Contacts of the strand formed by residues 198 - 208 (chain I) in PDB entry 1MWA


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 LYS 198 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193I  SER*     4.3     0.5    -      -       -      -
    194I  ARG*     2.9    45.4    +      -       -      +
    195I  PRO      2.9    10.8    +      -       -      +
    196I  GLU*     3.5    26.8    -      -       +      +
    197I  ASP*     1.3    79.9    -      -       -      +
    199I  VAL*     1.3    67.0    +      -       -      +
    248I  VAL*     4.0    19.3    -      -       +      +
    249I  VAL      3.3    15.0    -      -       -      +
    250I  PRO*     4.6     7.9    -      -       +      -
    251I  LEU*     5.3     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 199 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191I  HIS*     3.3    34.5    -      -       +      +
    192I  HIS      3.1    13.5    -      -       -      +
    193I  SER*     4.8     0.4    -      -       -      -
    194I  ARG*     4.1     1.8    -      -       -      -
    198I  LYS*     1.3    79.7    -      -       -      +
    200I  THR*     1.3    68.0    +      -       -      +
    201I  LEU*     3.3    31.2    -      -       +      -
    248I  VAL*     3.5     3.8    -      -       -      +
    249I  VAL*     2.8    38.7    +      -       +      +
    251I  LEU*     4.2    17.7    -      -       +      -
    254I  GLU*     4.1    13.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 200 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190I  THR      3.7     0.2    -      -       -      +
    192I  HIS*     2.9    49.3    +      -       +      +
    193I  SER      5.5     0.7    -      -       -      +
    194I  ARG*     4.2    23.8    -      -       +      +
    199I  VAL*     1.3    78.6    -      -       -      +
    201I  LEU*     1.3    63.0    +      -       -      +
    202I  ARG*     4.5    11.6    +      -       -      -
    246I  SER*     5.0     5.4    -      -       -      -
    247I  VAL      3.2     9.9    -      -       -      -
    248I  VAL*     4.2    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 201 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189I  VAL*     5.5     1.8    -      -       +      -
    190I  THR      3.6     4.0    -      -       -      +
    191I  HIS*     4.4    11.9    -      -       +      -
    199I  VAL*     3.3    28.7    +      -       +      -
    200I  THR*     1.3    72.8    -      -       -      +
    202I  ARG*     1.3    53.5    +      -       -      +
    203I  CYS      4.2     0.2    -      -       -      -
    217I  TRP*     3.6    36.9    -      -       +      -
    246I  SER*     2.7    34.1    -      -       -      -
    247I  VAL*     2.9    18.0    +      -       +      -
    249I  VAL*     4.4     6.1    -      -       +      -
    254I  GLU*     4.0    36.3    -      -       +      +
    257I  TYR*     4.3     8.7    -      -       +      +
    274I  TRP*     4.4    21.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 202 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189I  VAL*     3.1     5.8    -      -       -      +
    190I  THR*     2.9    47.7    +      -       -      +
    192I  HIS*     3.6    28.6    +      -       +      +
    200I  THR*     4.5     9.1    +      -       -      +
    201I  LEU*     1.3    74.0    -      -       -      +
    203I  CYS*     1.3    61.2    +      -       -      +
    204I  TRP*     3.2    24.8    -      -       +      +
    217I  TRP*     4.4     1.8    -      -       -      -
    244I  TRP*     3.3    40.2    -      -       +      -
    245I  ALA      3.7     1.8    -      -       -      -
    246I  SER*     3.7    16.0    +      -       -      -
     98M  ASP*     3.2    28.3    +      -       -      +
     99M  MET*     3.7    31.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 203 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188I  HIS      3.8     2.2    -      -       -      -
    189I  VAL*     4.1    10.5    -      -       -      -
    202I  ARG*     1.3    72.1    -      -       -      +
    204I  TRP*     1.3    64.2    +      -       -      +
    215I  LEU*     4.1     5.2    -      -       +      +
    217I  TRP*     3.7    15.0    -      -       +      +
    244I  TRP*     2.9    26.2    -      -       -      -
