Contacts of the strand formed by residues 118 - 124 (chain G) in PDB entry 1XBT


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 THR 118 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18G  ARG      4.7     7.4    +      -       -      -
     20G  GLN*     3.6    33.9    +      -       +      +
     22G  GLN*     4.2     5.2    -      -       -      +
     43G  PHE*     4.2    22.8    -      -       +      -
     92G  ALA      3.1    11.8    +      -       -      -
     93G  VAL*     3.4    13.7    -      -       +      +
     94G  ILE*     2.8    27.7    +      -       -      +
    116G  GLY      4.1     0.6    +      -       -      -
    117G  LYS*     1.3    71.9    -      -       -      +
    119G  VAL*     1.3    60.8    +      -       -      +
    120G  ILE*     4.2    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 119 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20G  GLN      2.8    16.6    +      -       -      +
     21G  ILE*     3.3     9.3    -      -       +      +
     22G  GLN*     2.8    27.5    +      -       -      +
     94G  ILE*     3.3    14.6    -      -       +      +
     96G  ILE*     3.8    18.6    -      -       +      -
    108G  PHE*     4.8     1.8    -      -       +      -
    109G  CYS*     3.7    39.0    -      -       -      +
    112G  MET*     3.8    27.8    -      -       +      -
    113G  ALA      4.1     1.3    -      -       -      +
    117G  LYS*     4.1     9.0    -      -       +      +
    118G  THR*     1.3    77.1    -      -       -      +
    120G  ILE*     1.3    65.3    +      -       -      +
    121G  VAL*     4.2     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 120 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22G  GLN*     3.4    27.8    -      -       +      +
     24G  ILE*     3.8    23.3    -      -       +      -
     36G  LEU*     3.4    21.1    -      -       +      +
     39G  ARG*     3.7    32.3    -      -       +      -
     40G  VAL*     4.2    14.8    -      -       +      -
     43G  PHE*     4.2    20.6    -      -       +      -
     93G  VAL*     4.6     4.9    -      -       +      -
     94G  ILE      2.8    11.4    +      -       -      +
     95G  GLY*     3.3     2.5    -      -       -      -
     96G  ILE*     2.8    31.9    +      -       -      +
    118G  THR*     4.2     8.7    -      -       +      -
    119G  VAL*     1.3    77.5    -      -       -      +
    121G  VAL*     1.3    59.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 121 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21G  ILE*     4.9     2.0    -      -       +      -
     22G  GLN      2.8    14.6    +      -       -      +
     23G  VAL*     3.5     3.2    -      -       +      +
     24G  ILE*     2.7    36.3    +      -       -      +
     96G  ILE*     3.5    17.9    -      -       +      +
     99G  GLY*     4.2    12.8    -      -       -      -
    105G  ILE*     4.3     3.6    -      -       +      -
    109G  CYS*     3.7    29.6    -      -       -      -
    119G  VAL*     4.2     4.9    -      -       +      -
    120G  ILE*     1.3    78.7    -      -       -      +
    122G  ALA*     1.3    65.9    +      -       -      +
    123G  ALA*     4.0    11.4    +      -       +      -
    136G  ILE*     4.3     4.5    -      -       +      -
    139G  LEU*     4.0    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 122 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24G  ILE*     3.4     8.7    -      -       +      +
     32G  LYS*     3.8    33.4    -      -       +      +
     36G  LEU*     4.1    12.4    -      -       +      +
     96G  ILE      2.9     9.9    +      -       -      +
     97G  ASP*     3.7    18.8    -      -       -      +
     98G  GLU*     3.0    11.0    +      -       -      -
     99G  GLY*     3.0    22.0    +      -       -      -
    120G  ILE      4.2     0.8    +      -       -      -
    121G  VAL*     1.3    71.0    -      -       -      +
    123G  ALA*     1.3    61.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 123 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24G  ILE      2.9     7.1    +      -       -      +
     25G  LEU*     3.3    27.6    -      -       +      +
     32G  LYS*     3.3    14.4    -      -       -      +
     98G  GLU*     4.7     1.1    -      -       -      +
     99G  GLY*     3.9     5.2    -      -       -      +
    100G  GLN*     3.3    12.8    -      -       -      +
    121G  VAL*     4.2     2.2    -      -       +      +
    122G  ALA*     1.3    77.8    -      -       -      +
    124G  LEU*     1.3    65.3    +      -       -      +
    125G  ASP      3.5     0.2    +      -       -      -
    136G  ILE*     3.5    39.3    -      -       +      -
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Residues in contact with LEU 124 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25G  LEU*     4.5     0.2    -      -       -      -
     26G  GLY      3.3    17.9    -      -       -      +
     27G  PRO*     3.8     1.6    -      -       +      -
     28G  MET*     3.7    17.3    -      -       +      +
     32G  LYS*     3.5     7.4    -      -       -      +
    100G  GLN*     3.0    23.0    +      -       -      +
    123G  ALA*     1.3    74.3    -      -       -      +
    125G  ASP*     1.3    61.8    +      -       -      +
    126G  GLY      3.6    13.0    -      -       -      +
    133G  PHE*     3.6    30.4    -      -       +      +
    136G  ILE*     3.4    17.3    -      -       -      +
    163G  THR*     4.6     1.3    -      -       -      +
   7195G  TTP      3.2    63.9    -      -       +      +
----------------------------------------------------------
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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