Contacts of the strand formed by residues 30 - 35 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  ARG*     4.2    12.8    -      -       -      +
     29B  THR*     1.3    81.2    -      -       -      +
     31B  LYS*     1.3    66.4    +      -       -      +
     32B  LEU*     3.6     3.3    +      -       +      +
    190B  LEU*     4.0    28.5    -      -       +      -
    191B  ASN      2.9    10.8    +      -       -      +
    192B  PHE*     3.6    16.6    -      -       +      -
    193B  ARG*     2.8    30.0    +      -       -      +
    215B  THR*     3.7    22.0    -      -       +      -
    216B  CYS      5.1     0.2    -      -       -      +
    339B  ILE*     3.9    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 31 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  LEU*     4.0    17.4    -      -       -      +
     60A  GLU*     2.8    28.9    +      -       -      +
     29B  THR*     4.2     3.0    +      -       +      +
     30B  VAL*     1.3    70.8    -      -       -      +
     32B  LEU*     1.3    61.7    +      -       -      +
     33B  LEU*     4.4     4.0    -      -       -      -
    193B  ARG*     3.4     9.0    -      -       +      -
    195B  PHE*     3.9    20.4    -      -       +      -
    210B  CYS*     2.9    28.2    +      -       -      +
    212B  GLU      2.8    28.7    +      -       -      +
    213B  GLY      3.7    19.1    -      -       -      +
    214B  VAL*     3.7     8.2    -      -       +      +
    215B  THR*     2.8    35.6    +      -       -      +
    216B  CYS      3.3     6.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 32 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  VAL*     3.6     3.5    +      -       +      -
     31B  LYS*     1.3    74.9    -      -       -      +
     33B  LEU*     1.3    75.5    +      -       -      +
     34B  LEU*     4.3     2.5    -      -       +      +
    192B  PHE*     4.1    20.2    -      -       +      -
    193B  ARG      2.9    10.5    +      -       -      +
    194B  MET*     3.3    32.3    -      -       +      -
    195B  PHE*     2.8    29.6    +      -       -      -
    216B  CYS*     3.4    14.8    -      -       -      +
    218B  ILE*     3.8    24.5    -      -       +      -
    332B  PHE*     3.9    31.0    -      -       +      -
    335B  VAL*     4.9     0.7    -      -       +      -
    339B  ILE*     4.4    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 33 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  LYS*     4.2     5.4    +      -       -      -
     32B  LEU*     1.3    78.0    -      -       -      +
     34B  LEU*     1.3    61.6    +      -       -      +
     35B  LEU*     3.8    19.9    +      -       +      -
    195B  PHE*     3.6    30.7    -      -       +      +
    210B  CYS*     3.7    27.6    -      -       +      +
    211B  PHE*     3.8    24.7    -      -       +      -
    214B  VAL*     3.8    25.1    -      -       +      -
    216B  CYS      3.0     8.0    +      -       -      +
    217B  ILE*     3.4     7.5    -      -       +      +
    218B  ILE      2.9    26.9    +      -       -      +
    255B  PHE*     4.7     2.9    -      -       +      -
    354B  CAC      4.1    14.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 34 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  LEU*     4.2     2.9    +      -       +      +
     33B  LEU*     1.3    70.5    -      -       -      +
     35B  LEU*     1.3    69.7    +      -       -      +
     42B  LYS*     3.4    38.5    -      -       +      +
     45B  ILE*     4.2    13.5    -      -       +      -
     46B  VAL*     3.5    20.6    -      -       +      -
    194B  MET*     4.0    22.2    -      -       +      -
    195B  PHE      2.8    15.3    +      -       -      +
    196B  ASP*     3.8    19.9    -      -       +      -
    197B  VAL*     4.1     2.4    +      -       -      +
    218B  ILE*     3.6    26.0    -      -       +      +
    220B  ILE*     3.6    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 35 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  LEU*     3.8    14.6    +      -       +      -
     34B  LEU*     1.3    85.6    -      -       -      +
     36B  GLY*     1.3    60.2    +      -       -      +
     42B  LYS*     3.7     5.8    -      -       -      -
    197B  VAL*     4.3     6.7    -      -       +      -
    207B  TRP*     4.1    22.0    -      -       +      -
    211B  PHE*     4.3    10.8    -      -       +      -
    217B  ILE*     4.1    20.0    -      -       +      -
    218B  ILE      3.0     9.0    +      -       -      +
    219B  PHE*     3.4    15.1    -      -       +      -
    220B  ILE*     2.8    30.0    +      -       -      +
    249B  ILE*     3.9    39.0    -      -       +      -
    354B  CAC      4.0    20.9    -      -       -      +
----------------------------------------------------------
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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