Contacts of the strand formed by residues 188 - 197 (chain D) in PDB entry 3T0E


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 188 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149D  GLY      3.1    20.3    +      -       -      -
    150D  PHE*     2.9    35.5    +      -       +      -
    151D  TYR*     4.8     8.2    -      +       -      -
    152D  PRO*     4.1     7.4    -      -       +      -
    153D  ASP*     3.3    49.6    +      -       +      -
    176D  PRO*     4.4    12.3    -      -       +      -
    177D  LEU*     3.4     9.0    -      -       -      +
    178D  LYS*     3.1    56.2    -      -       +      -
    179D  GLU*     3.2     2.6    -      -       -      +
    184D  ASN      5.7     1.2    +      -       -      -
    186D  SER*     4.8    15.2    +      -       -      -
    187D  ARG*     1.3    76.4    -      -       -      +
    189D  SER*     1.3    67.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 189 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152C  TYR*     5.3     0.2    -      -       -      -
    174C  TRP*     3.5    28.9    -      -       -      -
    147D  ALA      3.5     6.1    -      -       -      -
    148D  THR*     2.9    23.6    -      -       -      +
    150D  PHE*     3.4     3.8    -      -       -      -
    176D  PRO*     3.4     4.7    -      -       -      +
    177D  LEU*     3.0    40.3    +      -       -      +
    179D  GLU*     3.1    15.7    +      -       -      +
    188D  TYR*     1.3    78.7    +      -       -      +
    190D  LEU*     1.3    60.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 190 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174C  TRP*     5.7     0.2    -      -       -      -
    145D  CYS      3.7     1.7    -      -       -      +
    146D  LEU*     3.6     3.8    -      -       -      +
    147D  ALA*     3.0    38.9    +      -       +      +
    150D  PHE*     4.3    10.3    -      -       +      -
    155D  VAL*     4.3    22.7    -      -       +      +
    157D  LEU*     4.1    33.4    -      -       +      +
    172D  THR*     4.0    11.9    -      -       +      -
    173D  ASP*     3.9    31.6    -      -       +      +
    176D  PRO*     4.0    26.9    -      -       +      -
    189D  SER*     1.3    75.4    -      -       -      +
    191D  SER*     1.3    65.0    +      -       -      +
    192D  SER      4.3     0.2    +      -       -      -
    212D  VAL*     6.2     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 191 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154C  THR*     3.8     5.6    -      -       -      +
    172C  VAL*     3.5    24.6    -      -       -      +
    174C  TRP*     4.6     6.0    -      -       -      -
    144D  VAL*     5.3     4.5    -      -       -      -
    145D  CYS      3.2     7.2    -      -       -      -
    146D  LEU*     3.8    20.2    -      -       -      -
    172D  THR*     4.8     0.9    -      -       -      -
    173D  ASP*     2.2    63.1    +      -       -      +
    190D  LEU*     1.3    78.6    -      -       -      +
    192D  SER*     1.3    60.4    +      -       -      +
    193D  ARG*     3.6     6.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 192 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144D  VAL*     3.7     1.0    -      -       -      +
    145D  CYS      2.9    32.3    +      -       -      -
    157D  LEU*     3.5    25.2    -      -       -      +
    159D  TRP*     3.4    27.3    +      -       -      -
    170D  VAL*     4.2     1.4    -      -       -      +
    171D  SER      3.9     3.8    -      -       -      -
    172D  THR*     2.2    36.5    +      -       -      +
    191D  SER*     1.3    74.5    -      -       -      +
    193D  ARG*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 193 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133C  LEU*     4.1    19.3    -      -       -      -
    154C  THR*     4.8     0.6    +      -       -      -
    157C  THR*     3.0    28.5    +      -       -      +
    159C  LEU*     5.8     2.9    -      -       +      -
    170C  SER*     2.9    48.9    +      -       -      +
