Contacts of the strand formed by residues 18 - 25 (chain A) in PDB entry 1T7P


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 PHE 18 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  ILE*     4.0    18.8    -      -       +      -
      7A  GLU      4.1     3.1    -      -       -      -
      8A  ALA*     4.4     0.4    -      -       -      -
     17A  LYS*     1.3    74.6    -      -       -      +
     19A  HIS*     1.3    62.6    +      -       -      +
     20A  CYS*     3.4    36.3    -      -       -      -
     21A  GLY*     3.6     6.5    -      -       -      -
     34A  TYR*     4.4     2.2    -      -       +      -
     35A  ARG      3.8    15.5    -      -       -      -
     36A  PRO*     4.0    15.3    -      -       -      +
     38A  ASP      4.6     0.4    -      -       -      -
     39A  PHE*     3.4    54.3    -      +       +      -
     42A  TYR*     4.0    29.4    -      +       +      -
     69A  LEU*     4.3     7.0    -      -       +      -
     72A  LEU*     3.9    12.1    -      -       +      -
     76A  GLN*     2.9    26.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  GLU      2.8    15.4    +      -       -      +
      8A  ALA      3.5    22.7    -      -       -      -
      9A  ASN*     3.4    12.1    -      -       +      +
     17A  LYS*     3.6    17.3    +      -       +      +
     18A  PHE*     1.3    79.0    +      -       -      +
     20A  CYS*     1.3    59.4    +      -       -      +
     36A  PRO*     2.9    37.0    -      -       -      +
    160A  TRP      2.9    22.6    +      -       -      -
    161A  TRP      3.5    19.3    +      -       -      -
    162A  ASN*     3.8     1.5    -      -       -      -
    163A  PHE*     3.7    25.7    +      -       +      +
    167A  MET*     3.5    38.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  ILE*     3.3     2.8    -      -       -      -
      7A  GLU*     2.8    51.4    +      -       -      +
     18A  PHE*     3.4    14.3    -      -       -      -
     19A  HIS*     1.3    83.4    -      -       -      +
     21A  GLY*     1.3    59.8    +      -       -      +
     34A  TYR      3.1    15.5    -      -       -      +
    163A  PHE*     3.8    18.8    -      -       +      -
    167A  MET*     4.3     3.4    -      -       -      -
    168A  MET*     3.8    21.3    -      -       +      -
    171A  ASN*     3.3    19.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  ASP      3.2     9.6    -      -       -      -
      6A  ILE*     4.1     1.8    -      -       -      -
     18A  PHE*     3.6    11.2    -      -       -      -
     20A  CYS*     1.3    76.2    -      -       -      +
     22A  VAL*     1.3    63.3    +      -       -      +
     34A  TYR*     2.9    38.8    +      -       -      +
     42A  TYR*     4.2     7.9    -      -       -      -
    168A  MET*     3.8     1.0    -      -       -      +
    171A  ASN*     3.0    10.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  SER*     2.7    33.1    +      -       -      -
      5A  ASP      3.0     8.1    +      -       -      -
     21A  GLY*     1.3    80.1    -      -       -      +
     23A  ILE*     1.3    65.3    +      -       -      +
     31A  TYR*     4.1    20.0    -      -       +      -
     32A  VAL      3.4    11.2    -      -       -      +
     33A  SER*     4.1     4.5    -      -       -      +
     34A  TYR*     4.5     0.4    -      -       -      -
     42A  TYR*     4.2     1.0    -      -       -      -
    168A  MET*     3.6    16.2    -      -       +      -
    171A  ASN*     3.6    17.7    -      -       -      +
    172A  VAL*     3.8    24.9    -      -       +      +
    175A  VAL*     3.8    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  ILE*     3.8    32.1    -      -       +      -
      3A  VAL      3.5     3.8    -      -       -      +
      4A  SER*     3.7     5.4    -      -       -      +
     22A  VAL*     1.3    84.7    -      -       -      +
     24A  TYR*     1.3    65.1    +      -       -      +
     25A  ASP*     4.5     4.2    -      -       +      +
     30A  GLU      3.6     2.1    -      -       -      +
     31A  TYR*     3.4     2.1    -      -       -      -
     32A  VAL*     2.9    35.2    +      -       +      +
     34A  TYR*     3.6    21.5    -      -       +      +
     42A  TYR*     3.5    23.3    -      -       +      -
     45A  ALA*     3.5    32.8    -      -       +      -
     46A  LEU*     3.8    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  ILE*     3.0     7.1    -      -       -      +
      3A  VAL*     2.8    45.6    +      -       +      +
     23A  ILE*     1.3    74.1    -      -       -      +
     25A  ASP*     1.3    59.7    +      -       -      +
     26A  TYR*     3.8    32.8    +      +       -      -
     29A  ALA*     3.5    41.7    -      -       -      +
     30A  GLU      3.5     9.6    -      -       -      -
     31A  TYR*     3.5    35.2    -      +       +      +
    175A  VAL*     3.7    22.9    -      -       +      +
    179A  LYS*     3.4    36.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET      3.6     8.8    +      -       -      +
      2A  ILE*     3.6    18.5    -      -       +      +
     23A  ILE*     4.0     4.7    -      -       +      -
     24A  TYR*     1.3    75.4    -      -       -      +
     26A  TYR*     1.3    56.9    +      -       -      +
     27A  SER*     3.0    29.1    +      -       -      -
     28A  THR*     3.4    18.5    +      -       -      +
     29A  ALA*     2.7    36.9    +      -       -      -
     30A  GLU      3.2     8.6    +      -       -      +
     32A  VAL*     6.6     0.2    -      -       +      -
     49A  GLU*     4.6     2.5    -      -       -      +
     52A  ARG*     4.7    14.2    +      -       -      -
----------------------------------------------------------
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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