Contacts of the strand formed by residues 168 - 176 (chain B) in PDB entry 1XU2


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 168 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166B  THR*     3.7     4.8    -      -       -      +
    167B  PHE*     1.3   108.9    -      -       +      +
    169B  MET*     1.3    69.4    +      -       -      +
    188B  ILE*     4.4     2.9    -      -       +      -
    189B  ARG      3.3     9.6    -      -       -      +
    190B  SER*     4.0    15.9    -      -       -      +
    222B  ARG*     3.0    41.0    +      -       -      -
    197D  ARG      4.2     1.3    -      -       -      +
    199D  TYR*     4.0    22.0    -      -       +      +
     17S  LEU*     4.4     2.9    -      -       -      -
     18S  LEU*     3.6    14.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 169 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162B  PHE*     3.7    37.9    -      -       +      -
    164B  ASP*     3.8    26.2    -      -       +      +
    166B  THR*     3.7    17.7    -      -       -      +
    168B  THR*     1.3    81.7    -      -       -      +
    170B  GLY*     1.3    58.8    +      -       -      +
    188B  ILE*     3.6     3.1    -      -       -      -
    189B  ARG*     2.8    32.2    +      -       -      +
    191B  MET*     3.9    22.0    -      -       +      +
    220B  ILE*     3.8     8.3    -      -       +      -
    222B  ARG*     3.5    19.1    -      -       +      +
    225B  ALA*     3.5    31.9    -      -       +      -
     17S  LEU*     3.6    10.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 170 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162B  PHE*     3.5    17.4    -      -       -      -
    169B  MET*     1.3    78.0    -      -       -      +
    171B  GLN*     1.3    65.1    +      -       -      +
    187B  CYS      3.1    15.3    -      -       -      -
    202B  CYS*     4.4     2.0    -      -       -      -
    220B  ILE*     3.6    22.7    -      -       -      +
    221B  PRO*     3.6     6.9    -      -       -      +
    222B  ARG*     5.1     0.4    -      -       -      +
     17S  LEU*     3.7     9.8    -      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
    158B  SER*     2.9    39.0    +      -       -      +
    160B  VAL*     3.6    25.7    -      -       +      +
    170B  GLY*     1.3    78.4    -      -       -      +
    172B  VAL*     1.3    64.5    +      -       -      +
    173B  VAL*     4.2     7.3    +      -       +      +
    185B  PHE*     5.3     1.8    -      -       +      -
    186B  ARG*     3.2     7.3    -      -       -      +
    187B  CYS*     3.1    41.2    +      -       +      +
    202B  CYS*     3.2    37.5    +      -       -      +
    204B  SER      4.5     1.0    -      -       -      +
    218B  VAL*     4.2    13.9    -      -       +      -
    219B  LYS      3.3    10.3    -      -       -      +
    220B  ILE*     4.3     4.3    -      -       +      -
     17S  LEU*     4.4     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 172 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171B  GLN*     1.3    77.7    -      -       -      +
    173B  VAL*     1.3    61.5    +      -       -      +
    174B  SER*     3.7    12.1    +      -       -      +
    181B  ARG*     4.3    10.7    +      -       -      +
    183B  THR*     3.6    29.4    -      -       +      +
    185B  PHE      3.8     3.4    -      -       -      +
    186B  ARG*     4.2    12.3    -      -       +      -
    217B  THR*     3.6     2.3    +      -       -      +
    218B  VAL*     3.6     1.9    -      -       -      -
    219B  LYS*     2.8    38.5    +      -       +      +
    221B  PRO*     3.7    24.7    -      -       +      -
     16S  SER      4.0    15.3    -      -       -      +
     17S  LEU*     4.2     6.1    -      -       +      -
     19S  HIS*     5.5     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 173 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156B  LEU*     3.9    27.8    -      -       +      -
    158B  SER*     4.0    17.7    -      -       -      +
    171B  GLN*     4.3     9.4    -      -       +      -
    172B  VAL*     1.3    74.3    -      -       -      +
    174B  SER*     1.3    64.9    +      -       -      +
    183B  THR*     3.8     1.0    -      -       -      +
    184B  LEU*     2.8    25.8    +      -       +      +
    185B  PHE*     3.0    51.1    +      -       +      +
    216B  ILE*     4.2     8.1    -      -       +      -
    217B  THR      3.3    10.1    -      -       -      +
    218B  VAL*     4.4    12.3    -      -       +      -
    236B  LEU*     5.3     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 174 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172B  VAL*     3.7    16.5    +      -       -      +
    173B  VAL*     1.3    77.1    +      -       -      +
    175B  ARG*     1.3    60.9    +      -       -      +
    176B  GLU*     5.3     0.2    -      -       -      -
    181B  ARG*     3.6    27.9    +      -       -      -
    182B  GLU      3.3    14.4    -      -       -      -
    183B  THR*     3.8     7.6    +      -       -      -
    184B  LEU*     4.1     7.2    -      -       -      +
    216B  ILE*     3.2    10.9    -      -       -      +
    217B  THR*     3.0    41.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 175 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174B  SER*     1.3    75.1    -      -       -      +
    176B  GLU*     1.3    67.8    +      -       -      +
    177B  GLY*     4.4     5.1    +      -       -      +
    178B  GLN*     4.7     7.5    +      -       -      -
    180B  ARG*     3.7     7.5    +      -       -      +
    181B  ARG*     3.5     2.4    -      -       -      +
    182B  GLU*     2.9    63.0    +      -       +      +
    184B  LEU*     4.0    17.9    -      -       +      +
    209B  HIS      4.1    10.0    +      -       -      -
    210B  LEU*     3.9    17.3    -      -       -      -
    211B  HIS*     3.7    20.8    +      -       -      -
    214B  ASP*     2.9    41.0    +      -       -      +
    215B  ILE      3.2     5.4    -      -       -      +
    216B  ILE*     3.6    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 176 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175B  ARG*     1.3    82.2    -      -       -      +
    177B  GLY*     1.3    58.7    +      -       -      +
    180B  ARG      3.6     8.5    -      -       -      +
    181B  ARG*     3.8    35.5    +      -       +      +
    213B  GLY      4.0     1.0    -      -       -      +
    214B  ASP*     3.2     4.7    -      -       -      -
    215B  ILE*     2.7    55.7    +      -       +      +
    217B  THR*     3.3    27.0    +      -       +      +
    219B  LYS*     4.5     7.8    +      -       -      -
----------------------------------------------------------
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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