Contacts of the strand formed by residues 191 - 197 (chain A) in PDB entry 1XL4


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 191 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  SER*     6.0     4.7    -      -       -      -
    184A  GLU      3.2     4.9    -      -       -      +
    185A  ILE*     3.8    29.2    -      -       +      -
    189A  GLY      5.3     2.7    -      -       -      +
    190A  MET*     1.3    86.0    -      -       +      +
    192A  PHE*     1.3    61.4    +      -       -      +
    273B  ASP*     6.0     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  ARG      3.7     0.3    -      -       -      +
    183A  SER*     3.4     3.2    -      -       -      +
    184A  GLU*     2.9    46.2    +      -       +      -
    185A  ILE      4.4     0.9    -      -       -      -
    186A  SER*     3.9    22.0    -      -       -      -
    190A  MET*     3.7    27.4    -      -       +      -
    191A  VAL*     1.3    75.2    -      -       -      +
    193A  ARG*     1.3    74.2    +      -       -      +
    194A  ARG*     3.6    43.9    +      -       +      -
    153B  PHE*     3.5    39.5    -      +       -      -
    154B  GLU*     4.5     1.6    -      -       -      -
    215B  MET*     5.8     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ILE*     3.6    38.4    -      -       +      +
    181A  VAL*     3.3    41.1    +      -       +      +
    182A  ARG*     3.2     4.6    -      -       -      +
    183A  SER*     3.1    42.1    +      -       -      +
    192A  PHE*     1.3    81.9    -      -       -      +
    194A  ARG*     1.3    59.4    +      -       -      +
    195A  PHE*     4.4    11.2    +      -       +      -
    235A  SER      3.4     1.4    +      -       -      -
    236A  HIS*     2.9    29.9    +      -       -      +
    238A  GLU*     4.2     5.1    +      -       -      +
    275B  PHE*     6.5     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  LEU      3.6     3.5    -      -       -      +
    181A  VAL*     3.7     1.2    -      -       -      -
    182A  ARG      3.0    30.5    +      -       -      +
    184A  GLU*     2.8    25.2    +      -       -      +
    192A  PHE*     3.6    31.5    +      -       +      +
    193A  ARG*     1.3    74.1    -      -       -      +
    195A  PHE*     1.3    72.6    -      -       -      +
    196A  HIS*     3.1    38.0    -      -       -      +
    153B  PHE*     3.9    13.7    -      -       -      -
    154B  GLU*     3.1    28.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  LEU*     6.1     1.6    -      -       +      -
    179A  VAL*     3.7    17.9    -      -       +      -
    180A  LEU      3.4     4.3    -      -       -      -
    181A  VAL*     4.2    27.8    -      -       +      -
    193A  ARG*     4.6    10.1    -      -       +      -
    194A  ARG*     1.3    90.2    -      -       -      +
    196A  HIS*     1.3    62.0    +      -       -      +
    240A  LEU*     4.3    18.2    -      -       +      -
    202B  ARG*     3.3    49.5    +      -       -      +
    205B  SER*     5.0     6.5    -      -       -      -
    206B  PRO*     5.1     7.6    -      -       +      -
    207B  ILE      4.6    12.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  VAL*     3.8     2.7    -      -       -      -
    180A  LEU*     2.8    55.1    +      -       +      -
    182A  ARG*     4.2     6.0    +      -       +      -
    184A  GLU*     3.0    24.8    +      -       -      -
    194A  ARG*     3.1    42.3    -      -       +      -
    195A  PHE*     1.3    75.9    +      -       -      +
    197A  ASP*     1.3    65.9    +      -       -      +
    198A  LEU*     3.3     3.1    +      -       -      +
    223A  PRO*     3.7    36.4    -      -       +      +
    202B  ARG*     4.8     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  HIS*     2.7    43.3    +      -       -      -
    178A  LEU      3.6    11.1    +      -       -      +
    179A  VAL*     4.2     8.6    -      -       +      +
    196A  HIS*     1.3    72.9    -      -       -      +
    198A  LEU*     1.3    79.5    +      -       -      +
    199A  THR*     3.9     1.9    +      -       -      -
    223A  PRO*     5.2     3.1    -      -       -      +
    202B  ARG*     3.9    19.1    +      -       -      +
    206B  PRO*     4.7     1.9    -      -       -      +
----------------------------------------------------------
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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