Contacts of the strand formed by residues 234 - 242 (chain A) in PDB entry 3MIB


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 MET 234 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  TYR*     4.0    11.4    -      -       +      -
    229A  TYR*     3.4    25.8    -      -       +      +
    232A  TYR      3.3     1.0    +      -       -      -
    233A  PRO*     1.3    74.9    -      -       -      +
    235A  HIS*     1.3    64.0    +      -       -      +
    236A  VAL*     4.4    10.8    -      -       +      -
    281A  VAL      3.9     0.2    -      -       -      +
    282A  ASP*     3.3     5.2    -      -       -      +
    283A  VAL*     2.9    65.1    +      -       +      -
    289A  LEU*     3.7    26.7    -      -       +      -
    319A  ILE*     4.6     2.5    -      -       +      -
    321A  TYR*     3.4    39.3    -      -       +      -
    322A  TYR      3.6     4.9    -      -       -      -
    323A  MET*     3.8    13.2    -      -       +      -
    332A  MET*     4.1     2.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  NO2      2.9     4.9    +      -       -      -
    233A  PRO*     5.1    11.6    +      -       +      -
    234A  MET*     1.3    75.3    +      -       -      +
    236A  VAL*     1.3    64.1    +      -       -      +
    237A  PHE*     3.5     4.0    +      -       -      -
    280A  PRO*     4.8    13.0    -      -       +      -
    281A  VAL      3.6     2.5    -      -       -      -
    282A  ASP*     3.4    21.2    -      -       +      +
    321A  TYR*     3.0     5.2    -      -       -      -
    322A  TYR*     2.8    78.8    +      +       +      -
    323A  MET*     6.2     0.2    -      -       -      -
    359A   NI      2.0    45.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  MET*     4.4     7.2    -      -       +      -
    235A  HIS*     1.3    71.9    -      -       -      +
    237A  PHE*     1.3    61.8    +      -       -      +
    238A  ALA      3.8     8.5    -      -       -      +
    263A  ILE*     3.6    19.1    -      -       +      -
    277A  VAL*     3.5    24.4    -      -       +      +
    280A  PRO*     3.6    10.1    -      -       -      +
    281A  VAL*     2.9    41.3    +      -       +      +
    283A  VAL*     4.3    18.2    -      -       +      -
    319A  ILE*     3.4    35.9    -      -       +      -
    320A  MET      3.5     4.7    -      -       -      +
    321A  TYR*     4.1     2.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  ARG      5.2     2.2    -      -       -      -
    150A  LEU*     3.8    18.8    -      -       +      -
    151A  PRO*     3.7    31.9    -      -       +      -
    154A  VAL*     4.4     5.4    -      -       +      -
    202A  ALA*     4.5     1.3    -      -       +      -
    235A  HIS      4.7     0.2    -      -       -      +
    236A  VAL*     1.3    74.2    -      -       -      +
    238A  ALA*     1.3    67.0    +      -       +      +
    276A  PRO*     3.5     7.1    -      -       -      +
    277A  VAL*     3.1    23.3    +      -       -      -
    280A  PRO*     5.5     4.0    -      -       +      -
    320A  MET*     3.0    42.7    +      -       +      -
    321A  TYR*     3.3    31.0    -      -       -      -
    322A  TYR*     3.6    33.0    -      +       +      -
    360A  GOL      4.7     5.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  THR*     6.4     0.4    -      -       -      -
    236A  VAL*     3.8     5.0    -      -       -      +
    237A  PHE*     1.3    89.8    -      -       +      +
    239A  TYR*     1.3    61.5    +      -       -      +
    274A  PHE*     4.2     8.3    -      -       +      -
    275A  TYR      3.3    15.0    -      -       -      +
    276A  PRO*     4.5     1.3    -      -       +      -
    277A  VAL*     3.8     5.0    -      -       -      +
    319A  ILE      3.7     0.5    -      -       -      -
    320A  MET*     2.8    43.4    +      -       +      +
    360A  GOL      3.8    22.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238A  ALA*     1.3    76.3    -      -       -      +
    240A  ARG*     1.3    63.2    +      -       -      +
    241A  VAL*     4.1    13.9    -      -       +      -
    263A  ILE*     4.0    19.7    -      -       +      -
    264A  GLY*     3.7    30.9    -      -       -      -
    265A  ARG      3.6    21.8    +      -       -      -
    266A  GLN*     4.1    23.8    +      -       +      -
    273A  ALA      3.7     0.7    -      -       -      +
    274A  PHE*     3.4     5.3    -      -       -      -
    275A  TYR*     2.8    60.5    +      +       +      +
    276A  PRO      3.8    12.8    -      -       -      -
    277A  VAL*     4.0     7.6    -      -       +      -
    317A  LEU*     4.3    10.8    -      -       +      -
    318A  TYR      3.0    12.8    -      -       -      +
    319A  ILE*     4.6     3.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  HIS*     5.3     4.9    +      -       -      -
    110A  LEU*     3.7    32.2    -      -       -      +
    137A  ILE*     3.8    13.9    -      -       -      +
    140A  ALA*     4.1     5.2    -      -       -      -
    239A  TYR*     1.3    75.1    -      -       -      +
    241A  VAL*     1.3    69.6    +      -       -      +
    242A  HIS*     4.1    13.6    +      -       -      +
    272A  GLN*     2.7    51.3    +      -       -      +
    273A  ALA      3.6    10.5    -      -       -      +
    274A  PHE*     3.6    36.1    -      -       +      -
    275A  TYR*     5.6     0.4    -      -       -      -
    317A  LEU*     3.5     4.2    -      -       -      +
    318A  TYR*     2.8    70.5    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239A  TYR*     4.1     9.0    -      -       +      -
    240A  ARG*     1.3    81.1    -      -       -      +
    242A  HIS*     1.3    62.7    +      -       -      +
    250A  VAL*     3.7    36.1    -      -       +      +
    265A  ARG*     5.7     0.7    -      -       -      +
    266A  GLN*     4.0    33.7    -      -       +      -
    268A  PRO*     3.7    30.3    -      -       +      -
    272A  GLN*     3.3    26.7    -      -       +      +
    273A  ALA      4.9     0.8    +      -       -      -
    275A  TYR*     6.0     1.6    -      -       +      -
    316A  ASN      3.5     3.8    -      -       -      -
    317A  LEU*     3.9    12.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  NO2      2.8    11.6    +      -       -      -
    240A  ARG*     4.1    22.6    +      -       -      +
    241A  VAL*     1.3    77.2    -      -       -      +
    243A  THR*     1.3    76.3    +      -       -      +
    244A  HIS*     3.3     4.7    +      +       -      -
    250A  VAL*     5.1     1.7    -      -       -      +
    272A  GLN*     2.7    25.7    +      -       -      +
    314A  MET*     3.5    21.5    -      -       +      +
    316A  ASN*     2.9    55.7    +      -       +      +
    318A  TYR*     4.1     3.1    -      -       +      -
    358A   CU      2.0    31.4    -      -       -      -
----------------------------------------------------------
 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