Contacts of the strand formed by residues 451 - 465 (chain T) in PDB entry 6O81


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 TRP 451 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262A  ASP      5.4     2.2    +      -       -      -
    263A  ASN*     4.8     4.2    -      -       -      +
    264A  PHE*     4.7     4.5    -      -       +      -
    265A  ASP*     3.5    43.1    -      -       +      -
     78T  THR*     6.0     6.7    -      -       -      -
     79T  ILE*     6.1     4.5    -      -       +      -
    139T  ASP*     3.6    14.9    -      -       -      +
    140T  ILE*     4.7     6.7    +      -       +      +
    403T  VAL*     4.8    12.3    -      -       +      -
    404T  LEU      4.7     1.8    -      -       -      -
    405T  MET*     3.7    56.0    -      -       +      +
    444T  SER*     4.5     6.1    -      -       -      -
    445T  ARG*     3.9    12.1    -      -       -      -
    446T  ARG*     3.1    55.6    -      -       +      +
    450T  HIS*     1.3    70.8    -      -       -      +
    452T  ARG*     1.3    60.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 452 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139T  ASP*     3.8    13.0    -      -       +      -
    381T  LEU*     5.5     4.9    -      -       -      +
    384T  VAL*     3.5    29.7    -      -       -      +
    444T  SER*     3.8     3.4    -      -       -      -
    445T  ARG*     2.8    40.1    +      -       -      +
    447T  VAL*     4.4    20.0    -      -       +      +
    448T  GLU      5.8     0.4    -      -       -      +
    450T  HIS*     3.3    27.3    +      -       +      +
    451T  TRP*     1.3    77.3    -      -       -      +
    453T  LEU*     1.3    65.2    +      -       -      +
    454T  ILE*     3.7     0.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 453 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139T  ASP*     4.0    15.2    +      -       +      +
    142T  MET*     5.8     3.6    -      -       +      -
    143T  ALA*     4.6    22.2    -      -       +      +
    381T  LEU*     5.8     4.7    -      -       -      +
    382T  LEU      5.8     0.9    +      -       -      -
    442T  ALA*     6.0     1.8    -      -       +      -
    443T  LEU      4.6     2.7    -      -       -      +
    444T  SER*     3.9    10.0    -      -       -      -
    452T  ARG*     1.3    78.3    -      -       -      +
    454T  ILE*     1.3    60.1    +      -       -      +
    455T  GLY      4.9     4.5    -      -       -      +
    456T  TRP*     5.5    13.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 454 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377T  LEU*     3.5     9.1    -      -       +      +
    378T  LEU*     2.9    31.6    +      -       -      +
    395T  VAL*     4.6    18.8    -      -       +      +
    443T  LEU*     2.9    12.6    +      -       +      +
    444T  SER      4.6     0.4    -      -       -      -
    445T  ARG*     4.6    26.7    -      -       +      +
    452T  ARG      3.7     0.6    +      -       -      +
    453T  LEU*     1.3    75.0    -      -       -      +
    455T  GLY*     1.3    59.2    +      -       -      +
    456T  TRP*     5.8     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 455 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    376T  PHE      3.4    13.2    -      -       -      -
    377T  LEU*     4.1     3.1    -      -       -      -
    378T  LEU      4.5     1.1    -      -       -      -
    442T  ALA*     3.6     2.4    -      -       -      +
    443T  LEU*     2.9    34.5    +      -       -      +
    453T  LEU*     4.9     2.8    -      -       -      +
    454T  ILE*     1.3    80.8    +      -       -      +
    456T  TRP*     1.3    79.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 456 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    573A  ASN*     6.2     4.3    -      -       +      -
    576A  LEU*     6.0     8.3    -      -       +      -
    142T  MET      5.1     2.0    +      -       -      -
    143T  ALA*     5.4     3.2    -      -       -      +
    146T  LEU*     3.4    40.1    -      -       +      +
    177T  ILE*     4.5    23.3    -      -       +      -
    374T  SER      3.6     0.7    -      -       -      +
    376T  PHE*     3.1    36.6    +      -       -      +
    378T  LEU*     5.1    15.0    -      -       +      -
    382T  LEU*     6.1     4.7    -      -       +      -
    440T  LYS*     6.2     3.1    -      -       +      -
    441T  ILE      3.6     8.5    -      -       -      +
    442T  ALA*     4.1    13.9    -      -       +      +
    443T  LEU*     4.7     1.8    -      -       -      +
    453T  LEU*     5.5    12.8    -      -       +      +
    454T  ILE      6.0     0.9    -      -       -      -
    455T  GLY*     1.3    88.8    +      -       -      -
