Contacts of the strand formed by residues 89 - 96 (chain Y) in PDB entry 1T6B


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 ALA 89 (chain Y).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83Y  ILE*     4.8     0.2    -      -       +      -
     84Y  VAL      3.3     8.3    -      -       -      +
     85Y  PHE*     4.2     1.8    -      -       +      -
     88Y  GLN*     1.3    81.4    +      -       -      +
     90Y  THR*     1.3    66.3    +      -       -      +
    122Y  GLU*     3.3    44.2    -      -       +      +
    123Y  GLY*     3.7     6.3    -      -       -      +
    126Y  LEU*     3.6    17.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 90 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83Y  ILE*     3.5     2.1    -      -       -      -
     84Y  VAL*     2.8    45.5    +      -       -      +
     88Y  GLN*     5.0     5.9    -      -       -      +
     89Y  ALA*     1.3    80.5    +      -       -      +
     91Y  ILE*     1.3    76.2    +      -       -      +
     92Y  ILE*     3.4     9.5    +      -       +      +
    126Y  LEU*     3.9     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 91 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81Y  SER*     4.4     2.2    -      -       -      +
     82Y  PHE      3.8     4.9    -      -       -      +
     83Y  ILE*     4.4     4.9    -      -       +      +
     90Y  THR*     1.3    80.0    -      -       -      +
     92Y  ILE*     1.3    60.4    +      -       -      +
     93Y  LEU      3.6     4.7    -      -       -      +
     94Y  PRO*     3.4    41.7    -      -       +      +
    126Y  LEU*     3.9    36.2    -      -       +      +
    130Y  GLN*     4.0    29.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 92 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82Y  PHE*     2.9    22.2    +      -       +      +
     84Y  VAL*     3.7    37.5    -      -       +      -
     90Y  THR*     3.4     8.0    +      -       +      +
     91Y  ILE*     1.3    76.5    -      -       -      +
     93Y  LEU*     1.3    59.5    +      -       -      +
     94Y  PRO*     4.3     3.9    -      -       -      +
    105Y  GLY*     3.9    11.8    -      -       -      +
    108Y  ASP*     3.6    43.8    -      -       +      +
    109Y  LEU*     4.5     6.3    -      -       +      -
    112Y  VAL*     5.1    10.3    -      -       +      -
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Residues in contact with LEU 93 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80Y  LEU      4.0    12.6    -      -       -      +
     81Y  SER*     2.7    26.7    +      -       -      -
     82Y  PHE*     3.0    56.5    +      -       +      +
     91Y  ILE*     3.6     3.6    -      -       -      -
     92Y  ILE*     1.3    80.4    -      -       -      +
     94Y  PRO*     1.3    68.4    -      -       +      +
     96Y  THR*     3.6    21.8    -      -       +      -
    101Y  LYS*     3.6    26.5    -      -       +      +
    102Y  ILE*     3.9    25.4    -      -       +      -
    105Y  GLY*     4.4     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 94 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80Y  LEU      3.5     1.2    -      -       -      +
     91Y  ILE*     3.4    17.6    -      -       +      +
     92Y  ILE      4.3     3.8    -      -       -      +
     93Y  LEU*     1.3    91.2    -      -       +      +
     95Y  LEU*     1.3    72.0    +      -       -      +
     96Y  THR*     3.1    17.9    +      -       -      +
    130Y  GLN*     3.5     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 95 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44Y  ASP*     3.6    26.2    -      -       +      +
     45Y  LEU      4.3     1.3    -      -       -      +
     46Y  TYR*     3.4    39.0    -      -       +      +
     79Y  ARG*     3.6    50.2    -      -       +      +
     80Y  LEU*     3.2    13.7    -      -       -      -
     81Y  SER*     3.5     5.8    -      -       -      +
     94Y  PRO*     1.3    74.0    -      -       -      +
     96Y  THR*     1.3    61.0    +      -       -      +
    130Y  GLN*     2.7    21.6    +      -       +      +
    134Y  ALA*     4.4     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 96 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79Y  ARG*     3.2    11.1    -      -       -      +
     80Y  LEU      2.8    27.4    +      -       -      +
     93Y  LEU*     3.6    27.4    -      -       +      -
     94Y  PRO*     3.4    12.1    -      -       -      +
     95Y  LEU*     1.3    79.7    -      -       -      +
     97Y  GLY*     1.3    61.1    +      -       -      +
     98Y  ASP*     3.3    15.5    +      -       -      +
    101Y  LYS*     3.4    35.0    +      -       +      +
    102Y  ILE*     3.7     8.4    -      -       +      +
----------------------------------------------------------
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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