Contacts of the strand formed by residues 1033 - 1038 (chain B) in PDB entry 2IUI


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 THR1033 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1026B  LEU*     3.7    11.5    -      -       +      +
   1029B  THR*     3.7    25.4    -      -       +      +
   1030B  ALA*     2.8    25.3    +      -       -      +
   1031B  ASP      3.4     0.6    +      -       -      -
   1032B  GLY*     1.3    77.7    -      -       -      +
   1034B  PHE*     1.3    63.6    +      -       -      +
   1051B  LEU*     3.5     0.5    -      -       -      -
   1052B  ARG*     2.8    28.1    +      -       -      +
   1105B  TYR*     3.0    28.3    -      -       +      +
   1106B  PRO      5.2     0.4    -      -       -      -
   1107B  VAL*     3.4    25.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE1034 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1012B  TRP*     4.0    20.0    -      +       +      +
   1026B  LEU*     4.7     2.2    -      -       -      -
   1032B  GLY      3.4    14.6    -      -       -      +
   1033B  THR*     1.3    77.2    -      -       -      +
   1035B  LEU*     1.3    66.2    +      -       -      +
   1036B  VAL*     4.7     0.7    -      -       +      -
   1049B  LEU*     3.8    22.9    -      -       +      -
   1050B  THR      3.2    13.7    -      -       -      +
   1051B  LEU*     4.2     9.0    -      -       +      -
   1084B  ILE*     3.6    24.0    -      -       +      -
   1088B  ARG*     3.7    20.0    -      -       -      -
   1103B  LEU*     3.6    29.2    -      -       +      -
   1105B  TYR      3.0    10.6    +      -       -      -
   1106B  PRO*     3.7    34.6    -      -       +      +
   1107B  VAL*     3.0    27.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU1035 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1012B  TRP      3.5    13.7    -      -       -      +
   1014B  TRP*     3.9    16.8    -      -       +      +
   1017B  ILE*     4.4     5.4    -      -       +      -
   1022B  VAL*     3.8    40.6    -      -       +      -
   1025B  LYS*     3.8    32.5    -      -       +      -
   1026B  LEU*     4.5     3.4    -      -       +      -
   1034B  PHE*     1.3    78.6    -      -       -      +
   1036B  VAL*     1.3    81.5    +      -       -      +
   1037B  ARG*     4.2     3.8    -      -       +      +
   1049B  LEU*     3.6     1.9    -      -       -      +
   1050B  THR*     3.0    34.3    +      -       -      +
   1107B  VAL*     4.0    19.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1036 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1012B  TRP*     3.0    38.5    +      -       +      -
   1013B  TYR*     3.4    14.2    -      -       +      -
   1014B  TRP*     2.9    28.6    +      -       -      -
   1034B  PHE*     4.7     1.8    -      -       +      -
   1035B  LEU*     1.3    82.8    -      -       -      +
   1037B  ARG*     1.3    62.7    +      -       -      +
   1047B  TYR*     3.9    23.6    -      -       +      -
   1048B  THR      3.4     9.2    -      -       -      +
   1049B  LEU*     4.1     8.7    -      -       +      -
   1062B  ILE*     4.1     9.6    -      -       +      -
   1080B  VAL*     4.4     9.4    -      -       +      -
   1084B  ILE*     4.0    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG1037 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1013B  TYR*     4.6     0.9    -      -       -      -
   1015B  GLY      3.4    14.8    -      -       -      +
   1017B  ILE*     3.6    32.4    +      -       +      +
   1018B  SER      4.6     0.4    -      -       -      -
   1019B  ARG*     3.6    26.1    -      -       -      +
   1022B  VAL*     3.8    24.0    -      -       +      +
   1035B  LEU*     4.2     5.5    -      -       +      +
   1036B  VAL*     1.3    74.8    -      -       -      +
   1038B  ASP*     1.3    89.3    +      -       -      +
   1040B  SER*     3.9     5.5    -      -       -      +
   1047B  TYR*     3.3    11.5    -      -       -      +
   1048B  THR*     2.8    54.4    +      -       -      +
   1050B  THR*     4.5     5.5    +      -       -      +
   1059B  LEU*     3.7     9.9    -      -       -      +
   1204D  PTR      2.8    42.2    +      -       -      -
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Residues in contact with ASP1038 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1013B  TYR*     2.8    23.4    +      -       -      -
   1015B  GLY*     3.0    28.1    +      -       -      +
   1016B  ASP*     3.1    23.4    +      -       -      +
   1017B  ILE      5.1     1.9    -      -       -      +
   1037B  ARG*     1.3    98.7    +      -       -      +
   1039B  ALA*     1.3    67.5    +      -       -      +
   1040B  SER*     4.7     0.2    -      -       -      -
   1046B  ASP      3.9     6.5    -      -       -      +
   1047B  TYR*     3.3    16.0    -      -       -      -
   1048B  THR      4.2     0.2    -      -       -      -
----------------------------------------------------------
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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