    457T  GLY*     1.3    60.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 457 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    373T  ILE*     5.1     2.9    -      -       -      -
    374T  SER*     3.3    17.7    -      -       -      -
    376T  PHE*     5.1     1.8    -      -       -      -
    440T  LYS*     3.4     8.2    -      -       -      +
    441T  ILE*     2.9    34.0    +      -       -      -
    456T  TRP*     1.3    78.6    -      -       -      +
    458T  GLN*     1.3    60.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 458 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    373T  ILE*     4.0     2.9    -      -       -      -
    374T  SER*     3.0    32.5    +      -       -      -
    438T  GLY*     4.6     8.5    -      -       -      +
    439T  GLU      3.8     7.2    -      -       -      +
    440T  LYS*     5.4     1.1    -      -       -      -
    457T  GLY*     1.3    73.7    -      -       -      -
    459T  ILE*     1.3    66.9    +      -       -      +
    460T  ARG*     3.2     3.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 459 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371T  LEU*     5.5     7.9    -      -       +      -
    372T  GLU      4.1     1.6    -      -       -      +
    373T  ILE*     4.0    12.5    -      -       +      +
    436T  GLU      5.2     3.4    -      -       -      +
    437T  VAL      3.0    30.3    -      -       -      +
    438T  GLY*     3.6     8.5    -      -       -      -
    439T  GLU      3.4    16.9    +      -       -      +
    441T  ILE*     5.3     6.6    -      -       +      +
    457T  GLY      4.3     0.2    -      -       -      -
    458T  GLN*     1.3    71.3    -      -       -      +
    460T  ARG*     1.3    61.5    +      -       -      +
    461T  ARG      5.0     6.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 460 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372T  GLU*     2.8    15.0    +      -       +      +
    373T  ILE*     4.7     4.3    -      -       -      -
    374T  SER*     5.2     1.8    -      -       -      +
    437T  VAL      4.9     3.2    -      -       -      +
    458T  GLN      3.2     6.2    +      -       -      +
    459T  ILE*     1.3    75.2    -      -       -      +
    461T  ARG*     1.3    63.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 461 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371T  LEU*     3.5     4.9    -      -       -      +
    372T  GLU*     2.9    41.2    +      -       +      +
    437T  VAL      5.5     2.2    -      -       -      -
    459T  ILE*     3.7     4.9    -      -       -      +
    460T  ARG*     1.3    79.8    +      -       +      +
    462T  GLY*     1.3    59.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 462 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    368T  PHE*     4.8    14.8    -      -       -      -
    370T  GLU      3.3    10.1    -      -       -      -
    371T  LEU*     4.3     3.6    -      -       -      -
    461T  ARG*     1.3    77.8    -      -       -      +
    463T  VAL*     1.3    61.2    +      -       -      -
    464T  THR*     3.7     4.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 463 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    368T  PHE*     3.4     4.2    -      -       -      +
    369T  THR*     3.0    28.8    +      -       -      +
    370T  GLU*     2.9    29.5    +      -       +      +
    462T  GLY*     1.3    69.4    -      -       -      -
    464T  THR*     1.3    63.9    +      -       -      +
    465T  ILE*     5.3     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 464 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366T  GLU*     4.0    12.6    -      -       -      -
    367T  ILE      3.5     5.4    -      -       -      -
    368T  PHE*     3.7    25.4    -      -       -      -
    462T  GLY      3.7     4.1    +      -       -      -
    463T  VAL*     1.3    75.6    -      -       -      +
    465T  ILE*     1.3    64.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 465 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    309T  LEU      5.1    10.5    -      -       -      +
    310T  MET*     6.1     1.1    -      -       -      -
    311T  CYS*     5.1     7.3    -      -       +      +
    366T  GLU*     5.1     0.7    -      -       -      -
    367T  ILE*     2.9    37.8    +      -       +      +
    369T  THR*     6.2     3.6    -      -       -      -
    463T  VAL      5.3     0.7    -      -       -      +
    464T  THR*     1.3    77.1    -      -       -      +
    466T  LYS*     1.3    62.9    +      -       -      +
    467T  PRO      4.2     0.7    -      -       -      -
----------------------------------------------------------
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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