Contacts of the strand formed by residues 209 - 213 (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 THR 209 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  ASN*     3.9     1.8    -      -       -      -
    203T  ARG*     3.6     2.3    -      -       -      +
    204T  ILE*     2.9    34.3    +      -       -      +
    207T  PRO*     2.8    35.8    +      -       +      +
    208T  ARG*     1.3    77.2    -      -       -      +
    210T  THR*     1.3    63.8    +      -       -      +
    221T  CYS*     4.7     1.8    -      -       -      -
    222T  THR      3.2    16.2    -      -       -      +
    223T  GLY      4.0     0.2    -      -       -      -
    224T  ALA*     3.8    18.6    -      -       +      +
    233T  ALA*     3.3    25.9    -      -       +      +
    237T  TYR*     2.4    23.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 210 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  PHE*     4.5     1.6    -      -       +      -
     45A  ASN*     3.8    11.3    +      -       -      -
     46A  ILE      3.5    22.5    +      -       -      +
     47A  ASN*     4.4    13.3    +      -       -      +
     53A  GLU*     4.2    10.0    +      -       -      -
    201T  ILE*     4.4     7.6    -      -       +      -
    202T  MET      3.3    13.7    -      -       -      +
    203T  ARG*     3.9    14.0    -      -       +      +
    209T  THR*     1.3    77.4    +      -       -      +
    211T  ALA*     1.3    68.7    +      -       -      +
    212T  LEU*     5.5     1.3    -      -       +      -
    220T  VAL      4.1     0.5    -      -       -      +
    221T  CYS*     3.8     0.7    -      -       -      -
    222T  THR*     2.4    50.1    +      -       -      +
    237T  TYR*     3.9     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 211 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200T  VAL      3.4     2.6    -      -       -      +
    201T  ILE*     3.6     3.3    -      -       -      -
    202T  MET*     2.9    31.8    +      -       +      -
    210T  THR*     1.3    75.9    -      -       -      +
    212T  LEU*     1.3    66.1    +      -       -      +
    213T  ILE*     4.2     3.8    -      -       +      -
    219T  MET*     4.2    16.2    -      -       +      -
    220T  VAL      3.4     9.4    -      -       -      +
    221T  CYS*     4.9     3.8    -      -       +      -
    237T  TYR*     3.6    39.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 212 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  LEU*     4.0    23.6    -      -       +      -
     41A  PHE*     3.6    29.8    -      -       +      -
     47A  ASN      3.3    25.6    -      -       -      +
     81A  LEU      5.8     0.2    -      -       -      +
     82A  THR*     5.7     0.2    -      -       -      +
    197T  PHE*     3.6    34.1    -      -       +      -
    199T  ALA*     4.5     7.9    -      -       +      -
    200T  VAL      3.3     2.0    -      -       -      +
    201T  ILE*     3.7     9.4    -      -       +      -
    210T  THR*     5.5     1.6    -      -       +      -
    211T  ALA*     1.3    78.9    -      -       -      +
    213T  ILE*     1.3    62.5    +      -       -      +
    214T  PHE*     4.1     8.9    +      -       +      -
    218T  LYS      4.2     0.5    -      -       -      +
    219T  MET*     3.3     6.4    -      -       -      +
    220T  VAL*     2.9    40.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 213 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174T  LEU*     5.0     1.1    -      -       +      -
    178T  LEU*     3.7    27.1    -      -       +      -
    180T  LEU*     3.6    11.9    -      -       +      +
    183T  ILE*     4.7     7.0    -      -       +      -
    199T  ALA*     3.3     5.6    -      -       -      +
    200T  VAL*     2.9    44.1    +      -       +      +
    202T  MET*     3.8    37.0    -      -       +      -
    211T  ALA*     4.6     3.4    -      -       +      -
    212T  LEU*     1.3    76.4    -      -       -      +
    214T  PHE*     1.3    66.0    +      -       -      +
    218T  LYS      4.3     1.8    -      -       -      +
    219T  MET*     3.6    29.2    -      -       +      -
    237T  TYR*     5.0     4.3    -      -       +      +
    241T  VAL*     4.3    17.7    -      -       +      -
----------------------------------------------------------
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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