Contacts of the strand formed by residues 193 - 201 (chain K) in PDB entry 2O5J


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 ASP 193 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27K  PRO*     3.8     1.2    -      -       -      +
     28K  LEU*     3.0    43.2    +      -       +      +
     29K  GLU      3.0    13.0    -      -       -      +
     30K  ARG*     3.6     2.8    +      -       -      -
     31K  GLY*     2.7    39.6    +      -       -      -
     32K  PHE      3.7     0.9    -      -       -      -
     33K  GLY      3.6     8.7    +      -       -      +
    181K  VAL*     3.0    14.2    -      -       +      +
    182K  GLU      4.3     0.2    -      -       -      -
    184K  THR*     3.7     7.2    -      -       -      +
    192K  LEU*     1.3    75.4    -      -       -      +
    194K  LYS*     1.3    59.6    +      -       -      +
    938M  LYS*     2.6    36.6    +      -       -      +
    939M  ARG*     3.7     3.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 194 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24K  VAL*     4.2    20.0    -      -       +      -
     25K  LEU      4.1     0.2    -      -       -      -
     26K  GLU*     3.6    41.6    +      -       +      +
    180K  GLN      3.0    13.9    -      -       -      +
    181K  VAL*     3.2     4.9    -      -       -      +
    182K  GLU*     3.0    60.3    +      -       -      +
    183K  ASP      5.0     2.0    -      -       -      +
    184K  THR*     3.9    14.3    +      -       -      -
    193K  ASP*     1.3    75.0    -      -       -      +
    195K  LEU*     1.3    58.8    +      -       -      +
    196K  THR*     4.3     5.6    -      -       +      -
    934M  PHE*     5.7     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 195 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23K  PHE      3.6     1.4    -      -       -      +
     24K  VAL*     3.6     0.7    -      -       -      -
     25K  LEU*     2.9    43.1    +      -       +      +
     28K  LEU*     3.8     8.7    -      -       +      +
     33K  GLY*     3.4    38.1    -      -       -      +
     36K  LEU*     3.9    18.8    -      -       +      -
     37K  GLY*     3.6    15.7    -      -       -      +
     40K  LEU*     6.0     2.0    -      -       +      -
    179K  PHE*     3.6    35.2    -      -       +      -
    180K  GLN      3.5     3.1    -      -       -      -
    181K  VAL*     4.7     0.4    -      -       +      +
    194K  LYS*     1.3    69.4    -      -       -      +
    196K  THR*     1.3    70.1    +      -       -      +
    197K  LEU*     3.7    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 196 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23K  PHE      3.0     7.2    -      -       -      -
     24K  VAL*     3.4    31.0    -      -       +      -
    178K  ALA      3.8     0.5    -      -       -      +
    179K  PHE*     3.4     1.2    -      -       -      -
    180K  GLN*     3.1    32.1    +      -       -      +
    182K  GLU*     3.1    25.1    -      -       -      +
    194K  LYS*     4.3     2.2    -      -       +      +
    195K  LEU*     1.3    80.0    -      -       -      +
    197K  LEU*     1.3    61.2    +      -       -      +
    198K  ARG*     4.0     2.4    +      -       -      +
    934M  PHE*     2.9    41.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 197 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21K  GLY      3.7     3.5    -      -       -      +
     22K  GLU*     4.8     1.1    -      -       -      -
     23K  PHE*     3.0    42.9    +      -       +      +
     37K  GLY*     4.2    11.9    -      -       -      +
     40K  LEU*     4.1    29.2    -      -       +      -
     44K  LEU*     3.9    16.6    -      -       +      -
    177K  VAL*     4.4     3.8    -      -       +      -
    178K  ALA      3.0    10.5    -      -       -      +
    179K  PHE*     3.7     9.6    -      -       +      -
    195K  LEU*     3.7    28.7    -      -       +      -
    196K  THR*     1.3    72.3    -      -       -      +
    198K  ARG*     1.3    61.4    +      -       -      +
    199K  ILE*     3.8    22.6    -      -       +      +
    211K  LEU*     4.9     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 198 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20K  TYR*     2.8    39.7    +      -       +      -
     21K  GLY      3.7     4.9    -      -       -      -
     22K  GLU*     4.1    22.8    +      -       +      +
    176K  ARG      3.9     1.2    -      -       -      +
    177K  VAL*     3.5     3.8    -      -       -      -
    178K  ALA*     2.6    64.9    +      -       +      +
    196K  THR      4.9     3.1    -      -       -      +
    197K  LEU*     1.3    71.0    -      -       -      +
    199K  ILE*     1.3    61.5    +      -       -      +
    200K  TRP*     4.2    18.6    -      -       +      -
    863M  ASP*     5.2     4.9    +      -       -      +
    929M  ARG*     4.3    22.6    +      -       -      +
    932M  GLU*     3.1    51.3    +      -       -      +
    933M  GLY      4.7     0.2    -      -       -      +
    934M  PHE*     4.5    17.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 199 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19K  GLU      3.2     4.3    -      -       -      +
     20K  TYR*     3.6     2.0    -      -       -      -
     21K  GLY      3.1    36.0    +      -       -      +
     23K  PHE*     5.0     5.8    -      -       +      -
     44K  LEU*     3.6    33.0    -      -       +      -
    174K  VAL*     4.4    12.6    -      -       +      -
    176K  ARG      3.8     1.8    -      -       -      -
    177K  VAL*     3.4    30.3    -      -       +      -
    197K  LEU*     3.8    23.6    -      -       +      +
    198K  ARG*     1.3    77.2    -      -       -      +
    200K  TRP*     1.3    68.1    +      -       -      +
    201K  THR*     3.7    17.5    -      -       -      +
    207K  PRO*     3.6    22.3    -      -       +      +
    210K  ALA*     4.7     0.9    -      -       +      -
    211K  LEU*     5.8     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 200 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19K  GLU*     3.1    13.5    -      -       +      -
     20K  TYR*     4.1    38.8    -      +       +      -
    174K  VAL*     3.1    26.3    -      -       -      +
    175K  ARG*     3.3    10.7    +      -       +      -
    176K  ARG*     2.9    67.3    +      -       +      +
    178K  ALA*     4.3    14.1    -      -       +      -
    198K  ARG*     4.2    25.6    -      -       -      -
    199K  ILE*     1.3    73.8    -      -       -      +
    201K  THR*     1.3    63.1    +      -       -      +
    863M  ASP*     3.0    34.5    -      -       -      -
    864M  GLY      4.4     1.1    -      -       -      -
    932M  GLU*     4.6     6.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 201 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18K  ARG      3.3    14.1    -      -       -      -
     19K  GLU*     2.7    28.7    +      -       -      +
    173K  PRO*     2.8    23.1    -      -       +      +
    174K  VAL*     4.1     6.1    -      -       +      +
    175K  ARG*     5.2     1.6    -      -       -      -
    199K  ILE*     3.7     3.6    -      -       -      +
    200K  TRP*     1.3    76.5    +      -       -      +
    202K  ASP*     1.3    59.8    +      -       -      +
    203K  GLY      3.0     8.5    +      -       -      +
    205K  VAL*     3.0    41.1    -      -       +      +
    206K  THR      4.4     1.3    -      -       -      +
    207K  PRO*     3.4    27.4    -      -       -      +
----------------------------------------------------------
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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