Contacts of the strand formed by residues 195 - 204 (chain D) 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 ARG 195 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191D  PRO*     3.8     1.6    -      -       -      -
    192D  ARG      2.8    34.5    +      -       -      +
    193D  HIS*     4.2     8.5    -      -       +      +
    194D  GLY*     1.3    83.7    -      -       -      +
    196D  LEU*     1.3    64.3    +      -       -      +
    197D  CYS*     3.3     4.0    +      -       -      +
    260D  VAL*     3.8    26.8    -      -       +      +
    261D  ILE      3.1    26.8    +      -       -      -
    262D  ASP*     3.5    21.0    -      -       -      +
    349D  LEU*     5.6     0.4    -      -       -      -
    350D  ASP*     4.3    22.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 196 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189D  ILE*     3.7    23.6    -      -       +      -
    190D  THR*     4.0    15.3    -      -       -      -
    191D  PRO*     3.9    13.5    -      -       +      +
    194D  GLY      4.0     2.0    +      -       -      -
    195D  ARG*     1.3    73.6    -      -       -      +
    197D  CYS*     1.3    58.2    +      -       -      +
    260D  VAL*     4.0     1.6    -      -       -      +
    261D  ILE*     3.0    36.9    +      -       +      +
    270D  LEU*     6.3     0.2    -      -       +      -
    311D  TRP*     3.6    33.7    -      -       +      -
    341D  THR*     4.5     7.6    -      -       -      +
    342D  PRO*     5.3     3.8    -      -       +      +
    344D  CYS      4.6     1.8    -      -       -      +
    346D  ALA*     4.0    34.3    -      -       +      +
    349D  LEU*     4.2    21.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 197 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189D  ILE*     3.3    10.0    -      -       -      +
    190D  THR      2.8    54.8    +      -       -      +
    192D  ARG*     3.7    18.2    -      -       -      -
    195D  ARG      4.1     2.5    -      -       -      +
    196D  LEU*     1.3    75.8    -      -       -      +
    198D  PHE*     1.3    58.7    +      -       -      +
    199D  MET*     3.5    33.4    -      -       -      -
    258D  TYR*     4.4     8.5    -      -       +      -
    259D  HIS      3.3    14.1    -      -       -      +
    260D  VAL*     4.0    15.5    -      -       +      -
    261D  ILE*     4.4     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 198 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187D  ALA*     3.3    27.4    -      -       +      -
    188D  VAL      3.5     8.3    -      -       -      -
    189D  ILE*     4.3    14.4    -      -       +      +
    197D  CYS*     1.3    71.0    -      -       -      +
    199D  MET*     1.3    63.1    +      -       -      +
    200D  LEU*     4.5     6.7    -      -       +      -
    217D  MET*     4.1    35.2    -      -       +      -
    257D  ILE      5.4     0.2    -      -       -      -
    258D  TYR*     2.8     8.1    -      -       -      +
    259D  HIS*     2.8    48.7    +      -       +      +
    261D  ILE*     4.8     1.8    -      -       +      +
    267D  LEU*     4.5    22.2    -      -       +      -
    270D  LEU*     6.1     0.2    -      -       +      -
    283D  ILE*     4.0    27.4    -      -       +      -
    304D  TYR*     5.0     1.8    -      +       +      -
    309D  ILE*     3.5    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 199 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229C  GLU*     6.0     6.1    -      -       +      -
    187D  ALA*     2.9    10.0    -      -       -      +
    188D  VAL*     2.7    51.1    +      -       +      -
    190D  THR*     3.7    21.3    -      -       +      -
    191D  PRO      5.4     0.2    -      -       -      +
    192D  ARG*     3.0    44.6    -      -       +      +
    197D  CYS*     3.5    24.9    -      -       -      -
    198D  PHE*     1.3    77.9    -      -       -      +
    200D  LEU*     1.3    62.1    +      -       -      +
    256D  ILE*     3.9    19.3    -      -       +      -
    257D  ILE      3.5     2.2    -      -       -      -
    258D  TYR*     3.8    11.9    -      -       +      -
