Contacts of the strand formed by residues 190 - 195 (chain E) in PDB entry 5FLM


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 VAL 190 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150E  VAL*     4.2     2.8    -      -       -      +
    151E  MET*     3.2    43.6    +      -       -      +
    156E  VAL*     3.8    37.2    -      -       +      +
    159E  LEU*     4.5     4.0    -      -       +      -
    160E  LEU*     6.2     0.2    -      -       +      -
    167E  GLU*     6.3     1.6    -      -       +      -
    170E  LEU*     4.3    16.6    -      -       +      -
    188E  GLY      4.4     2.7    -      -       -      +
    189E  GLN*     1.3    78.1    -      -       -      +
    191E  VAL*     1.3    76.5    +      -       -      +
    206E  TYR*     4.2    16.2    -      -       +      -
    207E  ARG      3.6     9.0    -      -       -      +
    208E  LEU*     3.7    20.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 191 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148E  HIS*     4.9    10.3    -      -       +      -
    149E  VAL      3.8     7.0    -      -       -      +
    150E  VAL*     4.4     8.7    -      -       +      -
    151E  MET*     4.6     0.4    -      -       -      -
    173E  ILE*     4.1    13.9    -      -       +      -
    185E  ILE*     3.5    34.3    -      -       +      -
    190E  VAL*     1.3    80.1    -      -       -      +
    192E  LYS*     1.3    59.5    +      -       -      +
    193E  ILE*     3.6    14.5    +      -       +      -
    205E  THR      3.7     0.9    -      -       -      +
    206E  TYR*     3.3     6.8    -      -       -      -
    207E  ARG*     2.9    58.4    +      -       +      +
    209E  VAL*     4.2    12.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 192 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1029A  LEU*     5.5     4.9    -      -       -      +
   1032A  GLN*     5.7     4.8    -      -       -      +
    147E  GLU      3.7     2.4    -      -       -      +
    148E  HIS*     4.6     0.2    -      -       -      -
    149E  VAL*     2.9    56.4    +      -       +      +
    151E  MET*     3.7    21.1    -      -       +      +
    155E  GLU*     6.0     1.3    -      -       -      +
    191E  VAL*     1.3    72.2    -      -       -      +
    193E  ILE*     1.3    60.9    +      -       -      +
    194E  ILE*     3.9    20.3    +      -       +      +
    204E  ILE*     3.9    35.9    -      -       +      +
    205E  THR      3.5     3.4    -      -       -      -
    206E  TYR*     3.8    23.8    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 193 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1372A  GLU*     4.2    17.9    -      -       +      +
    146E  PRO*     3.5    29.2    -      -       +      -
    147E  GLU      3.4     3.4    -      -       -      +
    148E  HIS*     3.4    29.6    -      -       +      +
    173E  ILE*     5.6     1.8    -      -       +      -
    191E  VAL*     3.6    22.4    -      -       +      +
    192E  LYS*     1.3    72.0    -      -       -      +
    194E  ILE*     1.3    66.7    +      -       -      +
    195E  ARG*     4.3    15.0    -      -       +      +
    203E  TYR      3.7     0.5    -      -       -      +
    204E  ILE*     3.3     7.3    -      -       -      +
    205E  THR*     2.9    40.5    +      -       -      +
    207E  ARG*     3.6    31.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 194 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146E  PRO*     3.6     0.7    -      -       -      +
    147E  GLU*     2.9    51.8    +      -       +      +
    149E  VAL*     4.8    16.2    -      -       +      -
    192E  LYS*     4.4    23.6    -      -       +      +
    193E  ILE*     1.3    75.8    -      -       -      +
    195E  ARG*     1.3    64.1    +      -       -      +
    196E  PRO*     4.4     2.6    -      -       +      +
    202E  ARG*     3.8    34.1    -      -       +      +
    203E  TYR      3.7     2.9    -      -       -      +
    204E  ILE*     4.3    14.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 195 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    893A  GLU*     2.9    28.9    +      -       -      -
   1372A  GLU*     4.2    17.1    +      -       -      -
   1375A  ARG*     4.3    17.4    -      -       -      +
   1376A  LYS*     5.2    13.9    -      -       -      +
   1403A  ASP*     4.2    17.6    +      -       -      -
    146E  PRO*     3.6    20.4    -      -       +      -
    193E  ILE*     3.9     6.1    -      -       +      +
    194E  ILE*     1.3    75.6    -      -       -      +
    196E  PRO*     1.3    73.9    -      -       +      +
    197E  SER*     3.7     1.0    +      -       -      -
    202E  ARG*     4.6     3.4    -      -       -      -
    203E  TYR*     2.9    56.3    +      -       +      +
    205E  THR*     2.3    33.5    +      -       -      +
    207E  ARG*     5.5     2.4    -      -       -      +
----------------------------------------------------------
 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