Contacts of the strand formed by residues 185 - 198 (chain A) in PDB entry 1UIR


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 185 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  ARG*     3.9    14.3    +      -       -      -
    152A  TYR      3.2    16.2    -      -       -      +
    153A  ASP      3.9    15.7    -      -       -      +
    155A  VAL*     3.7    23.3    -      -       +      -
    181A  VAL*     3.9    10.5    -      -       +      +
    182A  LYS*     3.1    19.6    +      -       +      +
    183A  ALA      3.2     2.2    -      -       -      +
    184A  HIS*     1.3    78.3    -      -       -      +
    186A  ASN*     1.3    70.7    +      -       -      +
    189A  GLY*     4.1    15.9    -      -       -      +
    190A  VAL      4.0    14.4    -      -       -      +
    191A  MET*     4.6     3.6    -      -       +      -
    217A  PHE*     3.9    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  ARG*     4.8     8.7    +      -       -      -
    151A  ARG*     3.0    46.6    -      -       -      +
    152A  TYR*     2.7    23.6    +      -       -      +
    153A  ASP*     3.4    26.3    +      -       -      +
    185A  LEU*     1.3    78.5    -      -       -      +
    187A  PRO*     1.3    78.3    -      -       +      +
    189A  GLY*     2.9    15.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  HIS*     5.3     2.3    +      -       -      -
    151A  ARG*     4.1    21.5    -      -       -      +
    153A  ASP*     5.4     0.5    -      -       -      +
    186A  ASN*     1.3    94.1    -      -       +      +
    188A  GLY*     1.3    59.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 188 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  HIS*     3.4    21.8    +      -       -      -
     76A  PRO*     5.3     1.6    -      -       -      +
    186A  ASN      3.3     0.4    +      -       -      -
    187A  PRO*     1.3    72.7    -      -       -      +
    189A  GLY*     1.3    63.3    +      -       -      +
    242A  ALA*     3.3    30.7    -      -       -      +
    243A  PHE*     3.7    14.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 189 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  HIS*     4.3     1.3    -      -       -      -
    153A  ASP*     3.1    19.1    -      -       -      -
    185A  LEU*     4.1    16.4    -      -       -      +
    186A  ASN      2.9    18.3    +      -       -      -
    187A  PRO      3.2     0.4    +      -       -      -
    188A  GLY*     1.3    79.9    -      -       -      +
    190A  VAL*     1.3    59.0    +      -       -      -
    240A  SER*     2.8    25.5    +      -       -      -
    241A  ASP      4.7     0.7    +      -       -      -
    242A  ALA*     4.6     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 190 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  ALA*     3.4    33.0    -      -       +      +
     74A  THR*     4.2     8.5    -      -       +      -
     75A  HIS*     4.1     6.5    -      -       +      -
    153A  ASP      2.9     6.7    +      -       -      -
    154A  VAL*     3.2    20.7    -      -       +      +
    155A  VAL      3.1    20.3    +      -       -      -
    185A  LEU*     4.0     5.6    -      -       -      +
    188A  GLY      4.1     2.0    -      -       -      +
    189A  GLY*     1.3    79.7    -      -       -      +
    191A  MET*     1.3    62.6    +      -       -      +
    238A  LEU*     5.6     1.6    -      -       +      -
    239A  ALA      3.6     6.5    -      -       -      +
    240A  SER*     3.9     8.5    -      -       -      +
    243A  PHE*     3.2    38.6    -      -       +      -
    245A  PRO*     5.0     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 191 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  ALA*     4.5     2.9    -      -       -      -
    155A  VAL*     3.2    15.7    -      -       +      +
    157A  ILE*     3.9    14.4    -      -       +      -
    178A  TYR*     4.0    21.5    -      -       +      -
    181A  VAL*     4.2    19.1    -      -       +      -
    185A  LEU*     4.6     2.9    -      -       +      -
    190A  VAL*     1.3    75.7    -      -       -      +
    192A  GLY*     1.3    74.5    +      -       -      +
    193A  MET*     3.9    25.1    -      -       -      +
    213A  VAL*     4.2    11.7    -      -       +      -
    217A  PHE*     4.1    28.5    -      -       +      -
    237A  LEU*     4.5     1.6    -      -       +      -
    238A  LEU*     3.3     6.6    -      -       -      +
    239A  ALA*     2.9    41.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  LEU      4.8     5.6    -      -       -      -
