Contacts of the strand formed by residues 199 - 210 (chain D) 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 TYR 199 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167B  PHE*     4.5     0.7    -      +       -      -
    168B  THR*     4.0     6.3    -      -       +      -
    188B  ILE*     3.9    18.8    -      -       +      +
    190B  SER*     2.8    27.6    +      -       -      -
    161D  LEU*     5.2     8.1    -      -       +      -
    162D  PHE      3.4     7.6    -      -       -      +
    163D  HIS*     3.3    48.1    +      +       +      -
    191D  MET*     4.0     0.4    -      -       -      +
    196D  ASP*     3.5    20.8    +      -       -      -
    197D  ARG      3.0    14.9    +      -       -      -
    198D  ALA*     1.3    76.3    -      -       -      +
    200D  ASN*     1.3    66.8    +      -       -      +
     18S  LEU*     3.8    44.6    -      -       +      -
     20S  ALA*     4.0    19.5    -      -       +      +
     21S  CYS      5.1     1.6    +      -       -      -
     22S  ILE*     4.7     6.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 200 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188B  ILE*     3.4     5.3    -      -       -      +
    189B  ARG*     3.5    17.7    -      -       -      +
    190B  SER*     3.0    26.0    +      -       -      +
    161D  LEU*     3.7     5.5    -      -       -      +
    162D  PHE*     2.9    34.9    +      -       +      +
    189D  ARG*     3.6    23.9    -      -       +      +
    190D  SER      3.1    24.9    +      -       -      -
    191D  MET*     3.4    20.4    -      -       -      +
    192D  PRO*     3.8    11.9    -      -       -      +
    199D  TYR*     1.3    78.4    +      -       -      +
    201D  SER*     1.3    60.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 201 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  ARG      4.6     0.2    -      -       -      -
    187B  CYS*     3.7    10.4    -      -       -      -
    188B  ILE*     2.9    34.8    +      -       -      -
    189B  ARG*     2.8    27.1    +      -       -      -
    159D  GLN*     3.8    26.9    +      -       -      -
    160D  VAL      3.4     7.2    -      -       -      -
    161D  LEU*     3.9    13.7    -      -       -      +
    189D  ARG*     3.0     6.9    +      -       -      -
    200D  ASN*     1.3    77.0    -      -       -      +
    202D  CYS*     1.3    61.0    +      -       -      +
    203D  TYR*     4.2     0.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 202 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159D  GLN*     3.2     1.9    -      -       -      -
    160D  VAL      2.8    34.2    +      -       -      +
    162D  PHE*     3.9    11.7    -      -       +      -
    170D  GLY*     4.5     2.7    -      -       -      -
    171D  GLN*     3.0    20.0    +      -       -      +
    187D  CYS*     2.0    59.5    -      -       -      -
    188D  ILE*     3.5    14.8    -      -       -      -
    189D  ARG*     3.8    15.0    -      -       +      +
    201D  SER*     1.3    74.4    -      -       -      +
    203D  TYR*     1.3    58.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 203 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  GLN*     4.5     0.3    -      -       -      +
    201A  SER*     5.3     0.2    +      -       -      -
    203A  TYR*     3.5    39.1    +      +       -      +
    155B  LEU*     5.8     0.7    -      -       -      +
    189B  ARG*     5.8     1.8    -      -       -      +
    203B  TYR*     3.5    35.7    +      +       -      +
    204B  SER*     4.0     0.7    -      -       -      -
    205B  ALA*     3.2    48.1    -      -       +      +
    157D  TYR*     3.3    32.8    -      +       +      +
    158D  SER      3.4     6.1    -      -       -      -
    159D  GLN*     3.7    32.5    -      -       +      +
    187D  CYS*     3.4     9.5    -      -       -      -
    189D  ARG*     4.8     3.9    +      -       -      +
    201D  SER*     4.2     1.3    -      -       -      +
    202D  CYS*     1.3    74.5    -      -       -      +
    204D  SER*     1.3    74.5    +      -       -      +
    205D  ALA*     3.8     5.5    -      -       +      +
    235D  PHE*     4.3     3.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 204 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  GLN*     2.7    27.7    +      -       -      -
    203A  TYR*     4.0     5.1    -      -       -      -
    235A  PHE*     3.7     7.4    -      -       -      -
    157D  TYR*     3.5     0.2    -      -       -      -
    158D  SER      2.9    33.0    +      -       -      +
    171D  GLN*     4.6     0.2    -      -       -      +
    185D  PHE*     3.4    28.4    -      -       -      -
