Contacts of the strand formed by residues 198 - 207 (chain J) 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 J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190J  GLY      4.4     5.4    -      -       -      +
    191J  ASN      4.1     5.4    -      -       -      +
    192J  GLU*     3.4    16.4    -      -       +      +
    193J  LEU      5.5     0.4    -      -       -      -
    196J  GLY      5.3     1.0    -      -       -      -
    197J  ASN*     1.3    87.1    +      -       +      +
    199J  THR*     1.3    69.0    +      -       -      +
    200J  LEU*     5.0     1.1    -      -       -      -
    270J  ARG*     4.0     6.6    -      -       -      -
    271J  THR*     2.9    52.5    +      -       +      +
    278J  GLN*     3.7    20.9    -      -       -      +
    296J  SER*     3.8     6.3    -      -       -      -
    297J  GLU*     3.0    49.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 199 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190J  GLY*     3.4     4.7    -      -       -      -
    191J  ASN*     3.0    55.1    +      -       +      +
    192J  GLU*     3.7     2.9    -      -       -      +
    193J  LEU*     4.1    27.0    -      -       +      +
    198J  MET*     1.3    79.1    -      -       -      +
    200J  LEU*     1.3    60.7    +      -       -      +
    268J  LEU*     3.8    29.2    -      -       +      +
    269J  VAL      3.2    14.6    +      -       -      -
    270J  ARG*     4.6     3.5    -      -       -      +
    271J  THR*     4.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 200 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188J  VAL*     3.9    15.7    -      -       +      -
    189J  THR      3.3    13.5    -      -       -      +
    190J  GLY*     3.9     3.1    -      -       -      -
    198J  MET*     5.0     2.2    -      -       +      -
    199J  THR*     1.3    73.2    -      -       -      +
    201J  GLU*     1.3    60.9    +      -       -      +
    216J  TRP*     3.8    16.9    -      -       +      -
    267J  ASP      3.8     0.5    -      -       -      +
    268J  LEU*     3.3     4.9    -      -       -      +
    269J  VAL*     2.7    42.7    +      -       +      +
    271J  THR*     3.6    16.7    +      -       +      +
    278J  GLN*     4.0     4.7    -      -       +      +
    279J  PRO*     3.4    46.9    -      -       +      +
    295J  CYS      4.1     0.4    -      -       -      +
    296J  SER*     2.9    34.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 201 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187J  LYS      3.5     2.1    -      -       -      +
    188J  VAL*     3.2     5.3    -      -       -      -
    189J  THR*     2.7    44.8    +      -       -      +
    191J  ASN*     3.5    23.2    +      -       -      +
    200J  LEU*     1.3    74.8    -      -       -      +
    202J  CYS*     1.3    61.7    +      -       -      +
    203J  THR*     3.4    22.2    +      -       +      +
    266J  THR*     3.9    27.8    +      -       +      +
    267J  ASP      3.4     4.0    -      -       -      +
    268J  LEU*     3.4    20.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 202 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186J  VAL*     4.0    21.1    -      -       -      -
    187J  LYS      3.7     3.4    -      -       -      -
    188J  VAL*     4.1     4.0    -      -       -      +
    201J  GLU*     1.3    72.0    -      -       -      +
    203J  THR*     1.3    61.6    +      -       -      +
    204J  VAL*     4.2     5.1    +      -       -      +
    214J  THR*     4.2     2.5    -      -       -      +
    216J  TRP*     3.3    18.2    -      -       +      -
    265J  LEU*     4.1     0.7    -      -       -      +
    266J  THR*     3.5     1.6    -      -       -      -
    267J  ASP*     2.7    44.2    +      -       +      +
    281J  CYS*     2.0    48.9    -      -       +      -
    283J  VAL*     4.1     6.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 203 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185J  THR      3.4     1.7    -      -       -      +
    186J  VAL*     3.3     5.4    -      -       -      +
    187J  LYS*     2.9    41.5    +      -       +      +
    189J  THR*     5.2     4.9    -      -       -      +
    201J  GLU*     3.4    32.3    -      -       +      +
    202J  CYS*     1.3    78.1    -      -       -      +
    204J  VAL*     1.3    61.0    +      -       -      +
    205J  ASN*     3.6    20.6    +      -       -      -
    265J  LEU      3.3     9.2    -      -       -      -
    266J  THR*     4.2     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 204 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184J  PRO*     3.2    35.2    -      -       +      -
    185J  THR      3.4     2.2    -      -       -      -
    186J  VAL*     4.1    10.5    -      -       +      -
    202J  CYS*     4.7     5.4    -      -       -      +
    203J  THR*     1.3    77.4    -      -       -      +
    205J  ASN*     1.3    60.7    +      -       -      +
    207J  PHE*     3.5    19.0    -      -       +      -
    212J  VAL*     4.9     4.0    -      -       +      -
    214J  THR*     5.5     0.7    -      -       -      +
    264J  SER*     3.4     4.7    -      -       -      -
    265J  LEU*     2.8    58.3    +      -       +      +
    283J  VAL*     4.0    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 205 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184J  PRO*     3.0    19.0    -      -       -      +
    185J  THR*     2.7    32.1    +      -       -      +
    187J  LYS*     4.2    22.2    -      -       -      +
    203J  THR*     3.6    21.6    +      -       -      -
    204J  VAL*     1.3    77.1    +      -       -      +
    206J  SER*     1.3    76.9    +      -       -      +
    207J  PHE      3.8     1.1    -      -       -      -
    264J  SER*     3.8    11.2    +      -       -      +
    265J  LEU      5.3     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 206 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182J  THR*     3.4    16.8    -      -       -      +
    183J  THR      3.6     7.1    -      -       -      +
    205J  ASN*     1.3    78.3    +      -       -      +
    207J  PHE*     1.3    56.9    +      -       -      +
    257J  ASP*     3.2    15.3    -      -       -      -
    258J  LYS*     4.6     9.4    +      -       -      -
    262J  THR*     2.6    28.6    +      -       -      -
    263J  TYR      2.8     9.9    +      -       -      -
    264J  SER*     3.0    11.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 207 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182J  THR      3.1    11.4    -      -       -      +
    184J  PRO*     3.5    17.0    -      -       +      -
    204J  VAL*     3.5    39.9    -      -       +      -
    206J  SER*     1.3    73.3    -      -       -      +
    208J  TYR*     1.3    62.8    +      -       -      +
    209J  PRO      3.5    13.7    -      -       -      -
    210J  PRO      3.6    17.7    -      -       -      -
    212J  VAL*     3.4    26.5    -      -       +      -
    254J  ILE*     4.3     6.3    -      -       +      -
    262J  THR*     3.3     4.3    -      -       -      -
    263J  TYR*     2.8    53.6    +      -       +      -
    264J  SER      4.0     1.8    -      -       -      -
    265J  LEU*     3.7    23.6    -      -       +      -
    285J  HIS*     3.7     9.9    -      -       +      +
----------------------------------------------------------
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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