Contacts of the strand formed by residues 170 - 174 (chain B) in PDB entry 1XVI


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 LEU 170 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95B  ILE*     4.0    16.8    -      -       +      -
    100B  ILE*     4.1    21.8    -      -       +      -
    103B  VAL*     3.9    36.3    -      -       +      -
    165B  LEU*     3.0    32.4    +      -       +      +
    166B  ASN*     3.0    20.8    +      -       -      +
    168B  LEU*     4.0     9.6    -      -       +      +
    169B  GLY*     1.3    87.3    -      -       -      +
    171B  GLN*     1.3    60.3    +      -       -      +
    181B  VAL*     3.9    20.2    -      -       +      -
    182B  LEU*     3.4    21.5    -      -       -      +
    183B  ASP      3.9     2.9    -      -       -      +
    184B  ALA*     3.8     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 171 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165B  LEU*     4.6     2.7    -      -       -      -
    166B  ASN*     4.0     7.2    -      -       -      +
    170B  LEU*     1.3    74.5    -      -       -      +
    172B  PHE*     1.3    61.4    +      -       -      +
    173B  MET*     3.0    34.5    -      -       +      +
    180B  HIS      3.7     0.3    -      -       -      +
    181B  VAL*     3.5     9.7    -      -       -      +
    182B  LEU*     2.8    49.5    +      -       +      +
    183B  ASP      2.7    23.2    +      -       -      +
    184B  ALA*     3.6    15.6    +      -       +      +
    186B  ALA      2.9    24.4    +      -       -      +
    187B  GLY*     4.9     0.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 172 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149B  LEU*     4.0    14.6    -      -       +      -
    151B  TRP*     4.2     7.6    -      +       -      -
    158B  MET*     3.7    31.4    -      -       +      -
    161B  PHE*     3.9    29.2    -      +       -      -
    162B  THR*     3.3    29.4    +      -       -      +
    165B  LEU*     3.7    12.3    -      -       +      -
    166B  ASN*     4.8     0.2    +      -       -      -
    171B  GLN*     1.3    73.9    -      -       -      +
    173B  MET*     1.3    66.1    +      -       -      +
    174B  GLN      4.1     0.3    +      -       -      -
    179B  TRP*     3.3    61.7    -      +       +      -
    180B  HIS      3.5     3.4    -      -       -      -
    181B  VAL*     3.7    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 173 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  ASN*     4.0    26.9    -      -       -      +
    171B  GLN*     3.0    38.4    -      -       +      +
    172B  PHE*     1.3    76.1    -      -       -      +
    174B  GLN*     1.3    65.5    +      -       -      +
    175B  GLY      3.7     1.2    +      -       -      -
    179B  TRP*     3.3     7.1    -      -       -      -
    180B  HIS*     2.8    51.4    +      -       +      +
    182B  LEU*     4.0    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 174 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172B  PHE      4.1     0.4    +      -       -      -
    173B  MET*     1.3    75.4    -      -       -      +
    175B  GLY*     1.3    74.7    +      -       -      +
    176B  ALA      5.2     2.8    +      -       -      -
    178B  PHE      4.7     1.8    -      -       -      +
    179B  TRP*     3.4    48.4    -      -       +      +
    180B  HIS*     5.0     0.2    -      -       -      -
    217B  ASN*     5.1    11.1    +      -       -      +
----------------------------------------------------------
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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