    186D  ARG      4.3     0.9    -      -       -      -
    187D  CYS*     4.0    15.5    -      -       -      -
    202D  CYS      4.4     0.2    +      -       -      -
    203D  TYR*     1.3    83.7    -      -       -      +
    205D  ALA*     1.3    69.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 205 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157A  TYR*     4.0     1.8    -      -       -      -
    203A  TYR*     3.3    29.3    -      -       -      +
    235A  PHE*     3.3    23.0    -      -       -      -
    155D  LEU*     4.6     9.0    -      -       +      -
    156D  LEU      3.1    15.5    -      -       -      +
    157D  TYR*     3.6    15.5    -      -       +      -
    185D  PHE*     3.9     9.2    -      -       -      -
    203D  TYR*     3.8     7.9    -      -       +      +
    204D  SER*     1.3    81.9    +      -       -      +
    206D  GLY*     1.3    58.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 206 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  HIS*     4.5     1.6    -      -       -      -
    157A  TYR*     3.9    15.3    -      -       -      -
    155D  LEU*     3.5     5.7    -      -       -      +
    156D  LEU      2.8    31.5    +      -       -      +
    185D  PHE*     4.1     0.4    -      -       -      -
    205D  ALA*     1.3    77.8    -      -       -      +
    207D  VAL*     1.3    62.4    +      -       -      -
    208D  PHE*     3.3    25.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 207 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  VAL*     4.2    11.0    -      -       +      -
    109A  LEU      5.9     0.7    -      -       -      +
    110A  HIS*     3.8    13.9    +      -       +      +
    133A  LEU*     3.5    18.6    -      -       +      +
    157A  TYR*     3.2    25.2    +      -       +      +
    238A  PHE      5.3     0.7    -      -       -      +
    239A  VAL*     3.8    26.9    -      -       +      -
    153D  ILE*     3.3    32.5    -      -       +      -
    154D  TYR      3.3     6.3    -      -       -      +
    155D  LEU*     4.2    10.1    -      -       +      -
    206D  GLY*     1.3    74.4    -      -       -      +
    208D  PHE*     1.3    72.0    +      -       -      +
    241D  LEU*     4.1    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 208 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  HIS*     3.9    24.2    -      +       -      -
    133A  LEU*     4.0     7.0    -      -       -      -
    235A  PHE*     5.8     0.4    -      +       -      -
    153D  ILE*     3.4     0.8    -      -       -      -
    154D  TYR*     2.9    32.5    +      -       -      +
    156D  LEU*     4.4    10.3    -      -       +      -
    184D  LEU*     3.5    57.0    -      -       +      -
    185D  PHE*     3.5    24.9    -      +       +      -
    206D  GLY*     3.3    34.5    -      -       -      -
    207D  VAL*     1.3    80.0    -      -       -      +
    209D  HIS*     1.3    63.2    +      -       -      +
    210D  LEU*     3.4    21.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 209 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  LEU*     3.9    24.6    -      -       +      +
    151D  THR*     4.0    16.9    -      -       +      +
    152D  GLY*     3.3    26.1    +      -       -      -
    153D  ILE*     4.0    15.2    -      -       +      +
    175D  ARG*     3.7    18.7    +      -       -      -
    208D  PHE*     1.3    71.4    -      -       -      +
    210D  LEU*     1.3    70.3    +      -       -      +
    211D  HIS*     4.2     6.7    +      +       +      -
----------------------------------------------------------
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Residues in contact with LEU 210 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139D  LEU*     5.0     0.7    -      -       +      -
    148D  VAL*     4.1    19.3    -      -       +      -
    151D  THR*     3.4     6.2    -      -       -      +
    152D  GLY      2.9    31.9    +      -       -      +
    154D  TYR*     3.7    39.0    -      -       +      -
    156D  LEU*     4.6     5.4    -      -       +      -
    175D  ARG*     3.8    19.1    -      -       -      +
    184D  LEU*     4.4     6.7    -      -       +      -
    208D  PHE*     4.0    18.8    -      -       +      +
    209D  HIS*     1.3    83.4    -      -       -      +
    211D  HIS*     1.3    60.0    +      -       -      +
    214D  ASP*     4.0     2.0    -      -       -      +
    216D  ILE*     4.0    24.5    -      -       +      -
    238D  PHE*     4.3    16.6    -      -       +      -
----------------------------------------------------------
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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