Contacts of the strand formed by residues 152 - 163 (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 GLY 152 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  ARG*     5.6     2.2    -      -       -      -
    150D  ASP      3.5     1.6    +      -       -      -
    151D  THR*     1.3    78.6    -      -       -      +
    153D  ILE*     1.3    60.2    +      -       -      -
    154D  TYR*     3.4    13.7    -      -       -      -
    209D  HIS*     3.3    11.4    -      -       -      -
    210D  LEU      2.9    32.1    +      -       -      +
    240D  LYS*     4.0    10.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 153 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  VAL*     4.2    17.3    -      -       +      -
    133A  LEU*     4.2    16.6    -      -       +      -
    134A  ARG      5.3     0.9    -      -       -      +
    135A  ARG*     3.4    56.9    -      -       +      +
    152D  GLY*     1.3    74.2    -      -       -      -
    154D  TYR*     1.3    59.6    +      -       -      +
    207D  VAL*     3.3    31.2    -      -       +      -
    208D  PHE      3.4     5.6    -      -       -      +
    209D  HIS*     4.0    24.2    -      -       +      +
    240D  LYS*     3.7     3.8    -      -       -      +
    241D  LEU*     2.9    31.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 154 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107D  SER*     5.1     3.5    +      -       -      -
    137D  ARG      5.3     0.2    +      -       -      -
    138D  GLY*     3.9    10.0    +      -       -      -
    139D  LEU*     3.6    34.8    -      -       +      -
    148D  VAL*     4.7     1.6    -      -       +      -
    150D  ASP*     2.6    35.2    +      -       -      +
    152D  GLY*     3.4    24.9    -      -       -      -
    153D  ILE*     1.3    73.9    -      -       -      +
    155D  LEU*     1.3    65.9    +      -       -      +
    156D  LEU*     3.6     3.1    +      -       +      +
    206D  GLY      3.7     0.2    -      -       -      +
    207D  VAL*     3.3     7.6    -      -       -      -
    208D  PHE*     2.9    33.4    +      -       -      +
    210D  LEU*     3.7    34.8    -      -       +      -
    238D  PHE*     4.3     7.6    -      +       +      -
    239D  VAL      3.3     5.8    -      -       -      +
    240D  LYS*     3.6    45.5    -      -       +      +
    241D  LEU*     4.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 155 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  LEU*     4.7    23.1    -      -       +      -
    157A  TYR*     5.4     4.0    -      -       +      -
    203A  TYR*     5.7     1.1    -      -       -      +
    239A  VAL*     5.8     0.2    -      -       +      -
    155B  LEU*     4.8    18.6    -      -       +      -
    241B  LEU*     6.4     0.4    -      -       +      -
    154D  TYR*     1.3    71.5    -      -       -      +
    156D  LEU*     1.3    66.6    +      -       -      +
    157D  TYR*     4.6    13.4    -      -       +      -
    205D  ALA*     4.6     8.3    -      -       +      -
    206D  GLY*     3.5    23.1    -      -       -      +
    207D  VAL*     4.2    10.8    -      -       +      -
    237D  GLY      3.8     0.5    -      -       -      +
    238D  PHE*     3.2     6.6    -      -       -      -
    239D  VAL*     2.8    55.0    +      -       +      +
    241D  LEU*     3.9    19.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 156 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154D  TYR*     3.6     3.3    +      -       +      +
    155D  LEU*     1.3    73.9    -      -       -      +
    157D  TYR*     1.3    64.6    +      -       -      +
    173D  VAL*     4.0    20.2    -      -       +      -
    184D  LEU*     3.7    30.1    -      -       +      -
    185D  PHE*     3.8    13.8    -      -       +      -
    205D  ALA*     3.1     4.2    -      -       -      +
    206D  GLY      2.8    36.2    +      -       -      +
    208D  PHE*     4.4     7.6    -      -       +      -
    210D  LEU*     4.6    10.3    -      -       +      -
    216D  ILE*     4.2     5.2    -      -       +      -
    236D  LEU*     3.8    26.9    -      -       +      -
    237D  GLY      3.4     4.5    -      -       -      +
    238D  PHE*     3.7    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 157 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155B  LEU*     5.8     2.9    -      -       +      -
    205B  ALA      3.9    11.0    -      -       -      -
    206B  GLY*     3.9     9.4    -      -       -      -
    207B  VAL*     3.1    41.6    +      -       +      +
    109D  LEU      4.6     0.7    +      -       -      -
    110D  HIS*     2.7    31.6    +      -       -      +
    155D  LEU*     4.6    16.2    -      -       +      -
    156D  LEU*     1.3    77.9    -      -       -      +
    158D  SER*     1.3    61.4    +      -       -      +
    203D  TYR*     3.3    25.1    -      +       +      +
    204D  SER      3.5     4.3    -      -       -      -
    205D  ALA*     3.6     7.6    -      -       +      -
    235D  PHE*     3.8    20.2    -      +       -      -
    236D  LEU*     3.5     7.6    -      -       -      +
    237D  GLY*     2.9    61.7    +      -       -      -
