Contacts of the strand formed by residues 411 - 421 (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 LEU 411 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257T  ILE*     5.6     0.8    -      -       -      +
    355T  GLY*     5.0    22.4    -      -       -      +
    406T  VAL      3.2     4.0    -      -       -      +
    407T  ASN*     4.3     0.7    -      -       -      -
    408T  ILE*     2.9    42.7    +      -       +      +
    410T  SER*     1.3    75.2    -      -       -      +
    412T  SER*     1.3    60.8    +      -       -      +
    413T  THR*     3.6     4.4    +      -       -      -
    433T  VAL*     5.3    13.0    -      -       +      -
    434T  CYS      6.1     1.8    -      -       -      +
    435T  THR*     5.9     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 412 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264A  PHE*     5.0     4.2    -      -       -      -
     79T  ILE*     5.4    13.7    -      -       -      -
    355T  GLY*     6.0     0.8    -      -       -      -
    405T  MET*     3.9    24.2    -      -       -      +
    406T  VAL      3.4     6.3    -      -       -      -
    407T  ASN*     4.1    12.3    -      -       -      +
    410T  SER      3.4     6.9    +      -       -      -
    411T  LEU*     1.3    70.7    -      -       -      +
    413T  THR*     1.3    59.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 413 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264A  PHE*     5.0     3.4    -      -       -      -
    405T  MET*     3.7     3.4    -      -       -      -
    406T  VAL*     2.9    38.0    +      -       -      +
    411T  LEU*     3.6     4.6    +      -       -      -
    412T  SER*     1.3    75.6    -      -       -      +
    414T  GLY*     1.3    66.2    +      -       -      +
    429T  LEU*     5.0     5.2    -      -       -      -
    431T  ASN*     4.9    19.1    -      -       -      -
    432T  PRO      6.2     0.2    -      -       -      -
    433T  VAL*     4.9    18.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 414 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264A  PHE*     3.8    35.6    -      -       -      -
    404T  LEU      3.4     8.7    -      -       -      -
    405T  MET*     3.8     8.5    -      -       -      -
    413T  THR*     1.3    75.1    -      -       -      +
    415T  GLY*     1.3    58.1    +      -       -      -
    429T  LEU*     3.6     4.5    -      -       -      +
    430T  THR*     2.9    30.1    +      -       -      -
    431T  ASN      4.6     0.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 415 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264A  PHE*     5.6     0.2    -      -       -      +
    402T  GLU      3.5     1.2    -      -       -      +
    403T  VAL*     3.5     4.3    -      -       -      +
    404T  LEU*     2.9    38.9    +      -       -      +
    406T  VAL*     5.9     1.3    -      -       -      +
    413T  THR      3.9     0.2    +      -       -      -
    414T  GLY*     1.3    75.4    -      -       -      -
    416T  ARG*     1.3    62.6    +      -       -      -
    427T  ILE*     4.9     9.6    -      -       -      +
    428T  VAL      3.3    14.1    -      -       -      -
    429T  LEU*     3.8     5.4    -      -       -      -
    430T  THR*     4.4     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 416 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    401T  ASN*     4.8     6.5    -      -       -      -
    402T  GLU      3.4    14.1    -      -       -      +
    403T  VAL*     4.5     1.3    -      -       -      +
    415T  GLY*     1.3    73.2    -      -       -      -
    417T  VAL*     1.3    62.4    +      -       -      +
    418T  SER*     3.1     4.9    +      -       -      +
    427T  ILE*     3.3     3.0    -      -       -      -
    428T  VAL*     2.9    38.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 417 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398T  LEU*     5.0    12.1    -      -       +      +
    399T  SER      3.4    21.3    -      -       -      +
    400T  LYS*     3.6     3.9    -      -       -      -
    401T  ASN*     2.9    24.6    +      -       -      -
    402T  GLU*     3.0    18.1    +      -       +      +
    415T  GLY      4.0     0.4    +      -       -      -
    416T  ARG*     1.3    69.1    -      -       -      +
    418T  SER*     1.3    64.2    +      -       -      +
    419T  ALA*     3.5     6.3    -      -       -      +
    420T  VAL*     5.9     2.5    -      -       +      -
    426T  LYS      4.3     4.5    -      -       -      -
    427T  ILE*     4.5     5.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 418 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    400T  LYS*     4.8     8.9    -      -       -      +
    401T  ASN*     5.8     0.2    -      -       -      +
    416T  ARG*     3.1    10.5    +      -       -      -
    417T  VAL*     1.3    73.0    -      -       -      +
    419T  ALA*     1.3    63.3    +      -       -      +
    426T  LYS*     3.2    14.8    +      -       -      -
    428T  VAL*     4.7    13.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 419 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    400T  LYS*     6.3     0.4    -      -       -      -
    417T  VAL*     3.5     4.4    -      -       -      +
    418T  SER*     1.3    81.8    +      -       -      +
    420T  VAL*     1.3    64.1    +      -       -      +
    424T  LEU      4.6     0.2    -      -       -      -
    425T  GLY*     3.5     0.9    -      -       -      -
    426T  LYS*     2.9    38.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 420 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398T  LEU*     4.3    26.5    -      -       +      +
    417T  VAL*     5.9     3.4    -      -       +      -
    419T  ALA*     1.3    79.8    -      -       -      +
    421T  LYS*     1.3    61.6    +      -       -      +
    422T  ALA      3.9     3.3    +      -       -      +
    424T  LEU      3.3     9.2    -      -       -      +
    425T  GLY*     4.4     6.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 421 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    420T  VAL*     1.3    71.9    -      -       -      +
    422T  ALA*     1.3    56.4    +      -       +      +
    423T  ASP*     2.5    19.4    +      -       -      +
    424T  LEU*     2.9    24.3    +      -       +      +
----------------------------------------------------------
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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