Contacts of the strand formed by residues 1033 - 1042 (chain B) in PDB entry 2OOQ


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 ILE1033 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    994B  TRP*     4.1    31.9    -      -       +      +
    995B  ARG*     4.7     6.1    -      -       +      +
    998B  TRP*     3.8    22.7    -      -       +      -
   1028B  GLU      3.8     0.5    -      -       -      +
   1029B  VAL*     3.3     2.4    -      -       -      +
   1030B  TYR*     2.9    43.9    +      -       -      +
   1031B  GLY      3.7     0.4    -      -       -      -
   1032B  ASP*     1.3    93.3    -      -       -      +
   1034B  LYS*     1.3    59.4    +      -       -      +
   1035B  VAL*     3.7    11.5    +      -       +      -
   1053B  VAL*     3.5    32.3    -      -       +      -
   1054B  GLN      3.5     2.2    -      -       -      +
   1055B  LYS*     3.7    28.0    -      -       +      +
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Residues in contact with LYS1034 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1027B  THR*     3.6    25.8    -      -       -      +
   1028B  GLU      3.6     3.4    -      -       -      -
   1029B  VAL*     4.2    16.4    -      -       +      -
   1032B  ASP      3.7     2.0    +      -       -      -
   1033B  ILE*     1.3    69.2    -      -       -      +
   1035B  VAL*     1.3    62.8    +      -       -      +
   1036B  THR*     3.8    11.6    +      -       -      +
   1052B  THR*     3.7     1.9    +      -       -      +
   1053B  VAL*     3.4     3.8    -      -       -      +
   1054B  GLN*     2.7    54.2    +      -       +      +
   1056B  LYS*     4.1    24.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1035 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    994B  TRP*     3.7    42.4    -      -       +      -
   1024B  PRO*     3.4    15.7    -      -       +      +
   1027B  THR*     3.2     3.8    +      -       -      -
   1028B  GLU      3.0    31.1    +      -       -      -
   1030B  TYR*     3.9    24.2    -      -       +      -
   1033B  ILE*     4.0     9.4    -      -       +      -
   1034B  LYS*     1.3    77.1    -      -       -      +
   1036B  THR*     1.3    64.0    +      -       -      +
   1051B  PHE*     3.5    35.2    -      -       +      -
   1052B  THR      3.3     4.3    -      -       -      +
   1053B  VAL*     4.4     3.8    -      -       +      -
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Residues in contact with THR1036 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1026B  ASP*     3.3    15.3    -      -       -      +
   1027B  THR*     3.0    21.4    +      -       -      -
   1034B  LYS*     3.8    15.6    +      -       -      +
   1035B  VAL*     1.3    73.6    -      -       -      +
   1037B  LEU*     1.3    75.1    +      -       -      +
   1038B  ILE*     3.4     7.1    +      -       +      +
   1051B  PHE*     3.0     7.3    -      -       -      -
   1052B  THR*     2.9    49.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1037 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1024B  PRO*     4.1    10.9    -      -       -      +
   1025B  ASP*     3.2    26.7    -      -       -      +
   1026B  ASP*     2.9    19.9    +      -       -      +
   1036B  THR*     1.3    78.1    -      -       -      +
   1038B  ILE*     1.3    61.9    +      -       -      +
   1039B  GLU*     3.5    26.9    -      -       -      +
   1040B  THR*     3.8    18.6    -      -       -      +
   1049B  ARG*     4.1    10.8    -      -       +      -
   1050B  THR      3.5     7.6    -      -       -      +
   1051B  PHE*     3.6    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1038 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1036B  THR*     3.4    16.1    +      -       +      +
   1037B  LEU*     1.3    80.0    -      -       -      +
   1039B  GLU*     1.3    59.9    +      -       +      +
   1050B  THR*     2.8    44.3    +      -       +      +
   1051B  PHE*     4.2     4.0    -      -       -      +
   1052B  THR*     4.1    28.3    -      -       +      -
   1063B  GLU*     4.0    12.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1039 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301B  B3P      2.9    55.8    +      -       -      +
   1037B  LEU*     3.5    10.4    -      -       -      +
   1038B  ILE*     1.3    82.8    -      -       +      +
   1040B  THR*     1.3    73.6    +      -       -      +
   1041B  GLU*     4.3     5.3    -      -       -      +
   1048B  ILE      4.6     0.2    -      -       -      -
   1049B  ARG*     3.5     0.5    -      -       -      -
   1050B  THR*     2.8    41.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR1040 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1037B  LEU*     3.8    23.2    -      -       -      +
   1039B  GLU*     1.3    83.9    +      -       -      +
   1041B  GLU*     1.3    61.0    +      -       -      +
   1042B  PRO*     3.4    18.9    -      -       +      +
   1047B  VAL*     3.6    24.5    -      -       +      -
   1048B  ILE      3.6     2.9    -      -       -      -
   1049B  ARG*     4.4    10.2    -      -       +      +
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Residues in contact with GLU1041 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301B  B3P      2.6    92.1    +      -       +      +
   1039B  GLU*     4.3     5.1    -      -       -      +
   1040B  THR*     1.3    72.8    -      -       -      +
   1042B  PRO*     1.3    60.1    -      -       +      +
   1043B  LEU*     3.3    28.8    -      -       +      +
   1047B  VAL*     3.5     2.8    -      -       -      -
   1048B  ILE*     2.8    43.4    +      -       +      +
   1090B  GLN*     4.6    10.5    +      -       -      +
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Residues in contact with PRO1042 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1040B  THR*     3.4    18.8    -      -       +      +
   1041B  GLU*     1.3    83.7    -      -       +      +
   1043B  LEU*     1.3    64.9    +      -       -      +
   1047B  VAL*     3.7    19.0    -      -       +      -
----------------------------------------------------------
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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