Contacts of the strand formed by residues 468 - 476 (chain X) 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 ARG 468 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462X  TYR*     3.7     2.1    -      -       -      -
    463X  ASN*     2.9    30.5    +      -       -      +
    466X  ASN*     3.1    30.8    +      -       +      +
    467X  GLY*     1.3    83.5    -      -       -      +
    469X  VAL*     1.3    65.2    +      -       -      +
    470X  ARG*     4.0    38.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 469 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243X  ILE*     3.8    10.5    -      -       -      +
    244X  ASP*     3.7    32.5    -      -       +      +
    245X  LYS      5.3     0.4    -      -       -      +
    375X  TYR*     5.4     0.4    -      -       -      +
    460X  ALA*     3.8    24.0    -      -       +      -
    461X  THR      3.4     6.3    -      -       -      +
    462X  TYR*     4.2    13.9    -      -       +      -
    468X  ARG*     1.3    75.2    -      -       -      +
    470X  ARG*     1.3    76.0    +      -       -      +
    803X   NA      3.9    15.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 470 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    460X  ALA*     3.7     6.7    -      -       -      -
    461X  THR*     2.9    29.0    +      -       -      +
    463X  ASN*     5.8     5.1    -      -       +      +
    466X  ASN*     4.4    16.4    -      -       -      +
    468X  ARG*     4.0    38.2    +      -       +      +
    469X  VAL*     1.3    84.1    +      -       -      +
    471X  VAL*     1.3    69.2    +      -       -      +
    472X  ASP*     3.2     4.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 471 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375X  TYR*     3.8    36.1    -      -       +      -
    376X  ASN*     4.3    13.2    -      -       +      +
    458X  ASN*     3.7    30.1    -      -       +      +
    459X  ILE      3.5     6.7    -      -       -      +
    460X  ALA*     3.7     8.5    -      -       +      +
    470X  ARG*     1.3    73.1    -      -       -      +
    472X  ASP*     1.3    61.7    +      -       -      +
    473X  THR*     3.9     9.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 472 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458X  ASN*     3.6     6.0    -      -       -      +
    459X  ILE      2.9    10.9    +      -       -      +
    461X  THR*     3.7    22.2    +      -       -      +
    470X  ARG*     3.2     2.9    +      -       +      +
    471X  VAL*     1.3    72.1    -      -       -      +
    473X  THR*     1.3    67.2    +      -       -      +
    474X  GLY*     3.1    12.4    +      -       -      -
    475X  SER*     2.9    47.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 473 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    376X  ASN*     5.5     2.5    -      -       -      +
    458X  ASN*     3.3    26.5    +      -       -      +
    471X  VAL*     3.9    11.6    +      -       +      +
    472X  ASP*     1.3    75.0    +      -       -      +
    474X  GLY*     1.3    59.6    +      -       -      +
    475X  SER      3.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 474 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    472X  ASP*     3.1    13.3    +      -       -      -
    473X  THR*     1.3    80.1    +      -       -      +
    475X  SER*     1.3    57.3    +      -       -      +
    476X  ASN*     4.0     0.6    +      -       -      -
    479X  GLU*     3.9    16.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 475 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232X  PRO*     5.8     0.3    -      -       -      +
    458X  ASN*     3.1    13.9    +      -       -      -
    459X  ILE*     3.1    40.0    +      -       -      +
    461X  THR*     3.7    13.0    -      -       -      +
    472X  ASP*     2.9    31.9    +      -       -      +
    473X  THR      3.3     0.2    -      -       -      -
    474X  GLY*     1.3    76.9    -      -       -      +
    476X  ASN*     1.3    60.9    +      -       -      +
    479X  GLU*     4.6     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 476 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    455X  VAL*     6.0     0.7    -      -       -      +
    457X  GLY*     3.4    26.6    +      -       -      +
    458X  ASN*     4.0    11.0    +      -       -      +
    459X  ILE*     3.4    10.9    -      -       -      +
    474X  GLY      5.2     0.4    -      -       -      +
    475X  SER*     1.3    73.8    -      -       -      +
    477X  TRP*     1.3    66.1    +      -       -      +
    478X  SER*     2.8    38.8    +      -       -      +
    479X  GLU*     3.1    41.1    +      -       +      +
    480X  VAL*     3.7     4.9    +      -       -      +
----------------------------------------------------------
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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