Contacts of the helix formed by residues 204 - 212 (chain N) in PDB entry 6CET
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 ARG 204 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517M LEU* 4.1 17.3 + - - +
518M HIS* 3.8 37.2 - - - +
171N GLU 4.8 2.0 + - - -
172N TYR* 4.4 15.8 + - - +
173N ASP 3.8 7.2 - - - +
174N VAL* 3.8 11.2 - - + -
199N TYR* 5.2 0.3 - - - -
202N GLY 5.0 0.2 - - - -
203N PHE* 1.3 82.4 + - + +
205N HIS* 1.3 62.7 + - - +
206N ILE* 3.5 19.6 - - - +
207N GLN* 3.3 58.7 + - - +
208N LYS* 3.0 27.6 + - - +
237N SER* 4.9 9.2 - - - +
326N LEU* 3.4 44.8 + - + +
327N GLN* 6.0 0.2 - - - +
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Residues in contact with HIS 205 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170N GLN 5.1 5.8 + - - -
171N GLU* 2.9 48.0 + - + +
173N ASP* 3.6 15.2 + - + +
175N PRO* 5.0 2.7 - - + -
204N ARG* 1.3 75.7 - - - +
206N ILE* 1.3 62.2 + - - +
207N GLN 3.1 1.1 - - - -
208N LYS* 3.1 28.3 + - + +
209N ILE* 3.0 31.8 + - + +
217N LEU* 4.9 0.4 - - + -
220N VAL* 3.4 46.2 - - + +
221N ARG* 4.8 3.8 - - + -
224N ILE* 4.2 29.7 - - + +
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Residues in contact with ILE 206 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517M LEU 5.4 0.7 - - - +
518M HIS* 3.6 26.2 - - + +
519M TYR* 5.1 4.5 - - - +
557M GLU 5.1 10.1 - - - +
558M ASP* 5.9 4.0 - - + -
171N GLU* 3.1 29.1 + - - +
204N ARG* 3.5 31.4 - - - +
205N HIS* 1.3 73.1 - - - +
207N GLN* 1.3 64.1 + - + +
209N ILE* 3.7 11.8 - - + +
210N SER* 2.9 26.1 + - - +
217N LEU* 5.7 2.5 - - + -
327N GLN* 5.9 7.0 - - - -
328N LYS* 5.3 2.6 + - - +
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Residues in contact with GLN 207 (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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199N TYR* 4.7 12.9 + - - +
203N PHE* 5.0 3.3 + - - +
204N ARG* 3.3 42.3 + - - +
205N HIS 3.1 0.4 - - - -
206N ILE* 1.3 78.0 - - + +
208N LYS* 1.3 53.3 + - - +
210N SER* 3.8 1.4 + - - -
211N ALA* 2.7 43.0 + - + +
322N LEU 5.1 2.2 + - - -
325N ARG* 3.3 28.9 + - - +
326N LEU* 3.4 23.0 - - + +
327N GLN* 4.1 20.6 - - - +
328N LYS* 5.9 0.7 - - - +
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Residues in contact with LYS 208 (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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175N PRO* 3.4 26.2 - - + +
196N ILE* 6.1 4.3 - - + -
199N TYR* 3.5 38.9 - - + +
200N ILE* 4.3 12.1 - - + +
202N GLY 3.6 17.5 - - - -
203N PHE 3.0 24.5 + - - -
204N ARG 3.0 19.5 + - - +
205N HIS* 3.1 35.9 + - + +
207N GLN* 1.3 76.8 - - - +
209N ILE* 1.3 64.4 + - - +
212N GLU* 3.0 21.3 + - - +
213N ALA* 3.2 8.6 + - + +
220N VAL* 5.6 5.6 - - + -
224N ILE* 5.7 2.2 - - + -
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Residues in contact with ILE 209 (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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171N GLU* 4.0 7.4 - - - +
205N HIS* 3.0 23.0 + - - +
206N ILE* 3.7 20.4 - - + +
208N LYS* 1.3 77.8 - - + +
210N SER* 1.3 64.2 + - - +
213N ALA* 2.9 14.1 + - + -
214N ASP* 2.7 30.9 + - - -
215N VAL* 3.3 38.1 - - + +
216N GLU 3.8 10.8 - - - -
217N LEU* 3.8 14.1 - - + +
220N VAL* 3.7 29.6 - - + -
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Residues in contact with SER 210 (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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206N ILE* 2.9 24.5 + - - +
207N GLN 3.7 1.4 + - - -
209N ILE* 1.3 82.7 - - - +
211N ALA* 1.3 60.1 + - - +
214N ASP* 4.0 12.7 - - - +
328N LYS* 3.3 47.2 - - - +
329N TYR 5.5 0.9 - - - +
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Residues in contact with ALA 211 (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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199N TYR* 5.0 9.6 - - + +
207N GLN* 2.7 26.0 + - + +
208N LYS* 4.1 2.9 - - - +
210N SER* 1.3 80.9 - - - +
212N GLU* 1.3 68.0 + - + +
214N ASP* 4.9 2.7 - - - +
328N LYS* 5.6 2.7 - - + -
329N TYR 5.9 2.5 - - - -
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Residues in contact with GLU 212 (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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195N GLN 4.1 9.7 - - - +
196N ILE* 5.2 1.5 - - - +
198N PRO* 4.3 11.1 - - - +
199N TYR* 3.3 46.6 + - + +
208N LYS 3.0 7.3 + - - +
211N ALA* 1.3 82.0 - - + +
213N ALA* 1.3 68.6 + - - +
214N ASP* 3.5 11.1 - - - +
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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
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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