Contacts of the strand formed by residues 2 - 10 (chain E) in PDB entry 3IT8


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 THR 2 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1E  ILE*     1.3    78.0    +      -       -      +
      3E  LEU*     1.3    69.7    +      -       -      +
      4E  LYS*     4.3    10.3    -      -       +      +
     24E  HIS      4.4     0.2    -      -       -      +
     25E  TYR*     3.2    12.1    -      -       -      -
     26E  ASN*     2.7    53.9    +      -       -      +
     97E  CYS      3.9     4.1    +      -       -      +
     98E  TYR*     3.9    11.4    -      -       -      +
    107E  TYR*     5.5     1.6    -      -       -      +
    167E  ILE*     3.9     4.5    -      -       -      -
    210E  PRO*     6.3     0.9    -      -       +      -
    211E  ASP*     3.9    20.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 3 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2E  THR*     1.3    76.6    -      -       -      +
      4E  LYS*     1.3    60.1    +      -       -      +
      5E  TYR*     3.9    15.3    -      -       +      +
     23E  ASP*     3.6    24.2    -      -       -      +
     24E  HIS      3.4     9.4    -      -       -      +
     25E  TYR*     4.4     2.7    -      -       +      -
     96E  GLY*     3.1     4.7    -      -       -      -
     97E  CYS*     2.9    33.1    +      -       -      +
    107E  TYR*     3.5     2.1    +      -       -      -
    158E  PHE*     4.6     0.4    -      -       +      -
    163E  CYS*     3.9    21.5    -      -       -      -
    166E  ALA*     4.2     5.8    -      -       +      -
    167E  ILE*     3.8    42.8    -      -       +      +
    170E  TYR*     3.7    35.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 4 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2E  THR*     4.2     8.5    -      -       +      -
      3E  LEU*     1.3    74.9    -      -       -      +
      5E  TYR*     1.3    76.5    +      -       -      +
      6E  ASN*     5.1     7.0    -      -       +      +
     22E  TYR      3.6     3.1    -      -       -      +
     24E  HIS*     2.8    68.4    +      -       +      +
     94E  ILE*     4.7     4.7    -      -       +      -
     95E  THR      3.9     1.1    -      -       -      +
    107E  TYR*     3.6    16.6    -      -       +      +
    248E  PRO*     3.7    33.1    -      -       +      +
    325E  NAG      3.0    26.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 5 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3E  LEU*     3.9    13.9    -      -       +      +
      4E  LYS*     1.3    85.2    -      -       -      +
      6E  ASN*     1.3    61.4    +      -       -      +
      7E  TYR*     4.2     9.2    -      +       +      -
     21E  PHE*     3.8    18.4    -      +       +      -
     22E  TYR      3.5     2.7    -      -       -      -
     23E  ASP*     3.2    30.7    -      -       -      -
     59E  THR*     3.4    15.9    +      -       -      +
     60E  PRO*     3.7    18.3    -      -       +      +
     64E  TYR*     3.7     9.4    -      +       -      -
     93E  LEU      3.4     4.2    -      -       -      +
     94E  ILE*     3.6     2.4    -      -       -      -
     95E  THR*     2.7    46.9    +      -       +      +
    158E  PHE*     3.1    43.2    -      +       -      -
    166E  ALA*     5.2     0.2    -      -       -      +
    170E  TYR*     2.7    23.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 6 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4E  LYS*     5.1     8.7    -      -       -      +
      5E  TYR*     1.3    73.9    -      -       -      +
      7E  TYR*     1.3    64.5    +      -       -      +
      8E  THR*     2.8    16.3    +      -       -      -
     20E  VAL      3.7     0.7    -      -       -      +
     21E  PHE*     3.1     7.3    -      -       -      -
     22E  TYR*     2.9    52.1    +      -       +      +
     24E  HIS*     5.9     0.4    -      -       +      -
     92E  SER*     4.1     0.5    -      -       -      -
     93E  LEU      3.6     2.5    -      -       -      -
     94E  ILE*     3.4    18.2    -      -       +      +
    325E  NAG      1.4    64.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 7 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5E  TYR*     4.3    16.3    -      +       +      -
      6E  ASN*     1.3    74.4    +      -       -      +
      8E  THR*     1.3    62.3    +      -       -      +
     20E  VAL      3.5     4.5    -      -       -      +
     21E  PHE*     3.4    40.0    -      +       +      -
     60E  PRO*     5.3     3.3    -      -       -      +
     64E  TYR*     2.6    37.2    +      -       +      +
     66E  PHE*     4.5    14.4    -      +       +      -
     69E  TRP*     3.5    37.9    +      +       +      -
     70E  TYR      5.6     0.2    -      -       -      -
     73E  MET*     3.7    20.8    -      -       -      +
     92E  SER*     3.1     5.4    -      -       -      -
     93E  LEU*     2.8    60.7    +      -       +      -
     95E  THR*     4.7     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 8 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6E  ASN*     2.8    22.2    +      -       -      -
      7E  TYR*     1.3    70.9    -      -       -      +
      9E  VAL*     1.3    67.9    +      -       -      +
     10E  THR*     4.0    15.9    +      -       -      +
     18E  ASP      3.7     0.5    -      -       -      +
     19E  GLY*     3.2     3.1    -      -       -      -
     20E  VAL*     2.8    53.8    +      -       +      +
     22E  TYR*     6.0     0.2    -      -       -      -
     73E  MET*     4.6     0.4    -      -       -      -
     90E  SER*     4.3     9.4    -      -       -      +
     91E  LEU      3.3     6.3    -      -       -      +
     92E  SER*     3.0    20.8    +      -       -      +
    325E  NAG      3.4    22.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 9 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8E  THR*     1.3    75.1    -      -       -      +
     10E  THR*     1.3    62.0    +      -       -      +
     17E  TYR*     5.0     4.9    -      -       +      -
     18E  ASP      2.9     8.7    -      -       -      +
     19E  GLY*     4.5     0.4    -      -       -      -
     70E  TYR*     3.8    35.2    -      -       +      +
     73E  MET*     3.8    41.9    -      -       +      +
     74E  LYS*     4.4     5.2    -      -       -      +
     77E  LEU*     3.6    21.0    -      -       +      +
     90E  SER*     3.1     4.0    -      -       -      -
     91E  LEU*     3.0    36.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 10 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8E  THR*     4.0    10.2    +      -       -      +
      9E  VAL*     1.3    76.8    +      -       -      +
     11E  LEU*     1.3    63.0    +      -       -      +
     12E  LYS*     3.1    20.1    +      -       +      +
     17E  TYR*     3.0    11.5    -      -       -      -
     18E  ASP*     2.8    40.1    +      -       -      +
     20E  VAL*     5.7     2.3    -      -       -      +
     77E  LEU*     4.6     0.2    -      -       -      -
     89E  THR*     3.5    24.5    -      -       +      +
     90E  SER*     3.6    14.5    -      -       -      +
    325E  NAG      6.1     0.2    -      -       -      -
----------------------------------------------------------
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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