Contacts of the strand formed by residues 90 - 100 (chain L) 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 SER 90 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8L  THR*     4.3    10.2    -      -       -      +
      9L  VAL      3.1    15.7    -      -       -      -
     10L  THR*     3.5    19.0    -      -       -      +
     77L  LEU*     4.1     6.9    -      -       -      +
     88L  THR*     3.1    21.5    -      -       -      +
     89L  THR*     1.3    83.2    -      -       -      +
     91L  LEU*     1.3    63.7    -      -       -      +
     92L  SER*     5.1     1.4    +      -       -      -
    112L  THR*     3.8     3.3    +      -       -      -
    113L  ALA*     3.5    21.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 91 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8L  THR*     3.3     4.9    -      -       -      +
      9L  VAL*     3.0    40.5    +      -       +      -
     73L  MET*     3.4    18.4    -      -       +      +
     76L  THR*     3.6    36.8    -      -       +      -
     77L  LEU*     4.1    11.9    -      -       +      +
     80L  ILE*     4.1    14.4    -      -       +      -
     90L  SER*     1.3    76.7    -      -       -      +
     92L  SER*     1.3    63.6    +      -       -      +
    110L  VAL*     3.5    19.7    -      -       +      -
    111L  GLU      3.5    16.2    -      -       -      +
    112L  THR*     3.7    16.2    -      -       -      +
    117L  LEU*     4.5     0.9    -      -       +      -
    140L  MET*     4.0    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 92 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6L  ASN*     4.1     7.3    +      -       -      -
      7L  TYR      3.1     7.6    -      -       -      -
      8L  THR*     2.9    27.7    +      -       -      +
     73L  MET*     3.9     4.3    -      -       -      -
     90L  SER*     5.1     1.7    +      -       -      -
     91L  LEU*     1.3    73.4    -      -       -      +
     93L  LEU*     1.3    60.4    +      -       -      +
     94L  ILE*     3.8     5.7    +      -       -      -
    109L  TYR      3.8     0.2    -      -       -      +
    110L  VAL*     3.2     9.5    -      -       -      +
    111L  GLU*     2.9    53.7    +      -       -      +
    325L  NAG      4.5     7.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 93 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5L  TYR      3.4     6.2    -      -       -      +
      6L  ASN*     3.7     0.3    -      -       -      -
      7L  TYR*     2.8    54.3    +      -       +      -
     69L  TRP*     3.7    48.0    -      -       +      -
     73L  MET*     3.7    10.4    -      -       +      +
     92L  SER*     1.3    71.0    -      -       -      +
     94L  ILE*     1.3    64.4    +      -       -      +
     95L  THR*     3.8     3.5    +      -       +      -
    109L  TYR      3.6    14.4    -      -       -      +
    110L  VAL*     3.8    17.5    -      -       +      +
    140L  MET*     5.0     4.3    -      -       +      -
    155L  LEU*     4.3    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 94 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4L  LYS*     4.7     4.3    -      -       +      -
      5L  TYR      3.6     3.4    -      -       -      +
      6L  ASN*     3.3    33.0    -      -       +      +
     92L  SER*     4.2     5.2    -      -       -      -
     93L  LEU*     1.3    72.6    -      -       -      +
     95L  THR*     1.3    62.0    +      -       -      +
    107L  TYR*     3.8     5.3    -      -       +      -
    108L  GLY*     3.2     3.1    +      -       -      -
    109L  TYR*     2.7    72.5    +      -       +      +
    111L  GLU*     4.0    11.4    -      -       +      -
    248L  PRO*     3.4    33.0    -      -       +      -
    325L  NAG      3.5    28.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 95 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4L  LYS      3.7     0.2    -      -       -      -
      5L  TYR*     2.7    57.3    +      -       +      +
      7L  TYR*     4.7    10.5    -      -       +      -
     93L  LEU*     5.0     6.1    -      -       +      +
     94L  ILE*     1.3    76.0    -      -       -      +
