Contacts of the strand formed by residues 12 - 18 (chain A) in PDB entry 1TNF


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 PRO 12 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  ASP      4.1     5.2    -      -       -      +
     11A  LYS*     1.3    82.8    -      -       -      +
     13A  VAL*     1.3    58.9    +      -       -      +
     39A  ASN*     3.4    24.7    -      -       +      +
     41A  VAL*     3.5    24.2    -      -       +      -
     51A  PRO*     3.6     7.9    -      -       +      -
     52A  SER*     3.6    25.1    -      -       -      +
     56A  TYR*     4.0    13.6    -      -       +      +
    154A  ILE*     5.2     0.7    -      -       -      -
    155A  ILE*     3.2     2.6    -      -       -      -
    156A  ALA*     2.9    42.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 13 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  PRO      5.6     2.2    -      -       -      +
     11A  LYS*     3.6     6.9    +      -       +      +
     12A  PRO*     1.3    68.7    -      -       -      +
     14A  ALA*     1.3    64.8    +      -       -      +
     36A  LEU*     3.6    23.6    -      -       +      -
     38A  ALA*     3.3    42.6    +      -       +      +
     41A  VAL*     3.5    12.1    -      -       -      +
    154A  ILE*     3.3     9.0    -      -       -      +
    155A  ILE*     3.4    43.1    -      -       +      +
     55C  LEU*     3.7    18.2    -      -       +      -
    123C  VAL*     4.7     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 14 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  VAL*     1.3    78.0    -      -       -      +
     15A  HIS*     1.3    61.5    +      -       -      +
     16A  VAL*     4.7     2.5    -      -       +      -
     36A  LEU*     3.1    17.5    -      -       -      +
     37A  LEU*     4.7     5.2    -      -       +      -
     41A  VAL*     3.7    22.4    -      -       +      -
     48A  LEU*     4.5    10.5    -      -       +      -
     59A  TYR*     3.8     3.6    +      -       -      -
    153A  GLY*     3.0    19.2    -      -       -      -
    154A  ILE*     3.1    24.0    +      -       +      +
    123C  VAL*     5.5     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 15 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ALA*     1.3    74.7    -      -       -      +
     16A  VAL*     1.3    58.1    -      -       -      +
     17A  VAL*     4.7     7.3    -      -       +      +
     34A  ASN*     3.0    24.5    +      -       -      +
     35A  ALA*     2.8    30.9    -      -       -      -
     36A  LEU*     2.9    21.4    +      -       +      +
     59A  TYR*     3.0    22.2    +      +       -      +
    151A  TYR*     3.3    50.3    -      +       +      +
    152A  PHE      3.5     5.4    -      -       -      -
    153A  GLY*     3.9     0.9    -      -       -      -
    123C  VAL*     3.4    10.5    +      -       +      +
    124C  PHE*     3.7    32.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 16 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ALA*     4.7     2.2    -      -       +      -
     15A  HIS*     1.3    77.4    -      -       -      +
     17A  VAL*     1.3    59.5    +      -       -      +
     28A  TRP*     3.6    34.5    -      -       +      -
     29A  LEU      3.0    21.1    -      -       -      +
     30A  ASN*     4.4     3.6    -      -       +      +
     36A  LEU      4.3     1.6    -      -       -      +
     37A  LEU*     3.9    28.0    -      -       +      -
     43A  LEU*     4.5    10.5    -      -       +      -
     48A  LEU*     4.5    11.2    -      -       +      -
    151A  TYR*     3.1     8.1    -      -       -      +
    152A  PHE*     2.8    47.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 17 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  HIS*     4.7     7.0    -      -       +      +
     16A  VAL*     1.3    76.0    -      -       -      +
     18A  ALA*     1.3    60.2    +      -       -      +
     28A  TRP*     3.2     7.7    -      -       -      -
     29A  LEU*     2.7    59.4    +      -       +      +
     32A  ARG*     3.5    43.7    -      -       +      +
     34A  ASN      5.9     0.2    -      -       -      +
     35A  ALA*     4.4     5.8    -      -       +      -
    147A  SER*     4.1    21.8    -      -       -      +
    150A  VAL      3.3    18.6    -      -       -      +
    151A  TYR*     3.9     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 18 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  VAL*     1.3    72.9    -      -       -      +
     19A  ASN*     1.3    64.0    +      -       -      +
     20A  PRO*     3.1     9.7    -      -       -      +
     26A  LEU*     3.7    22.0    -      -       +      -
     27A  GLN      3.3     7.4    -      -       -      +
     28A  TRP*     3.6     3.9    -      -       -      -
     29A  LEU*     4.7     0.2    -      -       -      -
     32A  ARG*     3.5    10.6    +      -       -      -
    144A  PHE*     3.5    28.2    -      -       +      -
    150A  VAL*     3.3    24.8    +      -       +      -
----------------------------------------------------------
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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