     71A  ALA*     4.0    12.2    -      -       -      +
    155A  VAL      2.8     8.3    +      -       -      +
    156A  ILE*     3.2    11.1    -      -       -      +
    157A  ILE      2.8    23.7    +      -       -      -
    191A  MET*     1.3    77.6    -      -       -      +
    193A  MET*     1.3    61.7    +      -       -      +
    223A  TYR*     5.4     0.2    -      -       -      -
    237A  LEU      3.5     7.0    -      -       -      -
    238A  LEU*     4.0    12.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  LEU*     3.9    10.5    +      -       -      +
    157A  ILE*     3.2    30.3    -      -       +      +
    173A  TYR*     4.4     9.2    -      -       +      -
    178A  TYR*     3.5    27.4    -      -       +      +
    191A  MET*     3.9    18.8    -      -       -      -
    192A  GLY*     1.3    75.7    -      -       -      +
    194A  GLN*     1.3    73.2    +      -       -      +
    195A  THR*     3.4     9.0    -      -       -      +
    209A  VAL*     3.8    12.6    -      -       +      -
    213A  VAL*     4.0    11.9    -      -       -      -
    223A  TYR*     4.8     1.8    +      -       -      -
    236A  PHE*     3.1     8.4    -      -       -      +
    237A  LEU*     3.1    55.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  TYR*     3.3    26.5    -      -       +      +
     67A  LEU*     3.6     5.3    -      -       +      +
    157A  ILE*     3.3     7.5    +      -       -      +
    158A  ASP*     4.4     0.4    -      -       -      +
    159A  LEU      2.5    38.0    +      -       -      +
    160A  THR*     4.0     1.9    -      -       -      -
    161A  ASP*     3.3    17.2    -      -       -      +
    173A  TYR*     4.1     7.8    +      -       -      -
    193A  MET*     1.3    90.2    -      -       -      +
    195A  THR*     1.3    57.3    +      -       -      +
    196A  GLY      2.9    26.2    -      -       -      +
    234A  PHE*     3.1    28.6    -      -       -      -
    236A  PHE*     3.5    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  TYR*     5.7     2.5    -      -       -      -
    193A  MET*     3.4     9.7    +      -       -      +
    194A  GLN*     1.3    75.7    -      -       -      +
    196A  GLY*     1.3    60.2    +      -       -      +
    205A  VAL*     4.4     1.3    -      -       -      -
    206A  HIS*     3.0    50.3    +      -       +      +
    209A  VAL*     3.1    43.3    -      -       +      -
    235A  GLY      2.7    12.4    +      -       -      -
    237A  LEU*     3.3    28.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161A  ASP*     3.3    24.4    +      -       -      -
    173A  TYR*     5.9     1.0    +      -       -      -
    194A  GLN*     2.9    17.1    +      -       -      +
    195A  THR*     1.3    80.0    -      -       -      +
    197A  MET*     1.3    66.9    +      -       -      +
    205A  VAL*     4.2     4.9    -      -       -      -
    206A  HIS*     4.2     1.0    -      -       -      +
    234A  PHE*     3.7     6.5    -      -       -      -
    235A  GLY*     2.8    27.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  HIS*     5.3     4.9    -      -       +      -
     11A  VAL      3.7    23.3    -      -       -      +
     12A  THR*     5.1     2.0    -      -       +      -
    161A  ASP*     3.9    10.4    +      -       -      +
    196A  GLY*     1.3    77.9    -      -       -      +
    198A  ILE*     1.3    65.2    +      -       -      +
    199A  LEU*     4.2    23.9    +      -       +      +
    205A  VAL*     4.8     9.0    +      -       +      +
    206A  HIS*     4.1    12.6    +      -       -      +
    232A  LEU*     4.1    26.0    -      -       +      -
    233A  ASN      3.6     9.0    -      -       -      +
    234A  PHE*     3.6    28.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  MET*     1.3    78.0    -      -       -      +
    199A  LEU*     1.3    73.4    +      -       -      +
    200A  LEU      5.2     1.3    -      -       -      +
    206A  HIS*     4.2    19.5    -      -       +      +
    224A  LYS*     3.8    23.8    -      -       +      -
    232A  LEU*     5.6     1.4    -      -       -      +
    233A  ASN*     2.8    37.3    +      -       +      +
    234A  PHE      4.0     1.3    -      -       -      -
    235A  GLY*     3.6    30.7    -      -       -      +
    282A  LEU*     4.0    32.8    -      -       +      -
    226B  HIS*     5.6     0.9    -      -       -      -
    228B  PRO*     5.9     1.0    -      -       -      +
----------------------------------------------------------
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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