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


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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289B  GLY*     3.4    17.9    -      -       -      +
    290B  VAL*     4.2     9.0    -      -       -      +
    295B  GLY      3.8     4.0    +      -       -      -
    296B  ILE*     1.3    79.8    -      -       -      +
    298B  THR*     1.3    66.0    -      -       -      +
    211C  ILE*     3.2    41.3    -      -       +      +
    212C  SER*     4.6     5.6    -      -       -      +
    290C  VAL*     3.9    24.8    -      -       +      +
    291C  VAL      5.3     1.4    -      -       -      +
    292C  GLU*     4.5     7.4    -      -       -      +
    295C  GLY*     5.0     6.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 298 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174B  ALA*     3.2    49.7    +      -       +      +
    175B  HIS*     4.2     2.9    -      -       -      +
    177B  ARG*     5.2     1.2    -      -       -      +
    178B  ALA*     4.7    13.7    +      -       -      +
    181B  LEU*     5.3     3.3    -      -       -      +
    210B  ILE*     5.2     9.5    -      -       -      +
    287B  LEU      3.8     0.6    -      -       -      +
    288B  GLU*     3.4    23.4    -      -       -      +
    289B  GLY      2.8    17.1    +      -       -      -
    291B  VAL*     4.3     9.9    -      -       +      +
    296B  ILE*     3.8     5.2    -      -       +      +
    297B  THR*     1.3    78.2    -      -       -      +
    299B  GLN*     1.3    66.2    +      -       -      +
    211C  ILE*     3.4     9.5    -      -       -      +
    292C  GLU      6.0     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 299 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178B  ALA*     3.1    21.6    -      -       -      +
    181B  LEU*     5.2     0.7    -      -       -      -
    286B  ILE*     3.3    21.5    -      -       +      +
    287B  LEU      3.4     3.6    -      -       -      -
    288B  GLU*     2.8    29.8    +      -       +      -
    298B  THR*     1.3    75.1    -      -       -      +
    300B  ALA*     1.3    59.8    +      -       -      +
    301B  ARG*     3.1    45.1    +      -       +      +
    209C  MET*     4.3     8.9    -      -       -      +
    210C  ILE      5.0     1.8    +      -       -      -
    211C  ILE*     3.5    41.1    -      -       +      +
    212C  SER      4.5     0.2    -      -       -      +
    250C  PHE*     4.1    15.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 300 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178B  ALA*     4.5     6.1    -      -       -      +
    181B  LEU*     3.2    35.2    -      -       +      -
    183B  PHE*     3.5    26.2    -      -       +      -
    285B  VAL      3.5     5.0    -      -       -      +
    286B  ILE*     3.7     1.6    -      -       -      -
    287B  LEU*     2.9    35.0    +      -       +      -
    299B  GLN*     1.3    72.6    -      -       -      +
    301B  ARG*     1.3    61.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 301 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  VAL*     5.7     5.2    -      -       +      -
     38B  LYS      4.0     0.7    -      -       -      +
     39B  LYS*     3.4     4.7    -      -       -      -
     40B  GLY*     2.9    33.4    +      -       -      -
     41B  ASN*     4.4    18.4    -      -       -      +
     42B  CYS*     5.2     8.1    -      -       -      +
    183B  PHE*     4.7     2.4    -      -       -      -
    284B  ILE*     6.2     0.4    -      -       +      -
    285B  VAL      3.8     2.9    -      -       -      -
    286B  ILE*     3.7    19.1    -      -       +      -
    299B  GLN*     3.1    45.6    +      -       +      +
    300B  ALA*     1.3    75.9    -      -       -      +
    302B  THR*     1.3    62.9    +      -       -      +
    209C  MET*     4.4    16.7    -      -       -      +
    211C  ILE*     5.7     0.4    -      -       -      +
    250C  PHE*     3.8    28.9    -      -       +      -
    292C  GLU*     4.6    11.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 302 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  VAL*     4.0     6.0    -      -       -      +
     37B  SER      4.1     4.7    -      -       -      -
     38B  LYS*     3.0    22.9    +      -       -      +
    183B  PHE*     3.4    47.5    +      -       +      +
    184B  SER      5.3     0.3    +      -       -      -
    284B  ILE*     3.8     4.3    -      -       -      +
    285B  VAL*     3.1    40.5    +      -       +      +
    286B  ILE*     5.3     0.2    -      -       -      +
    301B  ARG*     1.3    76.6    -      -       -      +
    303B  SER*     1.3    74.0    +      -       -      +
    304B  TYR*     3.7    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 303 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  ARG*     4.8     0.7    -      -       -      -
     36B  VAL*     2.6    30.5    +      -       -      -
     37B  SER      3.2     9.5    +      -       -      -
     38B  LYS*     3.2    23.2    +      -       -      +
    282B  GLU*     3.0    26.3    +      -       -      -
    283B  ILE      3.1    11.2    -      -       -      -
    302B  THR*     1.3    82.4    +      -       -      +
    304B  TYR*     1.3    70.0    +      -       -      +
    305B  LEU*     4.2     8.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 304 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  LYS*     4.5     0.4    -      -       -      -
    183B  PHE*     3.6     7.3    -      -       -      +
    184B  SER*     2.4    37.3    +      -       -      -
    185B  LYS      3.1    21.5    -      -       -      -
    186B  HIS*     3.6     2.2    -      -       -      -
    187B  ALA*     3.5    28.3    -      -       +      -
    198B  PHE*     5.2     0.2    -      +       -      -
    200B  LEU*     3.3    39.2    -      -       +      +
    281B  LEU      4.7     0.2    -      -       -      -
    282B  GLU*     3.6     2.2    -      -       -      -
    283B  ILE*     3.0    45.8    +      -       +      +
    285B  VAL*     3.8    11.9    -      -       +      -
    302B  THR*     3.7    19.7    -      -       +      -
    303B  SER*     1.3    78.8    -      -       -      +
    305B  LEU*     1.3    67.1    +      -       -      +
    308B  GLU*     4.4     4.9    -      -       +      -
    309B  ILE*     3.6    19.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 305 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  ARG      5.5     2.9    -      -       -      +
     33B  ALA      5.1     2.7    -      -       -      +
     34B  ARG*     3.3    47.8    -      -       +      +
     38B  LYS*     5.3     4.3    -      -       +      +
    280B  ASP*     4.4    14.6    -      -       -      +
    281B  LEU      3.7    14.4    -      -       -      +
    282B  GLU*     4.1    18.8    -      -       +      +
    303B  SER*     4.2    14.8    -      -       -      +
    304B  TYR*     1.3    81.6    -      -       -      +
    306B  ALA*     1.3    66.7    +      -       -      +
    307B  ASP*     3.2    19.3    -      -       -      +
    308B  GLU*     3.0    16.5    +      -       +      +
    309B  ILE*     3.5    10.0    -      -       -      +
----------------------------------------------------------
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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