Contacts of the strand formed by residues 84 - 90 (chain L) in PDB entry 3INU


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 ALA 84 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37L  GLN*     3.7    28.3    -      -       +      +
     38L  GLN      3.3    16.4    -      -       -      +
     39L  LYS*     3.9     7.2    -      -       +      +
     40L  PRO*     5.1     3.1    -      -       -      -
     82L  ASP      3.3     4.7    +      -       -      +
     83L  VAL*     1.3    77.4    -      -       -      +
     85L  VAL*     1.3    65.7    +      -       -      +
     86L  TYR*     3.8    11.8    -      -       +      -
    102L  THR      3.8     0.3    -      -       -      +
    103L  LYS*     3.7     3.8    -      -       -      +
    104L  VAL*     2.8    29.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 85 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36L  TYR      4.0     0.2    -      -       -      +
     37L  GLN*     3.7     1.0    -      -       -      -
     38L  GLN*     2.7    48.7    +      -       +      +
     84L  ALA*     1.3    75.7    -      -       -      +
     86L  TYR*     1.3    63.0    +      -       -      +
     87L  TYR*     3.5    36.5    +      -       +      +
    100L  GLY      5.3     0.2    -      -       -      +
    101L  GLY*     3.9    13.5    -      -       -      -
    102L  THR      3.3    10.8    -      -       -      +
    103L  LYS*     4.4    22.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 86 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6L  GLN*     2.9     9.1    +      -       -      -
     21L  ILE*     3.5    22.2    -      -       +      -
     35L  TRP*     4.8     2.7    -      -       +      -
     36L  TYR      3.4     9.0    -      -       -      +
     37L  GLN*     2.9    29.5    +      -       +      -
     47L  LEU*     3.6    26.5    -      -       +      -
     62L  PHE*     3.6    16.0    -      +       -      -
     73L  LEU*     3.6    21.5    -      -       +      -
     75L  ILE*     3.6    11.7    -      -       +      +
     82L  ASP*     2.8    29.5    +      -       -      +
     84L  ALA*     3.8     8.7    -      -       +      -
     85L  VAL*     1.3    75.8    -      -       -      +
     87L  TYR*     1.3    61.0    +      -       -      +
    101L  GLY*     3.2     1.6    -      -       -      -
    102L  THR      2.8    33.9    +      -       -      +
    104L  VAL*     3.4    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 87 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39H  GLN*     3.6    17.8    +      -       -      -
     43H  LYS      3.7    10.0    +      -       -      -
     44H  GLY*     3.8    12.0    -      -       -      -
     45H  LEU*     3.8    28.3    -      -       +      -
      6L  GLN*     3.6     1.1    -      -       -      -
     35L  TRP*     3.3     6.7    -      -       -      -
     36L  TYR*     2.7    49.3    +      -       +      +
     38L  GLN*     3.4    27.8    +      -       +      -
     44L  PRO*     5.5     0.2    -      -       +      -
     85L  VAL*     3.5    30.6    -      -       +      +
     86L  TYR*     1.3    74.9    -      -       -      +
     88L  CYS*     1.3    64.6    +      -       -      +
     98L  PHE*     4.5     6.1    -      -       +      -
     99L  GLY      3.3    20.0    -      -       -      -
    100L  GLY      3.7     8.3    +      -       -      -
    101L  GLY*     3.4    21.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 88 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4L  MET*     4.0     6.5    -      -       -      -
      6L  GLN*     3.1    25.7    +      -       -      -
     23L  CYS*     2.1    46.2    -      -       +      -
     33L  LEU*     4.8     3.8    -      -       +      -
     34L  ALA      3.2     8.1    -      -       -      +
     35L  TRP*     3.5    24.8    -      -       +      -
     87L  TYR*     1.3    75.7    -      -       -      +
     89L  GLN*     1.3    63.0    +      -       -      +
     98L  PHE*     3.5     4.3    -      -       -      +
     99L  GLY*     2.9    30.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 89 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100H  PHE*     3.6    10.9    +      -       -      -
      4L  MET*     4.6     0.7    -      -       -      -
     33L  LEU*     3.5     7.2    -      -       -      +
     34L  ALA*     2.8    36.7    +      -       -      +
     36L  TYR*     2.7    37.2    +      -       +      -
     88L  CYS*     1.3    77.3    -      -       -      +
     90L  GLN*     1.3    68.7    +      -       -      +
     91L  TYR*     3.7    10.8    +      -       -      +
     96L  LEU*     3.4    35.6    -      -       -      +
     97L  THR      3.1    20.4    -      -       -      +
     98L  PHE*     3.6    29.2    -      -       +      -
     99L  GLY      4.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 90 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2L  LEU*     3.5    21.9    -      -       +      +
      4L  MET*     3.6    28.8    -      -       +      +
     27L  VAL*     4.0    19.5    -      -       -      -
     32L  TYR      3.5     4.7    -      -       -      -
     33L  LEU*     4.2     2.0    -      -       +      -
     89L  GLN*     1.3    84.3    +      -       -      +
     91L  TYR*     1.3    58.5    +      -       -      +
     92L  TYR*     2.8    33.1    +      -       -      +
     93L  SER      3.1    27.7    +      -       -      -
     95L  PRO      3.3    11.1    +      -       -      -
     96L  LEU*     3.8     1.9    -      -       -      +
     97L  THR*     3.1    37.3    +      -       -      +
----------------------------------------------------------
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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