Contacts of the strand formed by residues 88 - 95 (chain H) 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 88 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38H  ARG*     4.2    10.1    -      -       +      -
     39H  GLN      3.2    28.5    -      -       -      +
     40H  ALA*     3.5     8.5    -      -       +      +
     41H  PRO*     4.0     5.8    -      -       -      -
     85H  GLU      5.8     0.2    -      -       -      +
     86H  ASP      3.2     9.1    +      -       -      +
     87H  THR*     1.3    78.3    -      -       -      +
     89H  VAL*     1.3    60.2    +      -       -      +
     90H  TYR*     3.6    13.7    -      -       +      -
    108H  MET*     3.8     7.2    -      -       -      -
    109H  VAL*     2.7    38.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 89 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37H  VAL      3.9     0.3    -      -       -      +
     38H  ARG*     3.2     2.8    -      -       -      -
     39H  GLN*     2.7    48.9    +      -       +      +
     41H  PRO*     5.9     1.6    -      -       +      -
     88H  ALA*     1.3    70.6    -      -       -      +
     90H  TYR*     1.3    63.0    +      -       -      +
     91H  TYR*     3.7    33.4    +      -       +      +
    105H  GLN      4.9     1.1    -      -       -      +
    106H  GLY*     3.8    19.1    -      -       -      -
    107H  THR      3.4     8.5    -      -       -      +
    108H  MET*     3.7    30.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 90 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6H  GLU*     2.9     9.3    -      -       -      +
     20H  LEU*     3.5    28.9    -      -       +      -
     36H  TRP*     4.4     6.3    -      +       +      -
     37H  VAL      3.5     4.0    -      -       -      -
     38H  ARG*     3.1    41.4    +      -       +      -
     48H  VAL*     4.4     8.5    -      -       +      -
     67H  PHE*     4.1    13.7    -      +       -      -
     80H  LEU*     4.3    10.3    -      -       +      -
     82H  MET*     4.0    16.5    -      -       -      -
     86H  ASP*     2.8    33.6    +      -       -      +
     88H  ALA*     3.6    20.9    -      -       +      -
     89H  VAL*     1.3    73.0    -      -       -      +
     91H  TYR*     1.3    61.2    +      -       -      +
    106H  GLY*     3.3     0.2    -      -       -      -
    107H  THR*     2.8    37.1    +      -       -      +
    109H  VAL*     3.8    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 91 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6H  GLU*     3.3     5.2    -      -       -      +
     36H  TRP*     3.3     9.4    -      -       -      -
     37H  VAL      2.7    44.9    +      -       -      +
     39H  GLN*     3.5    34.9    +      -       +      -
     45H  LEU*     4.6     2.7    -      -       +      -
     89H  VAL*     3.7    24.5    -      -       +      +
     90H  TYR*     1.3    73.9    -      -       -      +
     92H  CYS*     1.3    62.2    +      -       -      +
     93H  VAL*     4.1     3.3    -      -       +      +
    103H  TRP*     3.8    27.6    -      +       +      -
    104H  GLY      3.3    18.8    -      -       -      +
    105H  GLN      3.7    16.3    +      -       -      -
    106H  GLY*     3.5     7.6    -      -       -      -
     38L  GLN*     3.6     8.7    +      -       -      -
     41L  GLY      5.8     0.3    -      -       -      -
     42L  GLN      3.7     6.9    +      -       -      -
     43L  PRO*     3.6    27.1    -      -       +      -
     44L  PRO*     4.5     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 92 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4H  LEU*     3.7    14.8    -      -       -      +
      6H  GLU*     3.2    15.3    +      -       -      -
     22H  CYS*     2.0    49.4    -      -       -      -
     34H  MET*     6.1     1.1    -      -       -      -
     35H  ASN      3.4     3.4    -      -       -      -
     36H  TRP*     3.5    19.9    -      -       +      -
     78H  LEU*     3.6    21.1    -      -       +      -
     91H  TYR*     1.3    71.2    -      -       -      +
     93H  VAL*     1.3    67.6    +      -       -      +
    104H  GLY      2.9    25.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 93 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4H  LEU*     4.1     3.8    -      -       -      -
     34H  MET*     3.8     6.5    -      -       -      +
     35H  ASN*     2.9    51.6    +      -       +      +
     37H  VAL*     4.0     8.1    -      -       +      -
     91H  TYR*     4.1     8.5    -      -       +      +
     92H  CYS*     1.3    83.5    -      -       -      +
     94H  ARG*     1.3    59.6    +      -       -      +
    100H  PHE*     3.3    35.7    -      -       +      +
    102H  ILE      3.1     9.0    -      -       -      +
    103H  TRP*     3.4    42.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 94 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2H  VAL*     4.1     6.9    -      -       -      +
      4H  LEU*     4.0     5.9    -      -       +      +
     27H  PHE*     3.5    41.2    -      -       +      +
     32H  TYR*     3.4    48.3    +      -       +      -
     34H  MET*     3.1    26.2    -      -       +      -
     93H  VAL*     1.3    73.4    -      -       -      +
     95H  GLU*     1.3    66.5    +      -       -      +
     97H  PRO*     5.3     1.6    -      -       -      +
    100H  PHE*     3.4     5.4    -      -       -      +
    101H  ASP*     2.9    60.5    +      -       -      +
    102H  ILE*     2.8    29.4    +      -       +      +
    229H  SO4      5.1     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 95 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32H  TYR*     3.4    11.1    -      -       -      +
     33H  ARG*     2.7    68.8    +      -       +      +
     35H  ASN*     2.9    28.5    +      -       -      +
     93H  VAL      3.9     1.0    +      -       -      -
     94H  ARG*     1.3    85.9    -      -       -      +
     96H  GLY*     1.3    68.9    +      -       -      +
     99H  ALA*     3.6     9.5    -      -       +      +
    100H  VAL*     3.1    50.3    +      -       +      +
    101H  ASP*     4.4     0.7    -      -       -      -
     96L  LEU*     4.7     3.5    -      -       -      +
----------------------------------------------------------
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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