Contacts of the strand formed by residues 296 - 307 (chain A) in PDB entry 3I7L


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 296 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  PHE*     3.7    11.9    -      -       -      +
    244A  LYS*     4.2    15.8    +      -       -      +
    287A  LYS*     3.5     9.2    -      -       -      +
    288A  GLU*     3.1    60.5    +      -       +      +
    290A  GLN*     4.2    15.3    +      -       -      +
    294A  THR*     3.4     6.9    +      -       -      -
    295A  VAL*     1.3    75.7    -      -       -      +
    297A  LEU*     1.3    74.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 297 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  PHE*     4.0    14.8    -      -       +      -
    239A  TYR*     3.5    46.2    -      -       +      -
    244A  LYS*     3.2    24.9    +      -       +      +
    246A  LEU*     3.2    29.2    -      -       +      +
    285A  LEU*     3.7    35.7    -      -       +      -
    286A  GLU      3.7     2.5    -      -       -      +
    296A  THR*     1.3    84.9    +      -       -      +
    298A  LYS*     1.3    63.3    +      -       -      +
    299A  ASP      3.7    17.5    -      -       -      +
    300A  LEU*     3.9     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 298 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  LEU*     3.3    16.2    -      -       -      +
    286A  GLU*     2.7    48.9    +      -       +      +
    288A  GLU*     4.0    32.6    -      -       +      +
    296A  THR*     4.1     2.7    -      -       -      -
    297A  LEU*     1.3    74.3    -      -       -      +
    299A  ASP*     1.3    87.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 299 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  LEU*     4.0    12.6    -      -       -      +
    248A  ILE*     4.5     7.7    -      -       -      +
    286A  GLU*     2.9    32.1    +      -       +      +
    297A  LEU*     3.7     4.9    -      -       -      +
    298A  LYS*     1.3   109.4    +      -       +      +
    300A  LEU*     1.3    86.7    +      -       -      +
    301A  ARG*     5.5     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 300 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  ILE*     5.6     3.1    -      -       +      -
    237A  ILE*     4.9     7.0    -      -       +      +
    238A  THR*     5.0     2.9    -      -       -      -
    239A  TYR*     3.9    33.2    -      -       +      +
    246A  LEU*     4.1    14.8    -      -       +      +
    247A  ALA      5.3     0.2    -      -       -      +
    248A  ILE*     3.1    41.9    -      -       +      +
    283A  LEU*     4.4    11.7    -      -       +      -
    284A  LEU      3.4     8.5    -      -       -      +
    285A  LEU*     3.2    39.0    -      -       +      -
    297A  LEU*     3.9    12.3    -      -       +      -
    299A  ASP*     1.3    92.5    +      -       -      +
    301A  ARG*     1.3    62.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 301 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248A  ILE*     4.2     3.8    -      -       -      +
    283A  LEU*     3.2     7.7    -      -       -      +
    284A  LEU*     2.6    74.5    +      -       +      +
    286A  GLU*     5.6    12.8    -      -       +      +
    299A  ASP*     5.5     2.9    -      -       -      +
    300A  LEU*     1.3    75.5    -      -       -      +
    302A  VAL*     1.3    72.8    +      -       -      +
    303A  GLU*     2.3    37.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 302 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237A  ILE*     4.0    26.0    -      -       +      -
    248A  ILE*     4.0    11.8    -      -       +      +
    250A  PRO*     4.3    17.0    -      -       +      -
    252A  ILE*     5.4    11.2    -      -       +      +
    253A  ILE*     4.1    12.6    -      -       +      -
    273A  LEU*     4.9     3.4    -      -       +      -
    281A  PHE*     3.4    34.5    -      -       +      -
    282A  MET      3.0     5.4    -      -       -      +
    283A  LEU*     4.3     8.7    -      -       +      -
    301A  ARG*     1.3    84.0    -      -       -      +
    303A  GLU*     1.3    73.9    +      -       -      +
    304A  LEU      4.2     1.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 303 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281A  PHE*     3.2     4.0    -      -       -      -
    282A  MET*     2.7    39.0    +      -       +      +
    284A  LEU*     3.3    22.4    -      -       +      -
    301A  ARG*     2.3    36.0    +      -       -      +
    302A  VAL*     1.3    79.2    -      -       -      +
    304A  LEU*     1.3    61.4    +      -       -      +
    305A  LEU*     3.0    23.0    +      -       +      +
    346A  TYR*     6.4     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 304 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252A  ILE*     4.4    27.8    -      -       +      +
    279A  ARG*     4.2    20.2    -      -       +      +
    280A  LEU      3.7     5.8    -      -       -      +
    281A  PHE*     3.7    25.2    -      -       +      -
    302A  VAL*     4.1     2.4    +      -       -      +
    303A  GLU*     1.3    68.2    -      -       -      +
    305A  LEU*     1.3    61.4    +      -       -      +
    306A  GLY*     3.6    29.6    -      -       -      +
    344A  GLY      4.7     3.1    -      -       -      +
    346A  TYR*     4.3    11.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 305 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272A  LEU*     4.3     8.5    -      -       +      -
    280A  LEU*     2.8    20.7    +      -       +      +
    281A  PHE      4.2     1.3    -      -       -      +
    282A  MET*     3.7    35.7    -      -       +      +
    303A  GLU*     3.0    26.1    +      -       +      +
    304A  LEU*     1.3    72.8    -      -       -      +
    306A  GLY*     1.3    55.7    +      -       -      +
    336A  LEU*     3.6    38.1    -      -       +      -
    344A  GLY      4.9     1.1    -      -       -      -
    345A  SER*     3.9     0.9    -      -       -      -
    346A  TYR*     2.9    49.0    +      -       +      +
    347A  VAL*     3.2    14.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 306 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279A  ARG*     3.2     8.5    -      -       -      +
    280A  LEU      2.8    25.9    +      -       -      -
    304A  LEU*     3.4    15.3    -      -       -      +
    305A  LEU*     1.3    80.7    -      -       -      +
    307A  GLU*     1.3    61.6    +      -       -      +
    344A  GLY      5.4     0.7    -      -       -      -
    345A  SER*     4.3    11.2    -      -       -      -
    347A  VAL*     3.6     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 307 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    277A  GLU      4.7     3.6    -      -       -      +
    278A  GLY      3.5     6.7    -      -       -      +
    279A  ARG*     5.1     6.1    -      -       +      +
    306A  GLY*     1.3    73.7    -      -       -      +
    308A  THR*     1.3    73.8    +      -       -      +
    334A  VAL*     5.8     0.3    -      -       -      +
    345A  SER*     4.7     3.2    +      -       -      -
    347A  VAL*     4.0    15.3    -      -       -      +
    383A  LYS*     3.7    32.4    +      -       -      +
    753A  ARG*     5.5     4.0    +      -       -      -
----------------------------------------------------------
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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