Contacts of the strand formed by residues 180 - 189 (chain B) in PDB entry 1TW8


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 180 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  LYS*     3.1     4.4    -      -       -      -
     20B  VAL*     2.8    54.1    +      -       +      +
     22B  ARG*     4.2     6.1    -      -       +      -
     23B  PRO*     6.2     1.6    -      -       +      -
     28B  LEU*     3.7    23.6    -      -       +      -
     33B  ALA      4.7     6.1    -      -       -      +
     34B  GLY*     4.5     9.0    -      -       -      -
     36B  PRO*     6.2     0.2    -      -       +      -
     37B  PHE*     3.2    11.4    -      -       +      -
    173B  TRP*     3.3    53.6    -      -       +      -
    174B  GLU      3.8     4.9    -      -       -      -
    175B  LEU*     3.9     8.7    -      -       +      -
    178B  GLU      3.7     9.4    -      -       -      +
    179B  ASP*     1.3    78.8    -      -       -      +
    181B  VAL*     1.3    59.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 181 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  GLY*     3.3    22.2    -      -       -      +
     18B  GLN      3.1    17.0    -      -       -      +
     19B  LYS*     4.7     4.9    -      -       +      -
    173B  TRP*     4.0     3.6    -      -       -      -
    174B  GLU*     3.2    35.5    +      -       +      +
    176B  ASN*     4.3    20.6    -      -       +      +
    179B  ASP      4.0     0.6    +      -       -      -
    180B  LEU*     1.3    73.3    -      -       -      +
    182B  CYS*     1.3    70.9    +      -       -      +
    183B  VAL*     3.1    15.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 182 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  LEU*     3.1    40.8    -      -       +      +
     16B  ILE*     3.5     8.2    -      -       -      +
     17B  GLY      2.9    26.2    +      -       -      -
     18B  GLN      3.2     6.8    +      -       -      +
     37B  PHE*     3.8    20.8    -      -       +      -
    171B  VAL*     3.9    14.6    -      -       +      -
    172B  ASP      3.2    11.0    -      -       -      +
    173B  TRP*     4.0     3.6    -      -       -      +
    181B  VAL*     1.3    72.9    -      -       -      +
    183B  VAL*     1.3    57.9    +      -       -      +
    184B  SER      3.1    27.1    -      -       -      -
    185B  THR*     4.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  ILE*     3.9    19.2    -      -       -      +
    133B  ILE*     3.7    30.7    -      -       +      -
    172B  ASP      2.8    10.9    +      -       -      +
    174B  GLU*     3.6    32.3    -      -       +      +
    181B  VAL*     3.2    20.0    -      -       +      +
    182B  CYS*     1.3    74.4    -      -       -      +
    184B  SER*     1.3    71.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 184 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  ILE*     4.2     9.6    -      -       -      -
    133B  ILE*     4.7     0.2    -      -       -      +
    171B  VAL*     4.0     0.2    -      -       -      -
    172B  ASP*     2.5    44.4    +      -       -      +
    182B  CYS*     3.1    15.3    -      -       -      -
    183B  VAL*     1.3    86.3    -      -       -      +
    185B  THR*     1.3    72.8    +      -       -      +
    213B  ARG*     3.6    11.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  TYR*     3.0    36.4    +      -       +      +
     11B  ILE*     6.3     0.2    -      -       +      -
     12B  ASN*     3.9    25.5    +      -       +      +
     15B  LEU*     3.9    21.0    -      -       +      +
    169B  LEU*     3.6    17.3    -      -       +      -
    170B  GLU      3.1    10.4    +      -       -      +
    171B  VAL*     4.5     1.6    -      -       -      -
    172B  ASP*     3.4     2.8    +      -       -      -
    182B  CYS*     4.1     4.9    -      -       -      -
    184B  SER*     1.3    86.1    +      -       -      +
    186B  SER*     1.3    72.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 186 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  TYR*     3.1     7.4    -      -       -      -
    168B  TYR      3.9     0.2    -      -       -      +
    169B  LEU*     3.3     5.5    -      -       -      +
    170B  GLU*     2.6    47.0    +      -       -      +
    172B  ASP*     4.7     1.0    +      -       -      -
    185B  THR*     1.3    83.9    +      -       -      +
    187B  PHE*     1.3    60.1    +      -       -      +
    212B  VAL*     3.9     3.3    -      -       -      +
    213B  ARG*     3.3    44.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 187 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  SER*     3.4    22.2    -      -       -      -
      4B  ILE*     4.0    30.1    -      -       +      -
      5B  LYS*     4.0    27.4    -      -       +      -
      8B  TYR*     3.5    31.2    +      +       +      -
    124B  GLU*     3.9     0.2    -      -       -      -
    126B  LEU*     4.2     2.2    -      -       +      -
    167B  ASN*     3.7    25.8    -      -       +      -
    168B  TYR      3.3    15.9    -      -       -      -
    169B  LEU*     4.5    12.6    -      -       +      -
    186B  SER*     1.3    75.7    -      -       -      +
    188B  ALA*     1.3    75.1    +      -       -      +
    189B  GLU*     3.8    24.7    -      -       +      -
    212B  VAL*     3.7     3.3    -      -       -      +
    217B  GLN*     5.0     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 188 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167B  ASN*     3.5     2.4    -      -       -      +
    168B  TYR*     2.8    40.1    +      -       +      +
    187B  PHE*     1.3    83.2    -      -       -      +
    189B  GLU*     1.3    63.0    +      -       -      +
    190B  LEU      3.9     0.3    +      -       -      -
    212B  VAL*     3.4    24.2    -      -       +      +
    215B  LEU*     3.8    24.7    -      -       +      +
    217B  GLN*     3.8    15.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 189 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  SER*     4.8    11.4    +      -       -      -
      5B  LYS*     5.0    10.4    +      -       -      +
    165B  ASP*     4.7    10.2    -      -       -      +
    167B  ASN*     3.1    29.4    +      -       -      +
    187B  PHE*     3.8    16.8    -      -       +      -
    188B  ALA*     1.3    73.9    -      -       -      +
    190B  LEU*     1.3    67.1    +      -       -      +
    191B  PHE*     4.6     2.2    -      -       +      +
    192B  LYS*     3.0    46.4    +      -       +      +
    193B  SER*     3.6     1.2    +      -       -      -
    215B  LEU*     4.5     1.7    -      -       -      +
    217B  GLN*     2.9    32.9    +      -       -      +
----------------------------------------------------------
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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