Contacts of the strand formed by residues 200 - 208 (chain B) in PDB entry 6MZL


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 CYS 200 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  LEU*     3.6    34.1    -      -       -      -
     29B  THR      3.1    16.6    -      -       -      +
     30B  HIS*     4.5     4.5    -      -       -      +
     31B  GLN*     5.5     3.4    -      -       +      -
    198B  GLU*     3.2    10.7    +      -       -      -
    199B  LEU*     1.3    81.3    -      -       -      +
    201B  THR*     1.3    62.2    -      -       -      +
    202B  TRP*     3.2    28.4    -      -       +      -
    241B  PRO*     3.2     6.9    -      -       -      +
    242B  THR      2.6    35.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 201 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  THR*     2.9    17.2    +      -       -      +
     30B  HIS*     2.7    37.3    +      -       +      +
     31B  GLN      2.9    15.2    +      -       -      -
    200B  CYS*     1.3    74.4    -      -       -      +
    202B  TRP*     1.3    64.3    +      -       -      +
    237B  MET*     5.2     1.0    -      -       -      +
    238B  LEU      2.3    30.9    +      -       -      -
    239B  THR*     3.4    19.8    -      -       -      +
    240B  ILE      4.9     0.4    -      -       -      -
    241B  PRO*     4.9     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 202 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  HIS*     3.4     6.5    -      -       -      -
     31B  GLN*     2.6    53.6    +      -       +      +
     32B  VAL*     5.1     0.4    -      -       -      -
     33B  VAL*     5.5     0.4    -      -       +      -
    190B  PHE*     4.9     3.5    -      +       -      -
    198B  GLU      4.5     0.7    -      -       -      -
    200B  CYS*     3.2    35.0    -      -       +      -
    201B  THR*     1.3    92.5    +      -       -      +
    203B  LYS*     1.3    58.2    +      -       -      +
    204B  LEU*     3.7    28.5    -      -       +      -
    236B  TYR      4.0     0.2    -      -       -      +
    237B  MET*     3.3     8.3    -      -       -      +
    238B  LEU*     2.9    44.4    +      -       +      +
    242B  THR*     3.1    41.5    -      -       -      -
    243B  ALA*     3.3    17.3    -      -       -      -
    244B  ALA*     4.0    11.4    -      -       +      -
    247B  ILE*     3.7    26.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 203 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  HIS*     3.3    17.3    -      -       +      +
     31B  GLN      2.9     5.9    +      -       -      -
     32B  VAL*     2.9    42.5    -      -       +      +
     33B  VAL      3.0     3.3    +      -       -      -
    202B  TRP*     1.3    73.9    -      -       -      +
    204B  LEU*     1.3    65.5    +      -       -      +
    205B  GLU*     6.3     0.2    -      -       +      -
    221B  VAL*     5.3     2.5    -      -       -      -
    222B  GLU*     5.8     2.9    -      -       -      +
    235B  HIS*     3.4    39.0    +      -       +      +
    236B  TYR      3.8     3.1    -      -       -      +
    237B  MET*     3.7    31.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 204 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  VAL*     3.6    24.5    -      -       +      +
    190B  PHE*     6.2     2.0    -      -       +      -
    202B  TRP*     3.7    31.6    -      -       +      +
    203B  LYS*     1.3    87.6    -      -       -      +
    205B  GLU*     1.3    59.7    +      -       -      +
    206B  PHE*     3.5    19.9    -      -       +      -
    216B  SER*     3.5    24.7    -      -       -      +
    217B  ASN*     4.5     9.9    -      -       +      +
    234B  PHE      3.1     5.7    -      -       -      +
    235B  HIS*     3.2     5.5    -      -       -      -
    236B  TYR*     2.9    45.9    +      -       +      +
    238B  LEU*     5.5     2.9    -      -       +      +
    247B  ILE*     4.4    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 205 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  VAL*     5.4     4.8    -      -       +      +
     33B  VAL*     2.8    17.6    +      -       -      +
     34B  CYS*     3.1    28.7    +      -       +      +
     35B  ILE      2.9    26.9    +      -       -      -
     36B  ASN*     5.3     1.4    -      -       -      +
     48B  PHE*     4.5     6.6    -      -       -      -
    203B  LYS*     6.3     0.4    -      -       +      -
    204B  LEU*     1.3    72.3    -      -       -      +
    206B  PHE*     1.3    68.6    -      -       -      +
    207B  THR      4.2     0.2    -      -       -      -
    233B  THR*     3.6    22.8    -      -       +      +
    234B  PHE      3.3     2.7    -      -       -      -
    235B  HIS*     4.2    23.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 206 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  VAL*     3.7    22.7    -      -       +      -
     35B  ILE*     3.5    15.9    -      -       +      -
    189B  TRP*     5.7     5.8    -      +       -      -
    204B  LEU*     3.5    17.7    -      -       +      -
    205B  GLU*     1.3    83.4    -      -       -      +
    207B  THR*     1.3    60.3    +      -       -      +
    208B  VAL*     3.3    15.8    +      -       +      +
    214B  ALA*     4.6     3.6    -      -       +      -
    216B  SER*     3.2    29.4    -      -       -      -
    233B  THR*     2.9    10.7    -      -       -      -
    234B  PHE*     2.9    58.7    +      -       +      +
    236B  TYR*     3.5    22.2    -      +       +      -
    249B  LEU*     3.6    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 207 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  CYS*     4.9     0.9    -      -       -      -
     35B  ILE*     2.5    21.8    +      -       -      +
     36B  ASN*     2.4    36.5    +      -       +      +
     37B  ASN*     4.1    15.0    -      -       -      +
     38B  ILE*     3.5    22.6    -      -       +      +
    206B  PHE*     1.3    68.2    -      -       -      +
    208B  VAL*     1.3    61.4    +      -       -      +
    227B  HIS*     5.7     2.0    -      -       +      +
    231B  LYS*     4.3    25.0    +      -       +      +
    232B  LYS      3.8     5.4    -      -       -      +
    233B  THR*     4.1    10.4    +      -       -      +
    251B  ILE*     5.9     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 208 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  ILE*     5.5     1.6    -      -       -      -
    206B  PHE*     3.7    15.9    -      -       +      +
    207B  THR*     1.3    78.0    -      -       -      +
    209B  ASP*     1.3    71.0    +      -       -      +
    212B  MET      3.4    10.5    -      -       -      +
    214B  ALA*     3.7    30.3    -      -       +      -
    231B  LYS*     3.2    13.4    -      -       -      +
    232B  LYS*     2.9    49.4    +      -       +      +
    233B  THR      4.1     0.7    -      -       -      +
    234B  PHE*     3.6    27.1    -      -       +      -
    249B  LEU*     5.9     0.4    -      -       +      -
    251B  ILE*     4.7    10.1    -      -       +      -
----------------------------------------------------------
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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