Contacts of the strand formed by residues 297 - 305 (chain D) in PDB entry 6C3P


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 THR 297 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211C  ILE*     3.7    34.2    -      -       +      +
    290C  VAL*     4.2    27.2    -      -       +      +
    292C  GLU      4.6     8.3    -      -       -      +
    295C  GLY*     4.4     7.3    +      -       -      -
    174D  ALA*     4.4     9.2    -      -       -      +
    288D  GLU*     5.0     1.6    -      -       +      -
    289D  GLY*     3.1    24.5    -      -       -      +
    290D  VAL*     3.5    19.0    -      -       +      +
    291D  VAL*     5.2     0.2    -      -       -      -
    295D  GLY      4.7     1.0    +      -       -      -
    296D  ILE*     1.3    78.4    -      -       -      +
    298D  THR*     1.3    63.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 298 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211C  ILE*     4.9     2.7    -      -       -      -
    174D  ALA*     4.3    13.8    -      -       -      +
    175D  HIS*     4.0     9.7    +      -       -      +
    177D  ARG*     5.0     3.1    -      -       +      -
    178D  ALA*     3.3    30.0    -      -       +      +
    181D  LEU*     4.9    12.3    -      -       +      -
    210D  ILE*     4.1    12.6    -      -       +      -
    287D  LEU      3.9     0.3    -      -       -      +
    288D  GLU*     3.5     3.5    -      -       -      -
    289D  GLY      3.0    29.7    +      -       -      +
    291D  VAL*     4.0    20.2    -      -       +      -
    296D  ILE      4.2     0.2    +      -       -      -
    297D  THR*     1.3    79.7    -      -       -      +
    299D  GLN*     1.3    68.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 299 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209C  MET*     4.1     6.8    -      -       -      +
    210C  ILE      4.0     9.0    -      -       -      +
    211C  ILE*     3.5    27.0    -      -       +      +
    250C  PHE*     3.3    19.8    -      -       -      -
    175D  HIS*     5.8     0.5    -      -       -      +
    178D  ALA*     3.8    11.6    -      -       -      +
    286D  ILE*     3.3    22.6    -      -       +      +
    287D  LEU      3.2    12.1    -      -       -      +
    288D  GLU*     3.2    20.6    +      -       +      +
    298D  THR*     1.3    82.5    +      -       -      +
    300D  ALA*     1.3    61.8    +      -       -      +
    301D  ARG*     2.5    53.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 300 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178D  ALA*     3.8    23.1    -      -       +      +
    181D  LEU*     4.2    21.5    -      -       +      +
    183D  PHE*     4.1    23.2    -      -       +      -
    285D  VAL      4.0     0.2    -      -       -      +
    286D  ILE*     3.9     0.5    -      -       -      -
    287D  LEU*     3.0    33.0    +      -       +      +
    299D  GLN*     1.3    74.0    -      -       -      +
    301D  ARG*     1.3    69.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 301 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209C  MET*     4.9    11.3    -      -       -      +
    250C  PHE*     3.9    22.2    -      -       +      -
    292C  GLU*     4.1    20.0    +      -       -      +
     36D  VAL*     3.9    12.3    -      -       +      -
     38D  LYS      4.8     0.3    -      -       -      +
     39D  LYS*     3.9     3.6    -      -       -      -
     40D  GLY*     3.3    50.7    +      -       -      -
     42D  CYS*     4.8    10.5    -      -       -      -
    183D  PHE*     4.8     4.7    -      -       -      -
    284D  ILE*     5.3     1.8    -      -       +      -
    285D  VAL      3.6     3.4    -      -       -      +
    286D  ILE*     4.3     7.4    -      -       +      -
    299D  GLN*     2.5    71.9    +      -       -      +
    300D  ALA*     1.3    77.0    -      -       -      +
    302D  THR*     1.3    64.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 302 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36D  VAL*     5.0     2.2    -      -       -      -
     37D  SER      4.4     6.3    -      -       -      -
     38D  LYS*     4.0    19.2    +      -       -      -
    183D  PHE*     3.5    47.2    +      -       +      +
    284D  ILE*     4.0     1.9    -      -       -      +
    285D  VAL*     2.8    49.3    +      -       +      +
    301D  ARG*     1.3    76.5    -      -       -      +
    303D  SER*     1.3    70.6    +      -       -      +
    304D  TYR*     4.2    14.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 303 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34D  ARG*     2.3    40.6    +      -       -      -
     36D  VAL*     2.4    26.6    +      -       -      -
     37D  SER      4.0     3.5    +      -       -      -
     38D  LYS*     3.2    14.4    -      -       -      +
    282D  GLU*     3.1    22.4    +      -       -      -
    283D  ILE      3.8     5.2    -      -       -      -
    284D  ILE*     3.8    13.5    -      -       -      -
    302D  THR*     1.3    78.2    +      -       -      +
    304D  TYR*     1.3    68.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 304 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  LYS*     4.0     5.8    -      -       -      -
    183D  PHE*     3.7    10.2    -      -       -      +
    184D  SER*     2.1    43.8    +      -       -      -
    185D  LYS      3.5    18.2    -      -       -      -
    186D  HIS      3.7     9.6    -      -       -      -
    187D  ALA*     4.2    14.4    -      -       +      -
    198D  PHE*     5.1     6.3    -      +       +      -
    200D  LEU*     3.5    31.8    -      -       +      +
    282D  GLU*     3.2     4.1    -      -       -      -
    283D  ILE*     2.9    33.3    +      -       +      +
    285D  VAL*     4.3    11.0    -      -       +      -
    302D  THR*     4.2    18.1    +      -       +      -
    303D  SER*     1.3    75.6    -      -       -      +
    305D  LEU*     1.3    62.0    +      -       -      +
    308D  GLU*     3.2    26.5    -      -       +      +
    309D  ILE*     4.1    22.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 305 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32D  ARG*     3.9    12.8    -      -       +      +
     33D  ALA      5.7     1.8    -      -       -      +
     34D  ARG*     3.1    46.7    -      -       +      +
    277D  HIS*     3.4    44.0    -      -       +      +
    281D  LEU      3.3    19.1    -      -       -      +
    282D  GLU*     4.0     8.5    -      -       +      +
    304D  TYR*     1.3    77.2    -      -       -      +
    306D  ALA*     1.3    75.3    +      -       -      +
    307D  ASP*     3.1    30.1    +      -       -      +
    308D  GLU*     3.4    10.7    +      -       -      -
    309D  ILE*     3.3    15.2    +      -       -      +
----------------------------------------------------------
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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