Contacts of the strand formed by residues 63 - 68 (chain C) in PDB entry 1TLF


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 63 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61C  SER      3.0    10.8    +      -       -      +
     62C  LEU*     1.3    69.1    -      -       -      +
     64C  ILE*     1.3    82.6    +      -       -      +
     93C  SER*     3.6    15.7    -      -       -      +
     94C  VAL      4.5     1.6    -      -       -      -
     95C  VAL*     3.5    26.7    -      -       +      +
    117C  GLN      3.9    19.7    -      -       -      +
    118C  ARG*     3.6    42.4    -      -       -      +
    119C  VAL*     4.2     5.2    -      -       +      +
    120C  SER*     2.9    43.1    +      -       -      +
    121C  GLY      3.6     2.1    +      -       -      -
    117D  GLN*     4.5    12.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 64 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62C  LEU*     3.3    13.7    -      -       +      +
     63C  LEU*     1.3    80.3    -      -       -      +
     65C  GLY*     1.3    63.0    +      -       -      +
     66C  VAL*     4.3    10.3    -      -       +      -
     83C  ILE*     4.7     0.4    -      -       +      -
     87C  ALA*     4.3     8.7    -      -       +      -
     92C  ALA*     4.3     9.6    -      -       +      -
     93C  SER      2.6    22.0    +      -       -      +
     94C  VAL*     4.1     6.5    -      -       +      -
     95C  VAL      2.8    27.0    +      -       -      +
    121C  GLY      3.8     6.1    -      -       -      +
    123C  ILE*     3.9    30.3    -      -       +      -
    301C  VAL*     4.0    36.3    -      -       +      +
    304C  LEU*     4.7    15.3    -      -       +      -
    305C  LEU*     5.2     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 65 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64C  ILE*     1.3    74.3    -      -       -      +
     66C  VAL*     1.3    61.2    +      -       -      -
     95C  VAL*     3.5     7.4    -      -       -      -
    114C  LEU*     4.1     4.9    -      -       -      -
    119C  VAL*     3.5    21.7    -      -       -      +
    121C  GLY      3.1    11.4    +      -       -      -
    122C  LEU*     3.2    13.5    -      -       -      +
    123C  ILE      2.8    25.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 66 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64C  ILE*     4.3     6.3    -      -       +      -
     65C  GLY*     1.3    75.6    -      -       -      +
     67C  ALA*     1.3    65.8    +      -       -      +
     68C  THR*     3.5     2.5    +      -       -      -
     80C  VAL*     4.3    16.4    -      -       +      -
     83C  ILE*     4.0    33.0    -      -       +      -
     94C  VAL*     3.3    33.7    -      -       +      -
     95C  VAL      3.0     8.2    +      -       -      +
     96C  VAL*     3.8    10.0    -      -       +      +
     97C  SER*     2.9    31.5    +      -       -      +
    114C  LEU*     4.1     3.7    -      -       -      +
    123C  ILE*     3.2    17.0    -      -       +      +
    125C  ASN*     4.9     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 67 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66C  VAL*     1.3    69.9    -      -       -      +
     68C  THR*     1.3    60.2    +      -       -      +
     97C  SER      3.4     6.1    -      -       -      -
     99C  VAL*     4.0    19.5    -      -       +      -
    107C  CYS      5.0     0.2    -      -       -      +
    110C  ALA*     4.5     5.8    -      -       +      -
    111C  VAL*     4.8     5.6    -      -       +      -
    114C  LEU*     4.0    19.1    -      -       +      +
    123C  ILE      3.0     7.5    +      -       -      -
    124C  ILE*     4.0    24.5    -      -       +      -
    125C  ASN*     2.8    31.4    +      -       -      +
    126C  TYR*     4.3     0.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 68 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66C  VAL*     4.5     4.9    -      -       -      -
     67C  ALA*     1.3    75.7    -      -       -      +
     69C  SER*     1.3    70.2    +      -       -      +
     71C  LEU*     3.4    29.0    -      -       +      +
     76C  PRO*     4.0     1.0    -      -       -      +
     80C  VAL*     3.5    16.5    -      -       -      +
     96C  VAL*     3.5    29.8    -      -       +      -
     97C  SER      3.1     7.0    +      -       -      +
     98C  MET*     3.5     7.9    -      -       +      -
     99C  VAL*     3.1    23.1    +      -       -      +
    125C  ASN*     3.3    15.8    +      -       -      -
    126C  TYR*     4.5     2.7    -      -       -      -
----------------------------------------------------------
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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