Contacts of the strand formed by residues 266 - 273 (chain A) in PDB entry 1TUB


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 HIS 266 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199A  ASP      3.8     4.8    +      -       -      +
    200A  CYS*     3.2    34.0    -      -       -      +
    201A  ALA*     3.4     4.2    +      -       -      -
    259A  LEU      4.6     1.8    -      -       -      +
    260A  VAL*     5.0     7.5    -      -       +      +
    261A  PRO*     4.3    23.2    -      -       +      +
    262A  TYR*     3.5    22.1    +      +       +      +
    264A  ARG*     2.3    42.2    +      -       +      -
    265A  GLY*     1.3    76.8    -      -       -      -
    267A  PHE*     1.3    65.7    -      +       -      +
    268A  PRO*     3.7     1.4    -      -       -      +
    380A  ASN*     4.3     9.6    -      -       +      +
    428A  LEU*     4.3     0.4    -      -       +      +
    432A  TYR*     2.3    57.4    -      +       -      -
    435A  VAL*     5.9     4.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 267 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  PHE*     4.9    10.8    -      +       -      -
    190A  THR*     4.7    11.7    -      -       +      -
    193A  THR*     5.3     8.7    -      -       -      -
    194A  THR*     5.7     2.9    -      -       -      -
    201A  ALA*     4.6    13.0    -      -       +      -
    203A  MET*     5.6     7.2    -      -       +      -
    264A  ARG      4.5     0.4    -      -       -      -
    265A  GLY*     2.9    25.4    -      -       -      -
    266A  HIS*     1.3    77.2    -      +       -      +
    268A  PRO*     1.3    72.3    -      -       +      +
    379A  SER      3.6     2.3    -      -       -      +
    380A  ASN*     2.2    30.2    -      -       -      +
    384A  ILE*     4.0    16.1    -      -       +      +
    388A  TRP*     2.9    50.7    -      +       +      -
    428A  LEU*     4.2    14.4    -      -       +      -
    432A  TYR*     3.7    21.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 268 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201A  ALA*     1.6    45.1    -      -       +      +
    202A  PHE*     3.6    18.8    -      -       +      +
    203A  MET*     4.0    17.5    +      -       +      +
    259A  LEU*     4.0    15.9    -      -       +      -
    266A  HIS      3.6     3.1    -      -       -      +
    267A  PHE*     1.3   103.1    -      -       +      +
    269A  LEU*     1.2    73.2    +      -       -      +
    379A  SER      2.9    14.6    -      -       -      +
    380A  ASN*     3.6     4.9    -      -       -      +
    384A  ILE*     4.6     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 269 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  PHE*     5.1     0.9    -      -       -      -
    203A  MET*     5.0     3.4    -      -       +      -
    268A  PRO*     1.2    81.5    -      -       -      +
    270A  ALA*     1.4    54.9    +      -       -      +
    271A  THR*     5.4     5.2    -      -       +      -
    301A  GLN*     3.9    26.7    -      -       +      +
    302A  MET*     6.2     0.7    -      -       +      +
    303A  VAL*     3.8    28.9    -      -       +      +
    305A  CYS*     3.9    10.3    -      -       +      -
    307A  PRO*     6.3     0.9    -      -       +      -
    312A  TYR*     6.1     0.9    -      -       +      -
    377A  MET      2.3    22.2    -      -       -      +
    378A  LEU*     2.6    23.3    -      -       -      +
    379A  SER*     2.9    24.4    +      -       -      +
    381A  THR*     3.8    22.9    -      -       +      +
    384A  ILE*     3.4    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 270 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  PHE*     5.3     2.2    -      -       +      -
    203A  MET      4.2    12.6    +      -       -      +
    234A  ILE*     3.3    43.3    -      -       +      -
    269A  LEU*     1.4    74.3    -      -       -      +
    271A  THR*     1.3    61.7    -      -       -      +
    302A  MET*     2.4    44.2    +      -       +      +
    376A  CYS*     6.3     0.2    -      -       -      -
    377A  MET      3.0     3.6    -      -       -      -
    378A  LEU*     3.9     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 271 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  ILE*     4.7     2.7    -      -       -      +
    269A  LEU*     5.2     4.3    -      -       +      -
    270A  ALA*     1.3    80.8    -      -       -      +
    272A  TYR*     1.3    55.1    +      -       -      +
    295A  CYS*     3.4    35.6    -      -       -      +
    300A  ASN*     4.2     9.0    -      -       -      -
    301A  GLN*     4.5    17.3    -      -       +      -
    375A  VAL      2.6    21.1    -      -       -      +
    376A  CYS*     2.9    12.1    -      -       -      +
    377A  MET*     2.3    62.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 272 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  LEU*     4.8    12.2    -      -       +      +
    233A  GLN*     3.9    38.6    +      -       +      -
    234A  ILE*     4.4    17.3    -      -       +      +
    236A  SER*     6.0     1.1    -      -       -      -
    237A  SER*     5.8     1.3    -      -       -      -
    271A  THR*     1.3    73.7    -      -       -      +
    273A  ALA*     1.3    58.8    +      -       -      +
    274A  PRO*     1.6    60.4    -      -       +      +
    275A  VAL*     2.7    31.3    -      -       +      +
    300A  ASN*     3.3    14.7    +      -       -      +
    302A  MET*     5.3     1.4    -      -       -      -
    320A  ARG*     5.4     7.6    -      -       -      -
    360A  PRO*     3.9    19.8    -      -       +      +
    361A  THR      5.1     3.5    +      -       -      -
    362A  VAL*     5.5     2.4    -      -       -      +
    371A  VAL*     5.1     1.0    -      -       -      +
    374A  ALA*     4.5     7.9    -      -       +      -
    375A  VAL      3.2     6.1    -      -       -      -
    376A  CYS*     4.7    11.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 273 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271A  THR      3.8     0.6    -      -       -      -
    272A  TYR*     1.3    74.5    -      -       -      +
    274A  PRO*     1.2    68.4    -      -       +      +
    275A  VAL*     3.4     8.8    +      -       -      +
    276A  ILE*     5.7     0.3    -      -       -      +
    286A  LEU*     5.0     7.8    -      -       +      +
    291A  ILE*     3.1    24.9    -      -       +      +
    294A  ALA*     2.8    39.2    -      -       +      +
    295A  CYS      3.9     3.1    -      -       -      +
    300A  ASN*     3.7     9.5    -      -       -      +
    375A  VAL*     3.1    10.8    +      -       +      -
----------------------------------------------------------
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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