Contacts of the strand formed by residues 62 - 70 (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 SER 62 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23X  TYR*     3.9     0.3    -      -       -      -
     24X  PHE*     2.8    35.1    +      -       -      +
     26X  ASP      3.2     5.8    +      -       -      -
     27X  LEU      3.4    26.0    -      -       -      -
     29X  PHE*     3.2    31.0    +      -       -      -
     60X  PHE*     3.6     4.2    -      -       -      +
     61X  GLN*     1.3    80.3    -      -       -      +
     63X  ALA*     1.3    56.4    +      -       -      +
    120X  TYR*     2.9    23.1    -      -       -      -
    121X  GLN*     4.1     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 63 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22X  TYR      3.0    14.6    -      -       -      +
     23X  TYR*     4.2    13.7    -      -       +      -
     24X  PHE*     4.0     2.5    -      -       -      -
     29X  PHE*     4.0     1.6    -      -       -      -
     60X  PHE*     6.1     0.4    -      -       +      -
     62X  SER*     1.3    75.1    +      -       -      +
     64X  ILE*     1.3    68.4    +      -       -      +
     65X  TRP*     3.6    32.5    -      -       +      -
    118X  ILE      4.0     0.2    -      -       -      +
    119X  GLN      3.7     0.5    -      -       -      -
    120X  TYR*     2.9    39.0    +      -       +      +
    130X  LEU*     4.6     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 64 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21X  GLY*     3.4     1.9    -      -       -      -
     22X  TYR*     2.8    55.1    +      -       +      +
     24X  PHE*     4.1     8.9    -      -       +      -
     29X  PHE*     3.3    48.2    -      -       +      -
     63X  ALA*     1.3    79.2    -      -       -      +
     65X  TRP*     1.3    78.0    +      -       -      +
     66X  SER*     4.9     2.2    -      -       -      +
    117X  LYS*     4.5    20.2    -      -       +      -
    118X  ILE      3.4     9.4    -      -       -      +
    119X  GLN*     4.7     5.2    -      -       +      -
    175X  VAL*     5.3    19.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 65 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19X  LEU*     4.3    20.9    -      -       +      -
     20X  LEU      3.2     6.7    -      -       -      -
     21X  GLY*     3.4    21.5    -      -       -      -
     23X  TYR*     3.2    42.2    +      +       -      -
     43X  LEU*     3.5    42.8    -      -       +      +
     63X  ALA*     3.6    24.2    -      -       +      -
     64X  ILE*     1.3    78.7    -      -       -      +
     66X  SER*     1.3    64.6    +      -       -      +
    116X  ILE*     5.5     0.2    -      -       -      -
    117X  LYS*     3.4     9.2    -      -       -      +
    118X  ILE*     2.9    55.1    +      -       +      +
    120X  TYR*     4.0    17.5    -      -       +      -
    130X  LEU*     3.8    15.5    -      -       +      -
    132X  PHE*     3.9    20.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 66 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19X  LEU*     3.7     7.7    -      -       -      +
     20X  LEU*     2.9    34.9    +      -       -      -
     22X  TYR*     5.4     7.6    -      -       -      -
     64X  ILE*     4.9     4.2    -      -       -      +
     65X  TRP*     1.3    74.9    -      -       -      +
     67X  GLY*     1.3    59.2    +      -       -      +
    116X  ILE      3.6     6.0    +      -       -      -
    117X  LYS*     3.1    28.9    +      -       -      +
    154X  PRO*     3.3    20.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 67 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19X  LEU*     3.5     5.0    -      -       -      +
     66X  SER*     1.3    75.7    +      -       -      +
     68X  PHE*     1.3    70.7    +      -       -      -
    115X  GLN*     3.6     6.1    -      -       -      +
    116X  ILE*     2.9    30.2    +      -       -      +
    152X  GLN      3.3    12.6    -      -       -      -
    154X  PRO*     3.7    15.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 68 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19X  LEU*     3.9     2.0    -      -       -      +
     67X  GLY*     1.3    75.6    -      -       -      -
     69X  ILE*     1.3    59.5    +      -       -      +
     92X  ASP*     5.7     0.2    -      -       -      -
    113X  LEU*     4.0    27.4    -      -       +      -
    114X  TYR      3.2    23.3    -      -       -      +
    115X  GLN*     3.4    31.4    -      -       +      -
    116X  ILE*     4.0     4.3    -      -       -      -
    151X  LEU*     3.3     7.3    -      -       -      +
    152X  GLN*     2.9    52.2    +      -       +      +
    153X  LEU      3.4    24.2    -      -       -      -
    154X  PRO*     4.0    12.3    -      -       +      -
    155X  GLU*     4.1    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 69 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68X  PHE*     1.3    75.2    -      -       -      +
     70X  LYS*     1.3    62.0    +      -       -      +
     71X  VAL*     5.0     1.3    -      -       +      +
     79X  PHE*     4.5     9.6    -      -       +      -
     91X  VAL*     4.9     2.2    -      -       +      -
    108X  LEU*     4.3    21.5    -      -       +      -
    113X  LEU*     3.7     3.3    -      -       -      -
    114X  TYR*     3.1    48.6    +      -       +      -
    116X  ILE*     3.5    32.3    -      -       +      -
    136X  TRP*     4.6    14.1    -      -       +      -
    146X  ILE*     4.9     2.7    -      -       +      -
    150X  ASN*     3.3    36.1    -      -       +      +
    151X  LEU*     3.9    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 70 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69X  ILE*     1.3    75.0    -      -       -      +
     71X  VAL*     1.3    64.5    +      -       -      +
     72X  LYS*     5.2    16.4    -      -       +      +
    111X  GLY*     5.1     7.0    -      -       -      +
    112X  ARG      3.7     8.5    -      -       -      +
    113X  LEU*     3.5    19.0    -      -       +      +
    149X  ASP*     3.3    39.4    +      -       -      +
    150X  ASN*     3.2    27.9    +      -       -      +
    152X  GLN*     3.4    30.9    -      -       -      +
----------------------------------------------------------
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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