Contacts of the strand formed by residues 30 - 35 (chain A) in PDB entry 1TAD


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 VAL 30 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  ARG*     3.7    29.2    -      -       -      +
     29A  THR*     1.3    82.6    -      -       -      +
     31A  LYS*     1.3    61.6    +      -       -      +
     32A  LEU*     3.7     1.6    +      -       +      -
    190A  LEU*     4.2    14.6    -      -       +      -
    191A  ASN      2.7    20.3    +      -       -      +
    192A  PHE*     3.5    38.7    -      -       +      +
    193A  ARG      2.9    24.8    +      -       -      +
    215A  THR*     3.6    20.6    -      -       +      +
    339A  ILE*     4.1    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  THR*     4.3     1.9    -      -       +      +
     30A  VAL*     1.3    71.8    -      -       -      +
     32A  LEU*     1.3    60.7    +      -       -      +
     33A  LEU*     3.8    15.5    -      -       +      -
    193A  ARG*     3.5     7.4    -      -       +      -
    195A  PHE*     3.9    23.1    -      -       +      -
    210A  CYS      2.9    27.5    +      -       -      -
    212A  GLU      2.8    28.3    +      -       -      +
    213A  GLY      3.5    20.0    -      -       -      +
    214A  VAL*     3.9     5.6    -      -       -      +
    215A  THR*     2.9    37.3    +      -       -      +
    216A  CYS      3.2     3.5    +      -       -      +
     59C  LEU*     3.9     5.0    -      -       -      +
     60C  GLU*     2.8    32.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  VAL*     3.7     1.8    +      -       +      +
     31A  LYS*     1.3    75.4    -      -       -      +
     33A  LEU*     1.3    71.1    +      -       -      +
     34A  LEU*     4.1     4.3    -      -       +      -
    192A  PHE*     3.8    34.5    -      -       +      -
    193A  ARG      2.8    13.6    +      -       -      +
    194A  MET*     3.3    21.8    -      -       +      -
    195A  PHE*     2.8    32.6    +      -       -      -
    216A  CYS*     3.3    15.3    -      -       +      +
    218A  ILE*     3.6    31.9    -      -       +      -
    332A  PHE*     4.0    16.6    -      -       +      -
    335A  VAL*     5.2     0.2    -      -       +      -
    339A  ILE*     4.3    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  LYS*     3.8    26.7    -      -       -      -
     32A  LEU*     1.3    83.0    -      -       -      +
     34A  LEU*     1.3    59.5    +      -       -      +
     35A  LEU*     3.8    18.9    +      -       +      -
    195A  PHE*     3.5    18.6    -      -       +      +
    210A  CYS*     3.7    16.6    -      -       +      +
    211A  PHE*     3.8    24.0    -      -       +      -
    214A  VAL*     3.6    28.7    -      -       +      +
    216A  CYS      3.0    10.8    +      -       -      +
    217A  ILE*     3.5     6.5    -      -       +      +
    218A  ILE*     2.9    28.6    +      -       -      +
    255A  PHE*     4.6     4.0    -      -       +      -
    354A  CAC      4.6     6.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  LEU*     4.1     3.1    -      -       +      -
     33A  LEU*     1.3    71.0    -      -       -      +
     35A  LEU*     1.3    69.2    +      -       -      +
     42A  LYS*     3.5    43.3    -      -       +      +
     45A  ILE*     4.0    15.3    -      -       +      -
     46A  VAL*     3.6    20.6    -      -       +      -
    194A  MET*     4.0    23.6    -      -       +      -
    195A  PHE      2.8    14.8    +      -       -      +
    196A  ASP*     3.9    18.0    -      -       +      -
    197A  VAL*     4.0     3.5    +      -       -      +
    218A  ILE*     3.4    43.5    -      -       +      +
    220A  ILE*     4.3     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  LEU*     4.4    14.8    -      -       +      -
     34A  LEU*     1.3    83.3    -      -       -      +
     36A  GLY*     1.3    60.2    +      -       -      +
     42A  LYS*     3.7     6.7    -      -       -      -
    197A  VAL*     3.9    11.2    -      -       +      -
    207A  TRP*     4.0    28.7    -      -       +      -
    211A  PHE*     4.4    11.2    -      -       +      -
    217A  ILE*     3.9    26.9    -      -       +      -
    218A  ILE      3.0     8.6    +      -       -      +
    219A  PHE*     3.3    13.7    -      -       +      -
    220A  ILE*     2.8    29.3    +      -       -      +
    249A  ILE*     4.1    20.6    -      -       +      -
    354A  CAC      3.9    22.4    -      -       +      +
----------------------------------------------------------
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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