    238D  PHE      4.1     2.2    -      -       -      -
    239D  VAL*     4.8     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 158 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129D  TRP*     5.9     0.9    -      -       -      -
    157D  TYR*     1.3    76.3    -      -       -      +
    159D  GLN*     1.3    62.0    +      -       -      +
    160D  VAL*     4.6     0.9    -      -       -      +
    171D  GLN*     3.2    26.5    +      -       -      +
    173D  VAL*     3.9    12.4    -      -       -      +
    185D  PHE*     3.9    21.3    -      -       -      -
    203D  TYR*     3.4     3.7    -      -       -      -
    204D  SER      2.9    30.5    +      -       -      -
    218D  VAL*     4.1     9.9    -      -       -      +
    235D  PHE      3.6     8.2    +      -       -      -
    236D  LEU*     4.2     8.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 159 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  ARG      2.7    26.0    +      -       -      +
    203B  TYR      4.5     0.3    -      -       -      +
    204B  SER*     2.7    29.0    +      -       -      -
    129D  TRP*     5.1     0.2    -      -       -      -
    158D  SER*     1.3    73.1    -      -       -      +
    160D  VAL*     1.3    76.3    +      -       -      +
    201D  SER*     3.8    18.6    +      -       -      -
    202D  CYS      3.2    11.2    -      -       -      +
    203D  TYR*     3.7    13.9    -      -       +      +
    232D  HIS      4.0     0.4    +      -       -      -
    233D  GLY*     3.0    24.5    +      -       -      +
    234D  THR*     3.3     2.6    -      -       -      +
    235D  PHE*     2.9    62.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 160 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127D  VAL*     6.0     1.6    -      -       +      -
    129D  TRP*     5.7     2.0    -      -       +      -
    158D  SER*     4.6     3.6    -      -       -      +
    159D  GLN*     1.3    81.5    -      -       -      +
    161D  LEU*     1.3    63.5    +      -       -      +
    162D  PHE*     3.6    30.5    -      -       +      -
    171D  GLN*     3.6    35.9    -      -       +      +
    201D  SER*     3.4     0.9    -      -       -      -
    202D  CYS*     2.8    33.9    +      -       -      +
    218D  VAL*     4.7     5.4    -      -       +      -
    220D  ILE*     4.5     8.5    -      -       +      -
    227D  LEU*     3.8    26.9    -      -       +      -
    233D  GLY      3.8     2.9    -      -       -      -
    234D  THR*     3.8    14.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 161 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  ARG*     3.7    32.8    -      -       -      +
    188B  ILE*     3.5    26.5    -      -       +      -
    160D  VAL*     1.3    74.0    -      -       -      +
    162D  PHE*     1.3    70.0    +      -       -      +
    163D  HIS*     6.4     0.4    -      -       +      -
    199D  TYR*     5.1     7.9    -      -       +      -
    200D  ASN      3.6    22.4    -      -       -      +
    201D  SER*     3.9     6.5    -      -       -      +
    227D  LEU*     3.2     5.2    -      -       -      +
    228D  SER*     2.8    50.5    +      -       -      -
    233D  GLY*     3.5    24.4    +      -       -      +
    234D  THR*     3.2     5.1    +      -       -      -
     18S  LEU*     5.6     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 162 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160D  VAL*     3.6    37.2    -      -       +      -
    161D  LEU*     1.3    79.2    -      -       -      +
    163D  HIS*     1.3    61.1    +      -       -      +
    164D  ASP*     3.9     1.6    -      -       +      -
    169D  MET*     3.7    42.2    -      -       +      -
    170D  GLY*     3.5    40.6    -      -       -      -
    171D  GLN*     4.0     0.2    -      -       -      -
    189D  ARG*     5.6     1.3    -      -       +      -
    191D  MET*     4.0    17.3    -      -       +      -
    198D  ALA      4.3     0.2    -      -       -      -
    199D  TYR*     3.4     5.7    -      -       -      +
    200D  ASN*     2.9    39.0    +      -       +      +
    202D  CYS*     3.9    15.7    -      -       +      -
    220D  ILE*     3.9    13.5    -      -       +      -
    226D  LYS      3.5    10.1    -      -       -      +
    227D  LEU*     4.3     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 163 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161D  LEU      4.2     0.2    +      -       -      -
    162D  PHE*     1.3    72.2    -      -       -      +
    164D  ASP*     1.3    58.8    +      -       -      +
    195D  PRO*     2.9    30.6    -      -       +      +
    196D  ASP*     4.9     1.6    -      -       -      -
    198D  ALA      3.1    14.1    +      -       -      -
    199D  TYR*     3.3    45.3    +      +       +      -
    226D  LYS*     3.0    34.5    +      -       +      +
    227D  LEU*     4.8     0.9    -      -       -      +
    228D  SER      5.6     0.9    -      -       -      +
----------------------------------------------------------
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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