    314D  ARG*     5.3     5.6    -      -       -      -
    315D  PHE*     4.2    10.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 200 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183D  PHE*     4.2     7.9    -      -       +      -
    184D  SER*     4.6     0.4    -      -       -      -
    187D  ALA*     4.1     8.1    -      -       +      -
    198D  PHE*     4.5     7.2    -      -       +      -
    199D  MET*     1.3    77.4    -      -       -      +
    201D  ARG*     1.3    75.8    +      -       -      +
    202D  VAL*     4.0    11.9    -      -       +      +
    217D  MET*     4.5     7.4    -      -       +      -
    256D  ILE*     3.4     5.4    -      -       -      +
    257D  ILE*     2.6    56.1    +      -       +      +
    285D  VAL*     3.4    27.4    -      -       +      -
    304D  TYR*     3.3    44.0    -      -       +      +
    315D  PHE*     4.5     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 201 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183D  PHE*     3.6     1.4    -      -       -      -
    184D  SER*     3.0    34.0    +      -       -      -
    200D  LEU*     1.3    81.6    -      -       -      +
    202D  VAL*     1.3    63.8    +      -       -      +
    254D  PRO*     4.1    17.7    +      -       +      +
    255D  LEU      3.2     7.2    -      -       -      +
    256D  ILE*     3.5    19.9    -      -       +      +
    315D  PHE*     3.2    51.9    -      -       +      +
    316D  VAL      2.9    27.9    +      -       -      -
    317D  PRO*     4.9     0.8    -      -       -      +
    318D  ILE*     3.2    22.9    -      -       -      +
    332D  LYS      5.0     0.2    +      -       -      -
    333D  PHE*     3.4    53.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 202 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182D  ILE      3.1    13.7    -      -       -      +
    183D  PHE*     4.0    18.8    -      -       +      -
    200D  LEU*     4.1     8.7    -      -       +      -
    201D  ARG*     1.3    76.8    -      -       -      +
    203D  GLY*     1.3    63.9    +      -       -      +
    215D  ILE*     4.5     6.3    -      -       +      -
    251D  LEU*     3.7    25.9    -      -       +      +
    254D  PRO*     3.3     2.4    -      -       -      +
    255D  LEU*     2.9    33.6    +      -       +      +
    257D  ILE*     3.5    32.5    -      -       +      -
    287D  LEU*     4.0    16.4    -      -       +      -
    333D  PHE*     4.3     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 203 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181D  LEU*     3.6     9.4    -      -       -      +
    182D  ILE*     2.8    34.8    +      -       -      +
    202D  VAL*     1.3    79.8    -      -       -      +
    204D  ASP*     1.3    59.8    +      -       -      +
    251D  LEU*     3.8    11.8    -      -       -      +
    254D  PRO*     4.4     6.5    -      -       -      -
    330D  TYR*     5.3     0.4    -      -       -      -
    333D  PHE*     4.0    17.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 204 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46C  HIS*     4.6     5.7    -      -       -      -
    177D  ARG*     3.3    23.6    +      -       -      -
    180D  THR*     3.9     7.4    +      -       -      -
    181D  LEU*     3.3    21.5    -      -       +      +
    203D  GLY*     1.3    75.2    -      -       -      +
    205D  LEU*     1.3    63.0    +      -       -      +
    206D  ARG*     2.9    26.7    +      -       -      +
    208D  SER      4.3     4.3    -      -       -      +
    209D  MET*     5.3     1.0    -      -       -      -
    210D  ILE*     3.4    13.2    +      -       -      +
    251D  LEU*     3.5    24.9    -      -       +      +
    252D  VAL      4.7     4.7    +      -       -      +
    253D  ALA      6.0     0.4    -      -       -      -
    254D  PRO*     5.8     0.2    -      -       -      +
    330D  TYR*     3.4    20.1    +      -       -      -
----------------------------------------------------------
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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