Contacts of the strand formed by residues 218 - 224 (chain T) 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 LYS 218 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171T  THR*     6.4     1.3    -      -       -      -
    172T  VAL      3.3     8.1    -      -       -      +
    173T  ASN*     3.8    29.6    -      -       +      +
    212T  LEU      4.2     0.2    -      -       -      +
    213T  ILE*     5.2     0.4    -      -       -      +
    214T  PHE*     3.2    47.2    +      -       +      +
    216T  SER*     3.7    11.0    +      -       -      +
    217T  GLY*     1.3    78.5    -      -       -      +
    219T  MET*     1.3    60.6    +      -       -      +
    220T  VAL*     5.2     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 219 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171T  THR*     3.3     5.3    -      -       -      -
    172T  VAL*     2.9    55.3    +      -       +      +
    174T  LEU*     4.3    23.3    -      -       +      -
    211T  ALA*     4.2     9.2    -      -       +      -
    212T  LEU      3.3    16.8    -      -       -      +
    213T  ILE*     3.6    27.8    -      -       +      -
    218T  LYS*     1.3    76.6    -      -       -      +
    220T  VAL*     1.3    64.2    +      -       -      +
    221T  CYS*     5.5     2.3    -      -       +      +
    234T  ALA*     3.4    30.3    -      -       +      +
    237T  TYR*     3.7    22.7    -      -       +      +
    238T  ALA      3.8     8.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 220 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  PHE*     3.5    28.8    -      -       +      -
     81A  LEU*     3.6    25.8    -      -       -      +
     82A  THR*     5.6     0.7    -      -       -      -
    169T  VAL*     4.4     6.3    -      -       +      -
    170T  SER      3.3    11.9    -      -       -      +
    171T  THR*     3.8    19.3    -      -       +      -
    211T  ALA*     3.4     3.3    -      -       -      +
    212T  LEU*     2.9    41.9    +      -       +      +
    214T  PHE*     4.8    19.7    -      -       +      -
    218T  LYS*     5.2     2.0    -      -       +      -
    219T  MET*     1.3    80.8    -      -       -      +
    221T  CYS*     1.3    62.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 221 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  PHE*     3.8     3.8    -      -       -      -
    168T  ILE      3.9     1.2    -      -       -      +
    169T  VAL*     3.2    14.0    -      -       -      +
    170T  SER*     2.8    46.5    +      -       -      +
    209T  THR*     4.7     2.5    -      -       -      -
    210T  THR      3.8     5.4    -      -       -      -
    211T  ALA*     4.5     3.6    -      -       +      +
    219T  MET*     5.5     2.9    -      -       +      +
    220T  VAL*     1.3    74.9    -      -       -      +
    222T  THR*     1.3    72.7    +      -       -      +
    224T  ALA      5.8     0.2    -      -       -      -
    230T  SER*     4.1    25.6    -      -       -      -
    233T  ALA*     4.4    16.8    -      -       -      -
    234T  ALA*     4.6    12.8    -      -       +      -
    237T  TYR*     5.0     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 222 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  PHE*     3.1    61.1    -      -       +      +
     45A  ASN*     4.1    15.7    -      -       -      +
     46A  ILE      4.1     2.0    +      -       -      +
    167T  ASN*     4.0     7.0    -      -       -      +
    168T  ILE      4.4     1.3    -      -       -      -
    169T  VAL*     4.6     0.2    -      -       +      -
    209T  THR*     3.2    11.6    -      -       -      +
    210T  THR*     2.4    61.8    +      -       -      +
    221T  CYS*     1.3    73.4    -      -       -      +
    223T  GLY*     1.3    59.8    +      -       -      +
    224T  ALA      3.6     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 223 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  GLY*     5.2     0.7    -      -       -      -
     45A  ASN*     3.3    36.2    +      -       -      -
     55A  GLU*     5.5     1.6    -      -       -      +
    166T  GLN      4.6     4.2    -      -       -      +
    167T  ASN*     3.0    15.4    +      -       -      -
    207T  PRO*     6.0     0.2    -      -       -      +
    208T  ARG      3.7    14.0    -      -       -      +
    209T  THR*     4.0     0.9    -      -       -      -
    222T  THR*     1.3    74.2    -      -       -      +
    224T  ALA*     1.3    63.7    +      -       -      +
    225T  LYS*     3.8    10.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 224 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167T  ASN*     3.3     8.1    +      -       -      -
    168T  ILE*     2.9    29.8    +      -       +      +
    207T  PRO*     5.3     1.3    -      -       -      -
    209T  THR*     3.8    10.7    -      -       +      +
    221T  CYS*     5.9     0.2    -      -       -      -
    222T  THR      3.6     2.4    -      -       -      -
    223T  GLY*     1.3    77.1    -      -       -      +
    225T  LYS*     1.3    59.7    +      -       -      +
    226T  SER      3.5     8.5    -      -       -      +
    229T  GLN*     3.8    11.4    -      -       +      -
    230T  SER*     3.4    42.0    -      -       -      +
----------------------------------------------------------
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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