Contacts of the strand formed by residues 117 - 121 (chain B) in PDB entry 4XIH


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 GLY 117 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  MET*     3.3    24.7    -      -       -      -
     36B  PHE*     2.9    35.7    +      -       -      +
    106B  VAL*     4.2     5.4    -      -       -      -
    115B  ASN      2.7    14.0    +      -       -      -
    116B  ALA*     1.3    72.1    -      -       -      +
    118B  THR*     1.3    58.4    +      -       -      -
    119B  PHE*     4.6     0.7    -      -       -      -
    131B  GLU      3.4     0.4    -      -       -      -
    132B  MET*     4.2     5.2    -      -       -      -
    139B  ARG*     3.0     6.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  MET*     3.6     1.1    -      -       -      +
     33B  LEU*     3.5    30.7    -      -       +      -
     34B  LEU      3.2     8.4    +      -       -      +
     35B  VAL*     4.3     2.5    -      -       +      -
    117B  GLY*     1.3    70.3    +      -       -      -
    119B  PHE*     1.3    69.9    +      -       -      +
    129B  PHE*     4.1     5.8    -      -       +      -
    130B  ALA*     3.4     4.7    -      -       -      -
    131B  GLU*     2.9    39.2    +      -       -      -
    139B  ARG*     2.7    25.8    +      -       -      -
    144B  TRP*     3.2    39.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 119 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  MET*     3.9    13.2    -      -       +      -
      2B  LEU      3.6    24.7    -      -       -      -
     32B  VAL      3.7     0.2    -      -       -      +
     33B  LEU*     3.4     6.8    -      -       -      +
     34B  LEU*     2.7    46.6    +      -       +      +
     36B  PHE*     3.7    31.9    -      +       -      -
    104B  TYR*     3.6    32.3    -      +       +      -
    106B  VAL*     3.7    24.2    -      -       +      -
    117B  GLY      4.6     0.4    -      -       -      -
    118B  THR*     1.3    75.1    -      -       -      +
    120B  VAL*     1.3    66.4    +      -       -      +
    121B  VAL*     4.1     2.9    -      -       +      -
    127B  ILE*     3.9    31.0    -      -       +      -
    129B  PHE*     3.2     9.2    -      -       -      +
    130B  ALA*     3.9    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  ASN*     4.7     0.2    -      -       +      -
     32B  VAL      3.2     4.0    -      -       -      +
     33B  LEU*     3.8    19.3    -      -       +      -
    119B  PHE*     1.3    77.4    -      -       -      +
    121B  VAL*     1.3    63.5    +      -       -      +
    127B  ILE*     3.5     3.1    -      -       -      -
    128B  ARG*     2.7    32.3    +      -       +      +
    129B  PHE*     3.1    36.6    +      -       +      +
    144B  TRP*     4.8     2.2    -      -       -      +
    147B  ALA*     4.3    12.1    -      -       +      +
    148B  LEU*     3.6    26.7    -      -       +      -
    151B  LEU*     3.6    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  ALA*     3.8    24.7    -      -       +      -
     23B  LEU*     4.4    14.6    -      -       +      -
     31B  ASN*     3.3     2.9    -      -       -      +
     32B  VAL*     2.7    49.1    +      -       +      +
     34B  LEU*     3.9    27.6    -      -       +      -
    119B  PHE*     4.9     2.0    -      -       +      -
    120B  VAL*     1.3    77.8    -      -       -      +
    122B  ASP*     1.3    64.9    +      -       -      +
    125B  GLY*     3.5    36.6    -      -       -      -
    126B  ILE      3.5     3.4    -      -       -      +
    127B  ILE*     4.6     7.4    -      -       +      -
----------------------------------------------------------
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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