Contacts of the strand formed by residues 185 - 189 (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 185 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183E  THR      5.2     0.7    +      -       -      -
    184E  PRO*     1.3    76.6    +      -       -      +
    186E  VAL*     1.3    63.2    +      -       -      +
    187E  LYS*     3.3    39.5    -      -       +      +
    203E  THR      3.4     1.6    -      -       -      +
    204E  VAL*     3.3     3.3    -      -       -      -
    205E  ASN*     2.7    45.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 186 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184E  PRO*     4.3     8.0    +      -       +      +
    185E  THR*     1.3    82.9    -      -       -      +
    187E  LYS*     1.3    76.9    +      -       -      +
    202E  CYS*     4.0    21.8    -      -       -      -
    203E  THR      3.3     8.5    -      -       -      +
    204E  VAL*     4.1    20.0    -      -       +      -
    283E  VAL*     4.2     7.4    -      -       +      -
    293E  TYR*     3.5    67.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 187 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185E  THR*     3.3    29.7    -      -       +      +
    186E  VAL*     1.3    83.7    -      -       -      +
    188E  VAL*     1.3    63.6    +      -       -      +
    189E  THR*     4.1     5.6    +      -       -      +
    201E  GLU      3.5     2.1    -      -       -      +
    203E  THR*     3.0    37.2    +      -       +      +
    205E  ASN*     4.2    16.0    -      -       -      +
    293E  TYR*     5.8     1.1    -      -       -      -
    299E  CYS*     6.0     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 188 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187E  LYS*     1.3    77.1    -      -       -      +
    189E  THR*     1.3    59.5    +      -       -      +
    200E  LEU*     3.9    18.4    -      -       +      -
    201E  GLU      3.2     8.3    -      -       -      +
    202E  CYS*     4.1     6.1    -      -       -      -
    216E  TRP*     4.0    17.7    -      -       +      -
    279E  PRO      5.9     0.7    -      -       -      +
    280E  VAL*     6.3     0.2    -      -       -      -
    281E  CYS*     3.7    25.8    -      -       +      +
    293E  TYR*     3.7    21.3    -      -       +      +
    294E  THR*     3.1    21.3    +      -       -      +
    295E  CYS*     3.2    12.4    -      -       -      +
    299E  CYS*     2.5    38.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 189 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187E  LYS*     4.9     6.1    +      -       -      +
    188E  VAL*     1.3    76.8    +      -       -      +
    190E  GLY*     1.3    63.3    +      -       -      +
    191E  ASN*     3.2    36.5    +      -       -      +
    199E  THR      3.5     1.2    -      -       -      +
    200E  LEU*     3.3     8.2    -      -       -      +
    201E  GLU*     2.7    48.5    +      -       -      +
    203E  THR*     5.2     4.5    -      -       -      +
    295E  CYS      4.6     0.2    -      -       -      -
    298E  GLY*     4.0    19.1    +      -       -      +
    299E  CYS*     4.7     0.4    -      -       -      +
----------------------------------------------------------
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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