Contacts of the helix formed by residues 196 - 204 (chain N) 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.
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 196 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C GLN* 3.7 17.5 - - - +
57C ALA* 5.6 1.2 - - - +
194N THR* 3.4 24.6 + - + +
195N LEU* 1.3 82.3 - - - +
197N MET* 1.3 59.9 + - - +
198N GLU* 3.3 16.0 + - - +
199N ASP* 3.0 28.1 + - - +
200N LEU* 2.8 26.9 + - - +
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Residues in contact with MET 197 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLN* 3.5 24.5 + - - +
56C SER* 5.8 3.4 - - - -
57C ALA* 5.6 2.9 - - - -
60C LEU* 6.4 0.7 - - - -
45L ARG* 5.3 10.8 - - - +
196N THR* 1.3 72.6 - - - +
198N GLU* 1.3 63.1 + - - +
200N LEU* 3.3 31.7 + - + +
201N THR* 2.8 28.6 + - - -
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Residues in contact with GLU 198 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173N HIS* 4.9 8.6 - - + +
176N MET* 3.8 17.2 - - - +
177N LYS 3.0 35.0 - - - +
196N THR* 3.2 13.3 + - - +
197N MET* 1.3 81.0 - - - +
199N ASP* 1.3 63.1 + - - +
201N THR* 3.6 6.7 + - - -
202N PRO* 3.3 17.3 - - - +
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Residues in contact with ASP 199 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C TRP* 4.3 0.3 - - - -
170N ALA* 3.2 40.6 + - + +
173N HIS* 3.2 32.6 - - - +
174N CYS* 3.6 8.2 - - - +
176N MET 5.3 0.2 - - - +
194N THR 2.9 25.8 - - - +
195N LEU* 3.8 5.9 - - + -
196N THR* 3.0 25.6 + - - +
198N GLU* 1.3 77.9 - - - +
200N LEU* 1.3 63.4 + - - +
201N THR 3.3 0.2 - - - -
202N PRO* 3.3 17.2 - - - +
203N ALA* 3.9 8.3 + - - +
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Residues in contact with LEU 200 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ALA* 4.8 18.8 - - + +
60C LEU* 5.1 16.4 - - + -
61C LEU* 4.6 24.0 - - + -
195N LEU* 5.3 6.1 - - + -
196N THR 2.8 16.2 + - - +
197N MET* 3.3 38.7 + - + +
199N ASP* 1.3 76.9 - - - +
201N THR* 1.3 62.1 + - - +
202N PRO 3.6 0.2 - - - -
203N ALA* 3.2 23.6 + - + +
204N LEU* 3.2 33.1 + - + +
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Residues in contact with THR 201 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197N MET 2.8 20.4 + - - -
198N GLU* 3.8 7.0 + - - -
200N LEU* 1.3 76.1 - - - +
202N PRO* 1.4 66.7 - - + +
204N LEU* 3.3 29.3 + - + +
205N SER* 4.4 0.3 + - - -
75S ILE* 6.0 6.3 - - + -
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Residues in contact with PRO 202 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169N ASP* 3.4 25.0 - - - +
173N HIS* 3.5 41.1 - - + +
198N GLU 3.3 17.0 - - - +
199N ASP 3.3 11.4 - - - +
201N THR* 1.4 90.5 - - + +
203N ALA* 1.3 59.3 + - - +
204N LEU 3.2 0.4 + - - -
205N SER* 3.2 24.1 + - - +
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Residues in contact with ALA 203 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C LEU* 5.6 2.0 - - + -
166N ILE* 3.7 42.5 - - + +
169N ASP* 4.3 5.1 + - + -
170N ALA* 6.0 0.9 - - + +
199N ASP 4.0 7.0 - - - +
200N LEU* 3.2 26.7 + - + +
202N PRO* 1.3 79.7 - - - +
204N LEU* 1.3 57.9 + - - +
205N SER* 3.2 7.2 + - - -
206N GLU* 4.2 9.5 + - - +
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Residues in contact with LEU 204 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200N LEU* 3.2 33.8 + - + +
201N THR* 3.6 21.1 - - + +
202N PRO 3.2 1.2 - - - -
203N ALA* 1.3 77.1 - - - +
205N SER* 1.3 58.2 + - - +
206N GLU 3.2 3.1 - - - -
208N GLY* 3.1 44.9 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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