Contacts of the strand formed by residues 191 - 201 (chain A) in PDB entry 4MDH


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 TYR 191 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  ILE      3.1    10.2    -      -       -      +
    182A  ILE*     3.6     2.6    -      -       -      -
    183A  TRP*     3.0    44.5    +      +       +      +
    190A  GLN*     1.3    74.8    -      -       -      +
    192A  PRO*     1.4    68.8    -      -       -      +
    193A  ASP*     2.9    46.4    +      -       -      -
    194A  VAL      5.2     0.5    +      -       -      -
    195A  ASN*     3.9     4.9    +      -       -      -
    209A  TYR*     4.9     3.6    +      -       -      -
    223A  ILE*     3.4    23.6    -      -       +      -
    307A  PHE*     3.4    25.7    -      +       -      -
    308A  SER*     3.6    25.6    +      -       -      -
    311A  LYS*     3.5    43.5    -      -       +      +
    312A  MET*     4.1     8.3    -      -       +      -
    315A  THR*     5.4     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  ALA*     4.1    14.1    -      -       +      -
    180A  VAL*     5.4     0.9    -      -       -      -
    181A  ILE      3.8     4.5    -      -       -      +
    182A  ILE*     4.1     7.9    -      -       +      -
    190A  GLN*     3.6    15.0    -      -       +      +
    191A  TYR*     1.4    93.4    -      -       +      +
    193A  ASP*     1.3    58.8    +      -       -      +
    194A  VAL*     3.8     2.5    +      -       -      +
    218A  LEU      5.3     0.7    -      -       -      +
    222A  PHE*     3.6    32.8    -      -       +      -
    223A  ILE*     4.1    27.9    -      -       +      +
    226A  VAL*     3.8    29.6    -      -       +      -
    227A  GLN*     5.5     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  ASN      4.7     1.2    -      -       -      +
    180A  VAL*     4.1     5.5    -      -       -      +
    181A  ILE*     2.9    36.1    +      -       +      +
    183A  TRP*     2.7    39.7    +      -       +      +
    191A  TYR*     2.9    28.9    +      -       +      -
    192A  PRO*     1.3    70.3    -      -       -      +
    194A  VAL*     1.3    64.3    +      -       -      +
    195A  ASN*     3.0    33.1    +      -       -      +
    196A  HIS*     4.9    10.3    +      -       -      -
    304A  ILE*     5.8     1.2    -      -       -      +
    308A  SER*     4.2     6.6    -      -       -      -
    312A  MET*     5.0     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  ILE*     4.1    14.8    -      -       +      -
    180A  VAL*     4.9     5.6    -      -       +      -
    191A  TYR*     5.2     0.6    +      -       -      -
    192A  PRO      3.8     1.7    +      -       -      +
    193A  ASP*     1.3    80.0    +      -       -      +
    195A  ASN*     1.3    60.3    +      -       -      +
    196A  HIS      3.1     6.8    +      -       -      -
    197A  ALA*     3.4    19.5    +      -       +      +
    208A  VAL*     3.7    27.6    +      -       +      +
    209A  TYR*     3.0    36.6    +      -       +      +
    218A  LEU*     4.2    10.5    -      -       +      -
    222A  PHE*     3.7    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191A  TYR*     3.9     5.4    +      -       -      -
    193A  ASP*     3.0    22.9    +      -       -      +
    194A  VAL*     1.3    76.3    +      -       -      +
    196A  HIS*     1.3    77.8    +      -       +      +
    197A  ALA      3.6     1.3    -      -       -      +
    209A  TYR*     3.9    29.1    +      -       -      -
    305A  ASN*     3.8    27.1    +      -       -      +
    307A  PHE*     5.8     0.5    -      -       -      -
    308A  SER*     3.8    14.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  ASN*     3.8    17.4    +      -       -      +
    181A  ILE*     3.8    31.9    -      -       +      -
    183A  TRP*     5.4     2.8    -      +       -      -
    193A  ASP*     4.6     9.2    +      -       -      -
    194A  VAL*     3.1     0.6    -      -       -      +
    195A  ASN*     1.3    95.1    +      -       +      +
    197A  ALA*     1.3    63.4    +      -       -      +
    198A  LYS*     4.3     8.9    -      -       -      +
    265A  PHE*     4.4    10.0    -      -       +      -
    302A  LEU*     3.7    34.4    -      -       +      +
    303A  PRO*     3.2    41.2    +      -       +      +
    304A  ILE*     5.4     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  VAL*     5.0     0.7    -      -       +      -
    178A  LYS      3.1    18.8    -      -       -      +
    179A  ASN      3.5     9.9    +      -       -      +
    180A  VAL*     4.3     9.0    -      -       +      -
    194A  VAL*     3.4    19.3    +      -       +      +
    195A  ASN      5.2     1.0    -      -       -      +
    196A  HIS*     1.3    80.5    -      -       -      +
    198A  LYS*     1.3    70.9    +      -       -      +
    207A  GLY*     3.7    16.6    -      -       -      -
    208A  VAL*     3.3    27.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  ASP      3.7     2.4    -      -       -      +
    177A  VAL*     4.0     0.3    -      -       -      -
    178A  LYS*     3.1    43.1    +      -       +      +
    179A  ASN*     5.4     2.7    -      -       -      +
    196A  HIS*     4.3     9.4    -      -       -      +
    197A  ALA*     1.3    88.1    -      -       -      +
    199A  VAL*     1.3    60.8    +      -       -      +
    205A  GLU*     3.5    37.3    +      -       +      +
    206A  VAL*     3.1    12.8    -      -       -      +
    207A  GLY*     4.1    17.7    -      -       -      +
    208A  VAL*     4.5     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  LEU*     3.6    18.4    -      -       +      -
    172A  VAL*     3.8    25.8    -      -       +      -
    176A  ASP      3.4    12.3    -      -       -      +
    177A  VAL*     4.4     6.5    -      -       +      -
    198A  LYS*     1.3    75.2    -      -       -      +
    200A  LYS*     1.3    70.5    +      -       -      +
    201A  LEU*     3.8    12.1    -      -       +      -
    204A  LYS      3.8     0.7    -      -       -      +
    205A  GLU*     2.8     8.3    -      -       -      -
    206A  VAL*     2.6    47.6    +      -       +      +
    207A  GLY      4.2     2.0    -      -       -      +
    208A  VAL*     4.4    10.5    -      -       +      +
    211A  ALA*     3.3    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172A  VAL*     3.6    19.8    -      -       -      +
    176A  ASP*     3.2    36.1    +      -       -      +
    199A  VAL*     1.3    74.8    -      -       -      +
    201A  LEU*     1.3    69.1    +      -       -      +
    202A  GLN*     5.6     2.1    +      -       -      -
    204A  LYS      5.4     0.2    -      -       -      -
    205A  GLU*     4.1    22.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  LEU*     5.1     7.0    -      -       +      +
    172A  VAL*     4.0    18.4    -      -       +      -
    199A  VAL*     4.1    14.4    -      -       +      -
    200A  LYS*     1.3    87.7    -      -       -      +
    202A  GLN*     1.3    70.1    +      -       -      +
    203A  ALA*     3.0     7.1    +      -       +      +
    204A  LYS*     3.0    27.8    +      -       -      +
    206A  VAL*     4.2    13.0    -      -       +      -
    211A  ALA*     3.9    25.1    -      -       +      +
----------------------------------------------------------
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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