Contacts of the strand formed by residues 75 - 81 (chain A) in PDB entry 3SE3


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 LEU 75 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  VAL*     4.3    19.1    -      -       +      -
     18A  PHE*     5.6    22.9    -      -       +      -
     37A  ASP      3.2    15.0    -      -       -      +
     38A  TYR*     3.5    18.4    -      -       +      -
     46A  TRP*     4.4     4.6    -      -       -      -
     73A  ILE*     3.7    22.9    -      -       +      +
     74A  LYS*     1.3    74.0    -      -       -      +
     76A  ARG*     1.3    63.3    +      -       -      +
     77A  ILE*     5.3     8.3    -      -       +      -
     89A  GLU*     3.4     5.2    -      -       -      +
     90A  VAL*     2.9    59.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  SER      4.0     0.3    -      -       -      +
     36A  PHE*     3.9     1.2    -      -       -      -
     37A  ASP*     2.7    66.4    +      -       +      +
     46A  TRP*     2.7    80.8    +      -       +      +
     75A  LEU*     1.3    75.6    -      -       -      +
     77A  ILE*     1.3    66.1    +      -       -      +
     78A  ARG*     4.2     1.0    +      -       +      -
     87A  TRP*     6.0     5.4    -      -       +      -
     88A  TYR      3.8     6.5    -      -       -      +
     89A  GLU*     4.7     2.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  VAL*     4.5    19.3    -      -       +      -
     11A  VAL*     5.6     1.8    -      -       +      -
     20A  LEU*     3.9    37.5    -      -       +      -
     34A  PHE*     4.1    26.7    -      -       +      -
     35A  SER      3.6    10.5    -      -       -      +
     36A  PHE*     5.5     2.7    -      -       +      -
     75A  LEU*     5.3     8.3    -      -       +      -
     76A  ARG*     1.3    80.8    -      -       -      +
     78A  ARG*     1.3    62.6    +      -       -      +
     79A  ALA      3.6     1.5    +      -       -      +
     86A  SER      3.5     5.0    -      -       -      +
     87A  TRP*     4.0     1.4    -      -       -      -
     88A  TYR*     3.0    48.1    +      -       +      +
     90A  VAL*     4.7    10.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  THR      3.5     1.6    -      -       -      +
     34A  PHE*     3.1     6.4    -      -       -      -
     35A  SER*     2.8    52.0    +      -       -      -
     37A  ASP*     6.1     1.6    -      -       -      +
     76A  ARG*     4.2     1.0    +      -       +      -
     77A  ILE*     1.3    72.3    -      -       -      +
     79A  ALA*     1.3    60.2    +      -       -      +
     80A  GLU*     3.9     2.3    +      -       +      +
     85A  SER*     5.3     8.5    -      -       -      -
     86A  SER      3.8     6.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  VAL*     4.5     5.4    -      -       +      -
     34A  PHE*     3.1    35.2    -      -       +      -
     77A  ILE*     3.6     1.2    +      -       +      -
     78A  ARG*     1.3    73.9    -      -       -      +
     80A  GLU*     1.3    59.1    +      -       -      +
     81A  LYS*     3.9     1.1    +      -       -      +
     84A  THR      3.9     1.0    -      -       -      +
     85A  SER*     3.3     1.0    -      -       -      -
     86A  SER*     2.8    37.4    +      -       -      +
     88A  TYR*     3.5    29.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  VAL*     3.6     1.0    -      -       -      -
     33A  THR*     2.7    43.6    +      -       -      +
     54A  ASN*     6.0     3.8    -      -       -      +
     78A  ARG*     5.0     2.2    -      -       +      +
     79A  ALA*     1.3    72.8    -      -       -      +
     81A  LYS*     1.3    60.8    +      -       -      +
     82A  GLU      4.0     8.4    +      -       -      +
     84A  THR      3.5     7.2    -      -       -      +
     85A  SER*     4.0    16.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  VAL*     4.1    21.8    -      -       +      +
     79A  ALA      3.9     2.0    +      -       -      +
     80A  GLU*     1.3    70.3    -      -       -      +
     82A  GLU*     1.3    72.4    +      -       -      +
     83A  ASN      3.4     1.9    +      -       -      -
     84A  THR*     3.1    18.4    +      -       -      +
----------------------------------------------------------
 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