Contacts of the strand formed by residues 188 - 196 (chain B) in PDB entry 5I75


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 VAL 188 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179B  TRP*     4.0    21.5    -      -       +      +
    184B  LEU      4.9     0.4    -      -       -      +
    185B  SER*     3.9    33.7    +      -       -      +
    186B  SER      3.9     0.2    -      -       -      -
    187B  SER*     1.3    76.8    -      -       -      +
    189B  HIS*     1.3    62.5    +      -       -      +
    190B  THR*     4.0    12.5    +      -       -      +
    204B  SER*     3.8    15.7    -      -       -      +
    205B  SER      3.2    15.9    -      -       -      +
    206B  VAL*     3.6    26.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 189 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187B  SER*     3.3    27.9    +      -       -      -
    188B  VAL*     1.3    74.9    +      -       -      +
    190B  THR*     1.3    61.6    +      -       -      +
    191B  PHE*     3.9    14.4    -      -       +      -
    204B  SER*     3.6     1.7    -      -       -      -
    205B  SER*     2.9    48.2    +      -       -      +
    207B  THR*     4.5    10.7    +      -       -      -
    157C  ASN*     4.6    11.9    -      -       +      +
    158C  ASN*     3.8    28.9    +      -       -      -
    184C  THR*     6.1     1.6    -      -       +      -
    187C  ASP*     4.8    13.9    +      -       -      -
    192C  THR*     5.4     3.1    -      -       -      -
    194C  SER*     3.4    28.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 190 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177B  VAL*     5.5     4.2    +      -       +      -
    188B  VAL*     4.0    11.8    +      -       -      +
    189B  HIS*     1.3    72.6    -      -       -      +
    191B  PHE*     1.3    67.8    +      -       -      +
    192B  PRO*     3.9     1.6    -      -       -      +
    202B  MET*     3.8    24.5    -      -       +      -
    203B  SER      4.2     2.5    -      -       -      +
    204B  SER*     3.9    12.7    +      -       -      -
    184C  THR*     3.4    16.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 191 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  HIS*     3.9    10.3    -      -       +      -
    190B  THR*     1.3    75.6    -      -       -      +
    192B  PRO*     1.3    73.4    -      -       +      +
    193B  ALA      3.6     1.6    +      -       -      -
    202B  MET*     3.7    16.3    -      -       -      +
    203B  SER*     3.0    41.8    +      -       -      +
    205B  SER*     3.8    16.6    -      -       -      -
    155C  PHE*     3.4    35.7    -      +       -      -
    157C  ASN*     4.0    14.4    -      -       -      -
    182C  SER*     4.0     5.4    -      -       -      +
    184C  THR*     3.6    16.4    -      -       +      -
    194C  SER*     4.1     6.7    -      -       -      -
    195C  MET*     3.3    31.2    -      -       -      -
    196C  SER*     3.5    24.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 192 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190B  THR      3.9     2.0    -      -       -      +
    191B  PHE*     1.3    86.3    -      -       -      +
    193B  ALA*     1.3    68.9    +      -       -      +
    194B  LEU*     3.7     7.8    +      -       +      +
    201B  THR      4.4     2.1    -      -       -      +
    202B  MET*     4.4     1.9    -      -       -      +
    182C  SER*     3.2    28.0    +      -       -      +
    183C  TRP      3.8    15.5    -      -       -      +
    184C  THR*     3.5    24.7    -      -       +      -
    185C  ASP*     5.3     2.9    -      -       -      +
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Residues in contact with ALA 193 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170B  TYR*     3.3    26.9    -      -       -      +
    173B  GLU*     5.8     3.4    -      -       +      -
    175B  VAL*     5.8     0.2    -      -       +      -
    191B  PHE      3.6     1.8    +      -       -      -
    192B  PRO*     1.3    79.3    -      -       -      +
    194B  LEU*     1.3    64.9    +      -       -      +
    195B  LEU      4.3     0.3    +      -       -      -
    200B  TYR*     4.3    19.2    -      -       +      -
    201B  THR      3.5     8.1    -      -       -      +
    202B  MET*     3.6    10.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 194 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192B  PRO*     4.1    12.6    -      -       +      +
    193B  ALA*     1.3    81.7    -      -       -      +
    195B  LEU*     1.3    63.4    +      -       -      +
    196B  GLN*     3.9     3.8    +      -       +      +
    199B  LEU      3.7     0.9    -      -       -      +
    200B  TYR*     3.3     4.0    -      -       -      -
    201B  THR*     2.9    38.6    +      -       -      +
    180C  LEU*     3.9    43.3    -      -       +      -
    181C  ASN      4.3     9.4    -      -       -      +
    182C  SER*     4.3    22.0    -      -       -      +
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Residues in contact with LEU 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171B  PHE*     4.6     5.6    -      -       +      -
    193B  ALA      4.3     0.2    +      -       -      -
    194B  LEU*     1.3    73.1    -      -       -      +
    196B  GLN*     1.3    64.0    +      -       -      +
    198B  GLY*     3.6    14.1    -      -       -      +
    199B  LEU      3.6    34.5    -      -       -      +
    200B  TYR*     3.6    43.9    -      -       +      +
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Residues in contact with GLN 196 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168B  LYS*     5.9     0.8    -      -       -      +
    194B  LEU*     4.3     4.9    -      -       +      +
    195B  LEU*     1.3    80.1    -      -       -      +
    197B  SER*     1.3    78.2    +      -       -      +
    198B  GLY      3.1     1.8    -      -       -      -
    199B  LEU*     2.9    29.2    +      -       +      +
    201B  THR*     3.6    27.4    +      -       -      +
    180C  LEU*     3.5    30.5    -      -       -      +
    200C  THR*     5.8     1.8    +      -       -      -
----------------------------------------------------------
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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