Contacts of the strand formed by residues 639 - 647 (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 LEU 639 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    612X  VAL*     4.6     4.7    -      -       +      -
    616X  HIS*     3.8    20.9    -      -       +      +
    631X  ILE*     5.6     0.7    -      -       +      -
    635X  ILE*     3.6    20.9    -      -       +      +
    636X  ARG*     3.2    17.4    +      -       -      +
    637X  LYS      3.5     1.9    -      -       -      +
    638X  ILE*     1.3    94.3    -      -       +      +
    640X  SER*     1.3    61.6    +      -       -      +
    641X  GLY      3.4     7.4    -      -       -      +
    642X  TYR*     3.4    32.5    -      -       +      +
    700X  ALA*     4.0    13.0    -      -       +      -
    701X  VAL      3.4    16.2    -      -       -      +
    702X  THR*     3.8    13.5    -      -       +      -
    703X  LYS*     5.4     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 640 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336X  HIS*     4.4    11.8    +      -       -      -
    337X  SER*     5.5     0.3    +      -       -      -
    638X  ILE      4.1     1.4    +      -       -      -
    639X  LEU*     1.3    73.0    -      -       -      +
    641X  GLY*     1.3    58.8    +      -       -      +
    663X  LEU*     4.5     6.2    -      -       -      +
    664X  ASN*     4.7    10.4    +      -       -      +
    701X  VAL*     2.8    17.8    +      -       -      +
    702X  THR      4.0     0.5    +      -       -      -
    703X  LYS*     4.2     6.2    -      -       -      +
    706X  THR*     2.5    38.3    +      -       -      +
    804X  PG4      3.8    23.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 641 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    639X  LEU*     3.4     3.4    -      -       -      +
    640X  SER*     1.3    83.9    +      -       -      +
    642X  TYR*     1.3    71.7    +      -       -      -
    663X  LEU*     3.2    22.2    -      -       -      -
    664X  ASN*     4.9     0.9    -      -       -      -
    666X  SER*     6.1     0.9    -      -       -      -
    700X  ALA*     3.7     1.2    -      -       -      +
    701X  VAL*     2.8    34.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 642 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    616X  HIS*     2.9    33.7    +      -       -      -
    631X  ILE*     3.8    11.4    -      -       -      +
    636X  ARG*     5.7     1.9    +      -       -      +
    639X  LEU*     3.4    22.4    -      -       +      +
    641X  GLY*     1.3    80.7    -      -       -      -
    643X  ILE*     1.3    58.2    +      -       -      +
    657X  ASN*     2.8    26.7    +      -       -      -
    663X  LEU*     3.0    16.2    +      -       -      +
    665X  ILE*     3.7    19.0    -      -       +      +
    666X  SER*     3.5    34.3    +      -       -      -
    674X  THR*     5.0     1.0    -      -       -      +
    676X  ILE*     3.7    23.3    -      -       +      -
    698X  VAL*     4.1    16.2    -      -       +      -
    699X  TYR      2.9    20.9    -      -       -      +
    700X  ALA*     3.8    13.7    -      -       +      -
    701X  VAL      4.7     0.4    -      -       -      +
    726X  ILE*     3.9     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 643 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    642X  TYR*     1.3    75.7    -      -       -      +
    644X  VAL*     1.3    67.7    +      -       -      +
    645X  GLU*     4.9     0.9    -      -       +      +
    655X  VAL*     3.4    33.2    -      -       +      -
    657X  ASN*     3.7     2.9    -      -       -      -
    663X  LEU*     3.6    24.7    -      -       +      -
    698X  VAL*     3.3     5.0    -      -       -      +
    699X  TYR*     2.8    54.3    +      -       +      -
    701X  VAL*     3.9    21.5    -      -       +      -
    718X  THR*     4.0    22.0    -      -       +      +
    721X  ILE*     4.3     7.9    -      -       +      -
    723X  LYS*     4.0    21.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 644 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    643X  ILE*     1.3    75.7    -      -       -      +
    645X  GLU*     1.3    64.6    +      -       -      +
    655X  VAL*     3.2     8.0    -      -       -      +
    656X  ILE*     2.9    45.1    +      -       +      -
    657X  ASN*     2.9    13.7    +      -       -      +
    665X  ILE*     3.7    26.9    -      -       +      -
    678X  PHE*     3.7    29.8    -      -       +      -
    687X  LEU*     4.0    19.5    -      -       +      -
    696X  VAL*     4.1    15.3    -      -       +      -
    697X  ASN      3.6     3.8    -      -       -      +
    698X  VAL*     4.4     5.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 645 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    643X  ILE*     4.9     0.7    -      -       +      -
    644X  VAL*     1.3    76.4    -      -       -      +
    646X  ILE*     1.3    76.1    +      -       -      +
    653X  LYS*     3.2    37.2    -      -       +      +
    654X  GLU      3.4    12.6    -      -       -      +
    655X  VAL*     4.5    13.9    -      -       +      +
    656X  ILE*     4.5     0.7    -      -       -      +
    696X  VAL*     3.4     6.9    -      -       -      +
    697X  ASN*     2.8    54.6    +      -       -      +
    699X  TYR*     2.4    36.4    +      -       +      -
    723X  LYS*     3.5    16.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 646 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    645X  GLU*     1.3    79.7    -      -       -      +
    647X  GLU*     1.3    65.3    +      -       -      +
    652X  LEU      3.9     0.5    -      -       -      +
    653X  LYS*     3.4     3.5    -      -       -      -
    654X  GLU*     2.8    40.6    +      -       +      +
    656X  ILE*     3.6    23.8    -      -       +      +
    687X  LEU*     4.6    12.1    -      -       +      -
    688X  TYR      4.9     8.1    -      -       -      +
    689X  ILE*     4.7    13.7    -      -       +      -
    694X  TYR*     4.0    28.7    -      -       +      -
    695X  LYS      3.4     9.9    -      -       -      +
    696X  VAL*     4.6    10.8    -      -       +      -
    113Y  SER*     5.0    14.8    -      -       -      +
    115Y  VAL*     4.4    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 647 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    646X  ILE*     1.3    80.6    -      -       -      +
    648X  ASP*     1.3    74.9    +      -       -      +
    651X  GLY*     4.0    18.3    +      -       -      +
    652X  LEU      3.3     9.6    -      -       -      +
    653X  LYS*     3.9    18.2    -      -       +      -
    694X  TYR*     3.3     9.4    -      -       -      +
    695X  LYS*     3.0    57.9    +      -       +      +
    697X  ASN*     3.0    29.7    +      -       -      +
----------------------------------------------------------
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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