Contacts of the strand formed by residues 92 - 100 (chain E) in PDB entry 6IAP


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 92 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38E  ARG*     4.0    10.5    -      -       -      -
     39E  GLN      3.2    31.4    -      -       -      +
     40E  ALA*     3.9     3.6    -      -       +      +
     41E  PRO*     4.5     3.6    -      -       -      -
     89E  GLU      5.6     0.4    -      -       -      +
     90E  ASP      3.2     4.4    +      -       -      +
     91E  THR*     1.3    77.9    -      -       -      +
     93E  VAL*     1.3    61.5    +      -       -      +
     94E  TYR*     3.5    19.3    -      -       +      -
    112E  LEU*     3.7     6.8    -      -       -      +
    113E  VAL      2.8    35.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 93 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38E  ARG*     3.2     3.8    -      -       -      -
     39E  GLN*     2.9    37.1    +      -       +      +
     92E  ALA*     1.3    74.9    -      -       -      +
     94E  TYR*     1.3    58.2    +      -       -      +
     95E  TYR*     3.9    27.3    -      -       +      +
    109E  GLN      5.0     1.3    -      -       -      +
    110E  GLY*     3.8    13.0    -      -       -      -
    111E  THR      3.2    27.1    -      -       -      +
    112E  LEU*     4.2    19.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 94 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6E  GLN*     2.8    20.6    +      -       -      -
     18E  VAL*     6.1     0.7    -      -       +      -
     20E  VAL*     5.0     1.8    -      -       +      -
     36E  TRP*     4.5    12.1    -      -       +      -
     37E  VAL      3.8     2.7    -      -       -      -
     38E  ARG*     2.9    39.1    +      -       +      -
     48E  ILE*     3.6    27.1    -      -       +      -
     81E  MET*     3.8    19.7    -      -       +      -
     83E  LEU*     3.5    22.7    -      -       +      +
     86E  LEU*     6.1     0.2    -      -       +      -
     90E  ASP      2.6    30.4    +      -       -      -
     92E  ALA*     3.5    22.7    -      -       +      -
     93E  VAL*     1.3    72.0    -      -       -      +
     95E  TYR*     1.3    61.1    +      -       -      +
    111E  THR*     2.8    28.0    +      -       -      +
    113E  VAL*     3.6    25.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 95 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  GLN*     3.4     8.1    +      -       -      -
     41D  GLY      5.2     2.3    +      -       -      -
     42D  LYS      4.4     3.2    +      -       -      -
     43D  ALA*     3.7    24.0    -      -       +      -
     44D  PRO*     4.2     5.8    -      -       +      -
      6E  GLN*     3.2     5.8    -      -       -      +
     36E  TRP*     3.5     8.2    -      -       -      -
     37E  VAL*     2.8    43.5    +      -       -      +
     39E  GLN*     3.0    34.0    +      -       +      -
     45E  LEU*     4.0    10.8    -      -       +      -
     93E  VAL*     3.9    31.2    -      -       +      +
     94E  TYR*     1.3    74.3    -      -       -      +
     96E  CYS*     1.3    63.7    +      -       -      +
     97E  VAL*     3.9     0.6    +      -       +      +
    107E  TRP*     3.7    30.3    -      +       +      -
    108E  GLY      3.6    18.8    -      -       -      +
    109E  GLN      4.1     3.4    -      -       -      -
    110E  GLY*     3.6    16.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 96 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4E  LEU*     3.7    12.1    -      -       -      +
      6E  GLN*     3.1    26.8    +      -       -      +
     22E  CYS*     2.0    54.1    -      -       +      -
     34E  MET*     4.4     5.6    -      -       -      -
     35E  HIS      3.4     5.8    -      -       -      +
     36E  TRP*     3.6    19.9    -      -       +      -
     95E  TYR*     1.3    73.5    -      -       -      +
     97E  VAL*     1.3    60.3    +      -       -      +
    107E  TRP*     3.5     0.9    -      -       -      -
    108E  GLY      3.0    25.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 97 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4E  LEU*     4.2     0.2    -      -       -      -
     34E  MET*     3.7     6.4    -      -       -      -
     35E  HIS*     2.7    63.9    +      -       +      +
     37E  VAL*     3.8    26.2    -      -       +      +
     95E  TYR      4.7     0.2    -      -       -      +
     96E  CYS*     1.3    76.3    -      -       -      +
     98E  ARG*     1.3    63.2    +      -       -      +
    104E  PHE*     3.4    38.1    -      -       +      -
    106E  TYR      3.3    12.3    -      -       -      +
    107E  TRP*     3.6    25.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 98 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2E  VAL*     3.7     8.5    -      -       -      +
      4E  LEU*     3.9    11.6    -      -       +      +
     27E  TYR*     3.4    51.8    -      -       +      +
     32E  PHE*     3.3    55.0    -      -       +      -
     33E  THR      3.5     5.6    -      -       -      +
     34E  MET*     4.5     2.7    -      -       -      -
     97E  VAL*     1.3    70.3    -      -       -      +
     99E  GLY*     1.3    63.2    +      -       -      +
    100E  SER*     4.2     1.0    -      -       -      -
    104E  PHE*     3.2    26.7    -      -       -      +
    105E  ASP*     2.7    43.2    +      -       -      +
    106E  TYR*     2.8    40.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 99 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  GLU*     3.7    21.4    -      -       -      +
     81A  LEU*     3.7     4.9    -      -       -      +
     32E  PHE*     3.6     4.9    -      -       -      +
     33E  THR*     2.8    46.1    +      -       -      -
     35E  HIS*     4.2     5.8    -      -       -      -
     97E  VAL      3.8     0.6    +      -       -      -
     98E  ARG*     1.3    74.6    -      -       -      +
    100E  SER*     1.3    63.3    +      -       -      -
    103E  GLY      3.8     2.2    -      -       -      -
    104E  PHE*     4.6     0.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 100 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  GLU*     3.0    19.4    +      -       -      +
     81A  LEU*     3.8     9.2    -      -       -      -
     32E  PHE*     3.6    24.0    -      -       -      -
     98E  ARG*     3.7     2.3    +      -       -      -
     99E  GLY*     1.3    76.4    -      -       -      +
    101E  SER*     1.3    65.8    +      -       -      +
    102E  ARG*     2.8     9.4    +      -       -      +
    103E  GLY      2.8    16.1    +      -       -      +
    105E  ASP*     2.6    38.7    +      -       -      -
----------------------------------------------------------
 Back to top of page


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