Contacts of the strand formed by residues 198 - 207 (chain F) 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 MET 198 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190F  GLY      4.4     5.4    -      -       -      +
    191F  ASN      4.1     5.8    -      -       -      +
    192F  GLU*     3.4    17.0    -      -       +      +
    193F  LEU      5.5     0.4    -      -       -      -
    196F  GLY      5.3     0.8    -      -       -      -
    197F  ASN*     1.3    86.8    -      -       +      +
    199F  THR*     1.3    69.6    +      -       -      +
    200F  LEU*     5.0     1.8    -      -       +      -
    270F  ARG*     4.0     6.8    -      -       -      -
    271F  THR*     2.9    51.2    +      -       +      +
    278F  GLN*     3.7    20.6    -      -       -      +
    296F  SER*     3.8     6.1    -      -       -      -
    297F  GLU*     3.0    49.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 199 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190F  GLY*     3.3     4.7    -      -       -      -
    191F  ASN*     3.1    54.5    +      -       +      +
    192F  GLU*     3.6     3.1    -      -       -      +
    193F  LEU*     4.1    28.0    -      -       +      +
    198F  MET*     1.3    78.2    -      -       -      +
    200F  LEU*     1.3    60.9    +      -       -      +
    268F  LEU*     3.8    30.3    -      -       +      +
    269F  VAL      3.2    15.9    +      -       -      -
    270F  ARG*     4.6     3.9    -      -       -      +
    271F  THR*     4.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 200 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188F  VAL*     3.9    16.2    -      -       +      -
    189F  THR      3.5    12.8    -      -       -      +
    190F  GLY*     3.9     2.9    -      -       -      -
    198F  MET*     5.0     2.0    -      -       +      -
    199F  THR*     1.3    73.2    -      -       -      +
    201F  GLU*     1.3    60.2    +      -       -      +
    202F  CYS      4.2     0.7    -      -       -      -
    216F  TRP*     3.8    17.9    -      -       +      -
    267F  ASP      3.9     0.5    -      -       -      +
    268F  LEU*     3.3     4.9    -      -       -      +
    269F  VAL*     2.7    43.0    +      -       +      +
    271F  THR*     3.6    16.3    +      -       -      +
    278F  GLN*     4.0     4.9    -      -       +      +
    279F  PRO*     3.4    46.7    -      -       +      +
    295F  CYS      4.1     0.2    -      -       -      +
    296F  SER*     2.9    35.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 201 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187F  LYS      3.6     1.9    -      -       -      +
    188F  VAL*     3.2     4.4    -      -       -      -
    189F  THR*     2.7    44.4    +      -       -      +
    191F  ASN*     3.5    23.4    +      -       -      +
    200F  LEU*     1.3    74.8    -      -       -      +
    202F  CYS*     1.3    61.4    +      -       -      +
    203F  THR*     3.4    21.7    +      -       +      +
    266F  THR*     3.8    28.2    +      -       +      +
    267F  ASP      3.4     3.4    -      -       -      +
    268F  LEU*     3.4    20.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 202 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186F  VAL*     4.0    21.5    -      -       -      -
    187F  LYS      3.8     2.9    -      -       -      -
    188F  VAL*     4.1     4.0    -      -       -      +
    201F  GLU*     1.3    69.7    -      -       -      +
    203F  THR*     1.3    62.2    +      -       -      +
    204F  VAL*     4.2     5.4    +      -       -      +
    214F  THR*     4.2     1.8    -      -       -      -
    216F  TRP*     3.3    17.5    -      -       +      -
    265F  LEU*     4.6     0.9    -      -       -      +
    266F  THR*     3.5     1.0    -      -       -      -
    267F  ASP*     2.7    45.5    +      -       +      +
    281F  CYS*     2.0    50.0    -      -       -      -
    283F  VAL*     4.1     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 203 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185F  THR      3.4     1.4    -      -       -      +
    186F  VAL*     3.3     5.9    -      -       -      +
    187F  LYS*     3.0    40.9    +      -       +      +
    189F  THR*     5.2     4.9    -      -       -      +
    201F  GLU*     3.4    32.1    -      -       +      +
    202F  CYS*     1.3    77.7    -      -       -      +
    204F  VAL*     1.3    60.8    +      -       -      +
    205F  ASN*     3.6    21.4    +      -       -      -
    265F  LEU      3.4    10.5    -      -       -      -
    266F  THR*     4.2     7.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 204 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184F  PRO*     3.2    35.2    -      -       +      -
    185F  THR      3.4     2.9    -      -       -      -
    186F  VAL*     4.2    10.1    -      -       +      -
    202F  CYS*     4.7     5.2    -      -       -      +
    203F  THR*     1.3    77.0    -      -       -      +
    205F  ASN*     1.3    60.7    +      -       -      +
    207F  PHE*     3.5    18.2    -      -       +      -
    212F  VAL*     4.9     3.6    -      -       +      -
    214F  THR*     5.6     0.7    -      -       -      +
    264F  SER*     3.4     4.3    -      -       -      -
    265F  LEU*     2.8    56.6    +      -       +      +
    283F  VAL*     4.0    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 205 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184F  PRO*     3.0    19.1    -      -       -      +
    185F  THR*     2.7    31.4    +      -       -      +
    187F  LYS*     4.2    23.0    -      -       -      +
    203F  THR*     3.6    21.7    +      -       -      -
    204F  VAL*     1.3    77.7    +      -       -      +
    206F  SER*     1.3    77.8    +      -       -      +
    207F  PHE      3.8     0.9    -      -       -      -
    264F  SER*     3.8    10.2    +      -       -      +
    265F  LEU      5.2     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 206 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182F  THR*     3.3    16.8    -      -       -      +
    183F  THR      3.7     6.8    -      -       -      +
    205F  ASN*     1.3    79.2    +      -       -      +
    207F  PHE*     1.3    56.6    +      -       -      +
    257F  ASP*     3.2    15.5    -      -       -      -
    258F  LYS*     4.6     9.0    +      -       -      -
    262F  THR*     2.6    28.8    +      -       -      -
    263F  TYR      2.8     9.1    +      -       -      -
    264F  SER*     3.0    11.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 207 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182F  THR*     3.1    11.7    -      -       -      +
    184F  PRO*     3.5    17.3    -      -       +      -
    204F  VAL*     3.5    41.7    -      -       +      -
    206F  SER*     1.3    72.5    -      -       -      +
    208F  TYR*     1.3    62.1    +      -       -      +
    209F  PRO      3.5    13.9    -      -       -      -
    210F  PRO*     3.6    17.5    -      -       +      -
    212F  VAL*     3.4    25.8    -      -       +      -
    254F  ILE*     4.3     6.3    -      -       +      -
    262F  THR*     3.4     4.5    -      -       -      -
    263F  TYR*     2.8    55.4    +      -       +      -
    264F  SER      4.0     1.6    -      -       -      -
    265F  LEU*     3.7    22.7    -      -       +      -
    285F  HIS*     3.7    10.8    -      -       +      -
----------------------------------------------------------
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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