Contacts of the strand formed by residues 304 - 309 (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 PHE 304 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264B  GLU      3.9     4.0    +      -       -      +
    265B  VAL*     3.9    14.3    -      -       +      -
    266B  THR*     2.9    29.8    +      -       -      +
    267B  HIS*     4.7     0.7    -      +       -      -
    284B  LEU*     4.4    13.9    -      -       +      -
    288B  PHE*     3.8    24.5    -      +       +      -
    299B  TYR*     3.3    17.7    -      +       +      +
    303B  CYS*     1.3    75.1    -      -       -      +
    305B  LYS*     1.3    75.1    +      -       -      +
    306B  THR*     3.1    25.1    -      -       +      -
    321B  SER      3.3     4.0    -      -       -      -
    323B  SER*     3.5    19.7    -      -       -      -
    346B  LEU*     5.8     3.8    -      -       +      -
    349B  SER*     4.3     4.0    -      -       -      -
    350B  LEU*     3.5    20.0    -      -       +      -
    353B  GLN*     3.3    36.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 305 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215B  VAL*     3.7    22.7    -      -       +      -
    216B  SER      2.4    32.3    +      -       -      +
    217B  ASN      3.2     9.1    +      -       -      -
    218B  GLY      2.9    28.7    +      -       -      +
    236B  TYR*     5.3     6.4    -      -       +      +
    266B  THR*     3.3    17.0    -      -       +      +
    268B  PHE*     4.8     4.3    -      -       +      -
    302B  SER*     6.1     0.2    -      -       -      -
    303B  CYS*     4.8     9.0    -      -       +      -
    304B  PHE*     1.3    81.9    -      -       -      +
    306B  THR*     1.3    65.3    +      -       -      +
    321B  SER*     2.6    32.3    +      -       -      +
    322B  MET*     2.8    32.4    -      -       +      -
    323B  SER      2.9     5.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 306 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266B  THR      3.0     6.3    +      -       -      -
    267B  HIS*     3.3    25.7    +      -       +      +
    268B  PHE*     2.9    29.0    +      -       -      +
    269B  CYS*     5.5     0.3    -      -       -      -
    304B  PHE*     3.1    33.4    -      -       +      -
    305B  LYS*     1.3    72.1    -      -       -      +
    307B  VAL*     1.3    66.0    +      -       -      +
    308B  PHE*     3.6    27.2    -      -       +      -
    323B  SER*     3.2    19.3    -      -       -      +
    325B  PHE*     3.6     7.6    -      -       +      -
    346B  LEU*     5.2     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 307 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215B  VAL*     4.5    15.9    -      -       +      -
    250B  ALA*     3.6    32.8    -      -       +      -
    253B  PRO*     4.9     5.8    -      -       +      -
    268B  PHE*     3.5    26.2    -      -       +      +
    306B  THR*     1.3    78.5    -      -       -      +
    308B  PHE*     1.3    73.9    +      -       -      +
    309B  ILE*     3.8    17.9    -      -       +      -
    322B  MET*     5.0     1.1    -      -       +      -
    323B  SER      3.0     6.3    +      -       -      +
    324B  ILE*     3.5    20.5    -      -       +      -
    325B  PHE*     2.9    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 308 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253B  PRO*     5.5     1.4    -      -       -      +
    267B  HIS*     5.4     2.7    -      +       -      -
    268B  PHE      3.0    11.8    +      -       -      +
    269B  CYS*     3.5    27.5    -      -       +      -
    270B  LEU*     4.5    13.7    +      -       -      +
    273B  LEU*     6.3     0.2    -      -       +      -
    277B  LEU*     3.6    15.9    -      -       +      -
    280B  THR*     4.5    12.8    -      -       +      -
    281B  THR*     5.6     0.4    -      -       -      -
    306B  THR*     3.6    14.6    -      -       +      -
    307B  VAL*     1.3    84.6    -      -       -      +
    309B  ILE*     1.3    68.0    +      -       -      +
    325B  PHE*     3.1    42.6    -      +       -      +
    326B  SER      4.1     8.7    -      -       -      +
    327B  THR*     3.2    14.5    +      -       +      +
    329B  LEU      4.5     6.3    -      -       -      -
    330B  LEU*     3.5    36.8    -      -       +      -
    346B  LEU*     5.7     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 309 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176B  HIS*     3.3    29.6    -      -       +      +
    178B  PHE*     3.5    45.1    -      -       +      -
    250B  ALA*     4.4     1.6    -      -       +      -
    270B  LEU*     5.0     1.6    -      -       -      -
    307B  VAL*     3.8    11.7    -      -       +      -
    308B  PHE*     1.3    79.6    -      -       -      +
    310B  ASP*     1.3    60.1    +      -       -      +
    311B  GLU      3.0    29.3    +      -       -      +
    324B  ILE*     3.6    26.0    -      -       +      -
    325B  PHE*     2.9     9.4    +      -       -      +
    326B  SER*     3.2     6.9    -      -       -      -
    327B  THR*     2.7    31.1    +      -       -      -
----------------------------------------------------------
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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