    171C  ALA*     4.7     1.1    -      -       -      -
    172C  VAL*     3.9    17.8    -      -       +      +
    142D  THR*     4.6     9.4    -      -       +      -
    143D  LEU      4.0     5.6    -      -       -      +
    144D  VAL*     3.7    22.2    -      -       +      -
    159D  TRP*     4.4     2.0    -      -       -      -
    169D  GLY      3.2     2.3    -      -       -      +
    170D  VAL*     3.2     5.7    -      -       -      +
    171D  SER*     2.9    60.5    +      -       -      +
    172D  THR      4.9     0.4    -      -       -      -
    173D  ASP*     3.9     7.7    +      -       -      -
    191D  SER*     3.6    21.0    +      -       -      -
    192D  SER*     1.3    76.2    -      -       -      +
    194D  LEU*     1.3    59.6    +      -       -      +
    195D  ARG      5.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 194 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142D  THR*     4.5     1.3    -      -       -      -
    143D  LEU*     2.9    37.3    +      -       +      +
    159D  TRP*     3.7    49.2    -      -       +      +
    161D  VAL*     4.0    24.5    -      -       +      -
    166D  VAL*     4.3     5.2    -      -       +      -
    168D  SER      3.8    22.0    -      -       -      +
    169D  GLY      3.6     1.8    -      -       -      -
    170D  VAL*     3.9     9.4    -      -       +      -
    192D  SER      4.3     0.6    +      -       -      -
    193D  ARG*     1.3    75.7    -      -       -      +
    195D  ARG*     1.3    69.8    +      -       -      +
    196D  VAL*     4.2    12.1    -      -       +      -
    208D  PHE*     4.2    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 195 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135C  THR*     3.0    43.1    +      -       -      +
    136C  ASP*     3.2    24.2    +      -       -      -
    159C  LEU*     3.3    31.0    -      -       +      +
    161C  MET*     3.7    30.8    -      -       -      +
    166C  PHE*     4.3     1.7    -      -       -      -
    168C  SER*     4.2     6.6    +      -       -      -
    170C  SER*     5.4     0.6    -      -       -      -
    134D  GLU*     3.5    13.9    +      -       -      +
    138D  THR*     4.3     2.8    +      -       -      -
    140D  LYS*     3.6    23.1    -      -       +      +
    141D  ALA      3.4     7.4    -      -       -      +
    142D  THR*     2.5    32.0    +      -       +      +
    168D  SER      5.0     0.2    -      -       -      +
    169D  GLY*     3.3    20.9    +      -       -      -
    194D  LEU*     1.3    74.0    -      -       -      +
    196D  VAL*     1.3    73.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 196 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161C  MET*     4.2     9.4    -      -       -      -
    140D  LYS*     3.6     5.9    -      -       -      +
    141D  ALA*     2.7    57.3    +      -       +      +
    143D  LEU*     4.6     5.4    -      -       +      -
    161D  VAL*     5.4     2.7    -      -       +      -
    194D  LEU*     4.2    16.4    -      -       +      -
    195D  ARG*     1.3    79.0    -      -       -      +
    197D  SER*     1.3    64.3    +      -       -      +
    200D  PHE*     3.6    35.9    -      -       +      -
    201D  TRP*     4.2     5.2    -      -       +      -
    208D  PHE*     4.1    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 197 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161C  MET*     4.4     9.7    -      -       -      +
    164C  MET*     6.1     4.7    -      -       -      -
    139D  GLN      4.6     3.6    -      -       -      -
    140D  LYS*     4.7     1.6    -      -       -      +
    196D  VAL*     1.3    76.5    -      -       -      +
    198D  ALA*     1.3    68.7    +      -       -      +
    199D  THR*     4.1     3.4    +      -       -      -
    200D  PHE*     2.7    49.7    +      -       -      +
    201D  TRP      3.4     2.9    +      -       -      -
----------------------------------------------------------
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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