     96L  GLY*     1.3    54.0    +      -       -      +
    107L  TYR*     2.8    26.0    +      -       -      -
    108L  GLY*     3.8     4.2    -      -       -      -
    155L  LEU*     3.7    22.9    -      -       +      +
    158L  PHE*     3.8    22.9    -      -       +      -
    159L  GLU*     4.7     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 96 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3L  LEU      3.1    13.9    -      -       -      -
      5L  TYR      4.6     0.2    -      -       -      -
     95L  THR*     1.3    77.8    +      -       -      +
     97L  CYS*     1.3    61.8    +      -       -      +
    106L  SER*     3.3     4.0    -      -       -      -
    107L  TYR*     2.8    43.5    +      -       -      +
    158L  PHE*     4.3     2.9    -      -       -      -
    159L  GLU*     5.8     0.2    -      -       -      -
    163L  CYS*     3.6    15.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 97 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2L  THR*     3.9     1.9    +      -       -      -
      3L  LEU*     2.9    30.4    +      -       -      +
     96L  GLY*     1.3    75.7    -      -       -      +
     98L  TYR*     1.3    68.8    +      -       -      +
    105L  GLY      3.2    16.2    -      -       -      +
    106L  SER*     3.9    10.3    -      -       -      +
    107L  TYR*     3.8     6.7    +      -       -      -
    163L  CYS*     3.2    40.6    -      -       +      -
    164L  SER*     3.9    10.1    -      -       -      +
    167L  ILE*     3.8    25.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 98 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1L  ILE      3.5    11.4    -      -       -      +
      2L  THR*     3.9     9.6    -      -       -      +
     97L  CYS*     1.3    86.2    -      -       -      +
     99L  GLU*     1.3    62.7    +      -       -      +
    100L  THR*     3.6    21.8    -      -       -      +
    103L  LEU*     4.0     5.0    -      -       +      +
    104L  PHE*     3.2    33.3    +      -       -      +
    105L  GLY*     3.0    42.1    +      -       -      +
    106L  SER      4.1     2.0    -      -       -      -
    107L  TYR*     4.5     6.1    -      +       +      -
    167L  ILE*     4.5     3.8    -      -       -      -
    211L  ASP*     5.7     0.2    -      -       +      -
    213L  ILE*     4.3    16.3    -      -       +      +
    245L  PRO      4.0    10.4    +      -       -      -
    246L  GLY*     3.6    36.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 99 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31I  ARG*     3.2    37.4    +      -       -      +
     32I  ARG*     2.7    45.1    +      -       -      -
      1L  ILE*     2.9    53.3    +      -       +      +
     98L  TYR*     1.3    75.8    -      -       -      +
    100L  THR*     1.3    60.1    +      -       -      +
    101L  GLY      3.5     3.2    +      -       -      +
    103L  LEU      3.5     5.2    -      -       -      -
    104L  PHE*     4.1     8.1    -      -       +      -
    164L  SER      5.4     0.7    -      -       -      +
    167L  ILE*     5.0     7.2    -      -       +      +
    168L  LEU*     4.0     8.1    -      -       -      +
    286L  ASP*     3.0     7.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 100 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98L  TYR*     3.6    22.5    -      -       -      +
     99L  GLU*     1.3    68.8    -      -       -      +
    101L  GLY*     1.3    65.0    +      -       -      +
    102L  LEU      3.2     0.3    +      -       -      -
    103L  LEU*     3.0    24.3    +      -       -      +
    211L  ASP*     3.0    41.7    +      -       -      +
    212L  VAL*     3.9     1.3    -      -       -      -
    213L  ILE*     3.9    27.8    -      -       +      +
    284L  PHE*     3.3    29.5    -      -       -      +
    285L  HIS*     4.3     1.6    -      -       -      -
    286L  ASP*     4.0     0.9    -      -       -      -
----------------------------------------------------------
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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