Contacts of the strand formed by residues 195 - 204 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191A  PRO*     3.8     1.6    -      -       -      -
    192A  ARG      2.8    36.2    +      -       -      +
    193A  HIS*     4.2     8.5    -      -       +      +
    194A  GLY*     1.3    84.8    -      -       -      +
    196A  LEU*     1.3    63.5    +      -       -      +
    197A  CYS*     3.3     4.3    +      -       -      +
    260A  VAL*     3.8    27.6    -      -       +      +
    261A  ILE      3.1    25.7    +      -       -      -
    262A  ASP*     3.5    22.2    -      -       -      +
    349A  LEU*     5.6     0.4    -      -       -      -
    350A  ASP*     4.3    22.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  ILE*     3.7    23.3    -      -       +      -
    190A  THR*     4.0    15.0    -      -       -      -
    191A  PRO*     3.9    13.3    -      -       +      +
    194A  GLY      4.0     2.0    +      -       -      -
    195A  ARG*     1.3    74.6    -      -       -      +
    197A  CYS*     1.3    59.3    +      -       -      +
    260A  VAL*     4.0     1.6    -      -       -      +
    261A  ILE*     3.0    37.3    +      -       +      +
    267A  LEU      5.8     0.2    -      -       -      +
    270A  LEU*     6.3     0.2    -      -       +      -
    311A  TRP*     3.6    33.4    -      -       +      -
    341A  THR*     4.5     7.6    -      -       -      +
    342A  PRO*     5.3     3.6    -      -       +      +
    344A  CYS      4.6     1.6    -      -       -      +
    346A  ALA*     4.0    33.9    -      -       +      +
    349A  LEU*     4.2    21.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  ILE*     3.3     9.4    -      -       -      +
    190A  THR      2.8    54.8    +      -       -      -
    192A  ARG*     3.7    17.7    -      -       -      -
    195A  ARG      4.1     2.2    -      -       -      +
    196A  LEU*     1.3    76.4    -      -       -      +
    198A  PHE*     1.3    59.9    +      -       -      +
    199A  MET*     3.5    34.5    -      -       -      -
    258A  TYR*     4.4     8.1    -      -       +      -
    259A  HIS      3.3    14.8    -      -       -      +
    260A  VAL*     4.0    15.5    -      -       +      +
    261A  ILE*     4.4     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187A  ALA*     3.3    26.5    -      -       +      -
    188A  VAL      3.5     7.2    -      -       -      -
    189A  ILE*     4.3    15.3    -      -       +      +
    197A  CYS*     1.3    72.9    -      -       -      +
    199A  MET*     1.3    63.0    +      -       -      +
    200A  LEU*     4.5     6.5    -      -       +      -
    217A  MET*     4.1    36.3    -      -       +      -
    258A  TYR*     2.8     7.6    -      -       -      +
    259A  HIS*     2.8    47.6    +      +       +      +
    261A  ILE*     4.8     2.0    -      -       +      +
    267A  LEU*     4.5    23.6    -      -       +      -
    283A  ILE*     4.0    27.1    -      -       +      -
    304A  TYR*     5.0     2.2    -      +       +      -
    309A  ILE*     3.5    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187A  ALA*     2.9    10.3    -      -       -      +
    188A  VAL*     2.7    50.3    +      -       +      -
    190A  THR*     3.7    22.0    -      -       +      -
    191A  PRO      5.4     0.2    -      -       -      +
    192A  ARG*     3.0    44.0    -      -       +      +
    197A  CYS*     3.5    25.4    -      -       -      -
    198A  PHE*     1.3    77.2    -      -       -      +
    200A  LEU*     1.3    62.3    +      -       -      +
    256A  ILE*     3.9    19.1    -      -       +      -
    257A  ILE      3.5     2.7    -      -       -      -
    258A  TYR*     3.8    11.7    -      -       +      -
    314A  ARG*     5.3     5.6    -      -       -      -
    315A  PHE*     4.2    10.3    -      -       +      -
    229D  GLU*     6.0     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  PHE*     4.2     8.5    -      -       +      -
    184A  SER*     4.6     0.7    -      -       -      +
    187A  ALA*     4.1     7.6    -      -       +      -
    198A  PHE*     4.5     7.6    -      -       +      -
    199A  MET*     1.3    77.6    -      -       -      +
    201A  ARG*     1.3    75.2    +      -       -      +
    202A  VAL*     4.0    12.3    -      -       +      +
    217A  MET*     4.5     7.6    -      -       +      -
    256A  ILE*     3.4     5.6    -      -       -      -
    257A  ILE*     2.6    55.7    +      -       +      +
    285A  VAL*     3.4    27.6    -      -       +      -
    304A  TYR*     3.3    43.1    -      -       +      +
    315A  PHE*     4.5     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  PHE*     3.6     1.0    -      -       -      -
    184A  SER*     3.0    33.6    +      -       -      -
    200A  LEU*     1.3    82.2    -      -       -      +
    202A  VAL*     1.3    62.8    +      -       -      +
    254A  PRO*     4.1    17.5    +      -       +      +
    255A  LEU      3.2     7.6    -      -       -      +
    256A  ILE*     3.5    20.4    -      -       +      +
    315A  PHE*     3.2    50.2    -      -       +      +
    316A  VAL      2.9    28.3    +      -       -      +
    317A  PRO*     4.9     0.4    -      -       -      +
    318A  ILE*     3.2    21.5    -      -       -      +
    332A  LYS      5.0     0.2    +      -       -      -
    333A  PHE*     3.4    53.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 202 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  ILE      3.1    13.9    -      -       -      +
    183A  PHE*     4.0    18.8    -      -       +      -
    200A  LEU*     4.1     8.7    -      -       +      -
    201A  ARG*     1.3    74.9    -      -       -      +
    203A  GLY*     1.3    64.5    +      -       -      +
    215A  ILE*     4.5     5.4    -      -       +      -
    251A  LEU*     3.7    25.1    -      -       +      +
    254A  PRO*     3.3     1.9    -      -       -      +
    255A  LEU*     2.9    34.3    +      -       +      +
    257A  ILE*     3.5    32.3    -      -       +      -
    287A  LEU*     4.0    15.9    -      -       +      -
    333A  PHE*     4.3     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 203 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  LEU*     3.6     9.0    -      -       -      +
    182A  ILE*     2.8    34.2    +      -       -      +
    202A  VAL*     1.3    79.1    -      -       -      +
    204A  ASP*     1.3    60.2    +      -       -      +
    251A  LEU*     3.8    12.0    -      -       -      +
    254A  PRO*     4.4     6.7    -      -       -      -
    330A  TYR*     5.3     0.7    -      -       -      -
    333A  PHE*     4.0    17.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  ARG*     3.3    23.6    +      -       -      -
    180A  THR*     3.9     7.1    +      -       -      -
    181A  LEU*     3.3    22.7    -      -       +      +
    203A  GLY*     1.3    74.5    -      -       -      +
    205A  LEU*     1.3    64.4    +      -       -      +
    206A  ARG*     2.9    27.1    +      -       -      +
    208A  SER      4.3     3.3    -      -       -      +
    209A  MET*     5.3     0.8    -      -       -      -
    210A  ILE*     3.4    13.2    +      -       -      +
    251A  LEU*     3.5    25.4    -      -       +      +
    252A  VAL      4.7     5.3    +      -       -      +
    254A  PRO      5.9     0.4    -      -       -      -
    330A  TYR*     3.4    20.3    +      -       -      -
     46D  HIS*     4.6     5.2    -      -       -      -
----------------------------------------------------------
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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