Contacts of the strand formed by residues 251 - 256 (chain A) in PDB entry 4MSL


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 251 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224A  CYS*     4.0    26.9    -      -       +      -
    237A  THR*     4.5    14.1    -      -       +      -
    238A  THR      3.4    16.2    -      -       -      +
    239A  TYR*     3.9    10.1    -      -       +      +
    244A  CYS      4.3     3.8    -      -       -      +
    247A  ASP*     3.5    32.3    -      -       +      +
    248A  LEU*     4.4    13.5    -      -       +      -
    249A  GLY      4.3     0.2    -      -       -      +
    250A  ALA*     1.3    81.4    -      -       -      +
    252A  GLU*     1.3    61.5    +      -       -      +
    269A  LYS      3.4     4.9    +      -       -      -
    270A  ILE*     2.6    52.4    +      -       +      +
    271A  TYR      4.1    15.5    -      -       -      +
    272A  SER*     6.0     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237A  THR*     3.3     3.1    -      -       -      -
    238A  THR*     2.8    51.7    +      -       -      +
    240A  ALA*     5.8     3.5    -      -       -      +
    250A  ALA      3.8     2.4    +      -       -      +
    251A  LEU*     1.3    74.6    -      -       -      +
    253A  LEU*     1.3    59.5    +      -       -      +
    254A  TRP*     3.4    19.2    +      -       +      +
    265A  THR*     4.0    17.7    +      -       -      +
    267A  GLY      3.6    14.4    -      -       -      +
    268A  VAL*     3.7    21.6    -      -       +      +
    269A  LYS      5.4     0.2    -      -       -      +
    270A  ILE*     4.2     1.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  PHE*     4.7     2.9    -      -       +      -
    236A  PHE      3.3    26.9    -      -       -      +
    237A  THR*     3.9    13.9    -      -       +      +
    252A  GLU*     1.3    70.1    -      -       -      +
    254A  TRP*     1.3    62.1    +      -       -      +
    265A  THR*     3.3     4.2    -      -       -      -
    266A  ILE*     2.6    57.1    +      -       +      -
    267A  GLY      2.8    17.0    +      -       -      +
    270A  ILE*     3.6    19.3    -      -       +      +
    273A  PHE*     4.0    31.6    -      -       +      -
    280A  LEU*     4.7     5.2    -      -       +      -
    282A  ALA*     4.5     7.2    -      -       +      -
    304A  TRP*     4.1    19.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 254 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  HIS*     3.6    37.2    -      +       -      -
    235A  PHE*     3.5     5.5    -      -       -      +
    236A  PHE*     2.8    50.8    +      +       +      -
    238A  THR*     3.2    24.6    +      -       -      -
    252A  GLU*     3.4    24.6    -      -       -      +
    253A  LEU*     1.3    86.7    -      -       -      +
    255A  ARG*     1.3    64.1    +      -       -      +
    263A  PHE*     3.5    33.7    -      +       +      -
    264A  LYS      3.4     5.8    -      -       -      +
    265A  THR*     3.3    30.0    -      -       +      +
    266A  ILE*     4.5     2.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233A  THR*     3.6    21.1    -      -       +      -
    234A  ILE      3.4     5.2    -      -       -      +
    235A  PHE*     3.6    16.8    -      -       +      -
    236A  PHE*     4.9     0.4    -      -       -      -
    254A  TRP*     1.3    75.9    -      -       -      +
    256A  THR*     1.3    63.6    +      -       -      +
    257A  SER*     4.1    11.9    +      -       -      +
    262A  SER      4.1     0.2    -      -       -      +
    263A  PHE*     3.4     8.7    -      -       -      -
    264A  LYS*     2.8    55.5    +      -       -      +
    266A  ILE*     3.8    19.3    -      -       +      -
    300A  GLN*     2.6    46.1    +      -       -      +
    301A  GLY      4.5     1.2    -      -       -      -
    302A  ASP*     3.3    40.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 256 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  ILE*     4.6     2.7    -      -       +      -
    232A  ASN      4.3     0.6    -      -       -      +
    233A  THR*     3.3     5.5    -      -       -      +
    234A  ILE*     2.8    60.0    +      -       +      +
    236A  PHE*     4.7     1.3    -      -       +      -
    255A  ARG*     1.3    74.4    -      -       -      +
    257A  SER*     1.3    59.8    +      -       -      +
    258A  ASP*     2.7    28.1    +      -       -      -
    259A  LEU      4.3     3.4    -      -       -      +
    260A  GLY*     2.9    15.6    +      -       -      +
    262A  SER      3.0    14.4    +      -       -      -
    263A  PHE*     3.7    17.3    -      -       +      -
----------------------------------------------------------
 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