    245I  ALA*     2.7    19.6    +      -       +      +
    259I  CYS*     2.0    50.3    -      -       -      -
    261I  VAL*     4.2     9.2    -      -       -      -
    272I  LEU*     4.2     9.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 204 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186I  LYS      4.3     0.2    -      -       -      -
    187I  ALA*     2.8    33.3    -      -       -      +
    188I  HIS*     2.9    47.0    +      +       +      +
    190I  THR*     3.1    23.6    +      -       +      +
    202I  ARG*     3.2    26.3    -      -       +      +
    203I  CYS*     1.3    76.1    -      -       -      +
    205I  ALA*     1.3    61.8    +      -       -      +
    206I  LEU*     4.2    18.6    -      -       +      -
    215I  LEU*     5.4     1.1    -      -       -      -
    234I  ARG*     3.5    18.4    -      -       -      -
    242I  GLN*     5.5     0.4    -      -       +      -
    243I  LYS      3.7     7.4    -      -       -      -
    244I  TRP*     3.2    31.6    -      +       +      -
     97M  ARG      4.8     3.6    -      -       -      -
     98M  ASP*     2.9    33.7    -      -       +      -
     99M  MET*     3.2    20.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 205 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185I  PRO*     4.2     5.4    -      -       +      -
    186I  LYS      3.5     5.4    -      -       -      -
    187I  ALA*     4.5     0.9    -      -       +      +
    204I  TRP*     1.3    74.4    -      -       -      +
    206I  LEU*     1.3    63.0    +      -       -      +
    208I  PHE*     3.7    20.9    -      -       +      -
    213I  ILE*     3.7    17.9    -      -       +      -
    215I  LEU*     4.0    14.8    -      -       +      -
    242I  GLN*     3.2     8.7    -      -       -      +
    243I  LYS      2.9    31.9    +      -       -      +
    261I  VAL*     4.4     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 206 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185I  PRO*     3.6     0.5    -      -       -      +
    186I  LYS*     2.9    47.1    +      -       +      +
    188I  HIS*     4.3    26.5    -      -       +      +
    204I  TRP*     4.9    14.4    -      -       +      -
    205I  ALA*     1.3    79.0    -      -       -      +
    207I  GLY*     1.3    67.1    +      -       -      +
    208I  PHE*     3.5     3.6    +      -       -      -
    241I  PHE      3.8     0.9    -      -       -      -
    242I  GLN*     3.1    46.4    -      -       +      +
     12M  ARG      4.9     2.7    -      -       -      +
     14M  PRO*     4.5    23.3    -      -       +      -
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Residues in contact with GLY 207 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183I  ASP*     3.7    10.6    -      -       -      +
    184I  SER      3.4    11.4    -      -       -      +
    186I  LYS*     4.5     8.9    +      -       -      -
    206I  LEU*     1.3    77.1    -      -       -      +
    208I  PHE*     1.3    57.5    +      -       -      +
    236I  ALA*     5.8     0.6    -      -       -      +
    240I  THR*     3.2    33.9    -      -       -      +
    241I  PHE      3.1     7.9    +      -       -      -
    242I  GLN*     4.6     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 208 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183I  ASP      3.2    11.0    -      -       -      +
    185I  PRO*     3.2    39.5    -      -       +      -
    205I  ALA*     3.6    24.2    -      -       +      -
    207I  GLY*     1.3    75.3    -      -       -      +
    209I  TYR*     1.3    63.0    +      -       -      +
    210I  PRO      3.3    11.8    -      -       -      +
    211I  ALA      3.7    22.0    -      -       -      -
    213I  ILE*     3.7    23.8    -      -       +      -
    233I  THR*     4.5     1.8    -      -       +      -
    240I  THR*     3.5     0.8    -      -       -      -
    241I  PHE*     3.0    63.1    +      -       +      -
    242I  GLN*     3.5    22.0    -      -       -      -
    243I  LYS*     3.9     1.6    -      -       +      -
    263I  HIS*     3.9     9.2    -      +       +      -
----------------------------------------------------------
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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