     3.8    26.9    -      -       +      -
    317D  VAL*     4.2    14.8    -      -       +      -
    335D  LEU*     4.1    20.0    -      -       +      -
    337D  LEU*     3.6    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 284 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251D  PHE*     4.5    13.0    -      -       +      -
    261D  LEU*     5.0     0.4    -      -       +      -
    267D  GLY*     3.2     3.1    -      -       -      -
    268D  ALA*     2.9    47.4    +      -       +      +
    270D  LEU*     3.9    29.2    -      -       +      -
    282D  TYR*     4.8     0.4    -      -       +      -
    283D  PHE*     1.3    82.5    -      -       -      +
    285D  PRO*     1.3    67.0    -      -       -      +
    288D  MET*     3.5    38.6    -      -       +      +
    290D  PRO*     3.7    35.4    -      -       +      -
    305D  ALA*     3.8    14.8    -      -       +      -
----------------------------------------------------------
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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