Contacts of the helix formed by residues 192 - 210 (chain N) in PDB entry 5MQF
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 LYS 192 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191N GLU* 1.3 73.4 - - - +
193N ARG* 1.3 65.2 + - - +
195N LYS* 3.2 12.1 - - + +
196N TYR* 2.9 24.1 + - - +
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Residues in contact with ARG 193 (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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190N ILE* 6.3 0.2 - - + -
191N GLU* 3.1 12.1 - - + +
192N LYS* 1.3 77.8 - - - +
194N ASP* 1.3 59.0 + - - +
195N LYS 3.1 0.5 + - - -
196N TYR* 3.1 5.2 + - - +
197N SER* 2.9 28.3 + - - -
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Residues in contact with ASP 194 (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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190N ILE* 3.7 28.0 - - + +
191N GLU 3.5 4.9 + - - +
192N LYS 3.5 0.4 - - - -
193N ARG* 1.3 78.1 - - - +
195N LYS* 1.3 56.9 + - - +
197N SER* 4.1 9.4 - - - -
198N ARG* 2.9 30.1 + - - +
322O MET 4.6 14.4 - - - +
323O LEU* 5.3 5.4 - - + -
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Residues in contact with LYS 195 (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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191N GLU 3.3 7.3 + - - +
192N LYS* 3.1 23.5 + - + +
193N ARG 3.0 1.2 - - - -
194N ASP* 1.3 75.4 - - - +
196N TYR* 1.3 59.9 + - - +
198N ARG* 3.3 5.5 + - - +
199N ARG* 2.9 27.3 + - - +
290O ARG 5.6 5.8 - - - +
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Residues in contact with TYR 196 (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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192N LYS 2.9 12.2 + - - +
193N ARG* 3.8 6.3 - - - +
195N LYS* 1.3 73.1 - - - +
197N SER* 1.3 61.6 + - - +
199N ARG* 2.9 22.5 + - - +
200N ARG* 2.9 15.9 + - - +
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Residues in contact with SER 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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193N ARG 2.9 16.8 + - - -
194N ASP* 4.1 8.7 - - - -
196N TYR* 1.3 76.9 - - - +
198N ARG* 1.3 57.4 + - - +
200N ARG* 4.2 5.4 - - - +
201N PRO* 3.1 21.2 - - - +
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Residues in contact with ARG 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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194N ASP 2.9 22.1 + - - +
195N LYS* 3.6 7.2 - - - +
196N TYR 3.1 0.2 - - - -
197N SER* 1.3 77.5 - - - +
199N ARG* 1.3 60.9 + - - +
200N ARG 3.3 0.7 - - - -
201N PRO* 3.3 16.7 - - - +
202N TYR* 3.9 7.6 + - - +
322O MET* 4.6 25.6 - - + +
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Residues in contact with ARG 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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195N LYS 2.9 16.9 + - - +
196N TYR* 2.9 10.0 + - - +
198N ARG* 1.3 76.1 - - - +
200N ARG* 1.3 63.7 + - - +
201N PRO 3.5 0.2 - - - -
202N TYR* 3.3 9.8 + - + +
203N ASN* 3.2 21.8 + - - +
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Residues in contact with ARG 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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196N TYR 2.9 14.1 + - - +
197N SER* 4.2 6.1 - - - +
199N ARG* 1.3 77.2 - - - +
201N PRO* 1.3 64.2 - - + +
203N ASN* 3.2 8.4 + - - +
204N ASP* 2.9 26.1 + - - +
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Residues in contact with PRO 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 SER 3.1 21.8 - - - +
198N ARG* 3.3 15.5 - - - +
200N ARG* 1.3 91.8 - - + +
202N TYR* 1.3 54.5 + - - -
204N ASP* 3.7 10.7 - - + +
205N ASP* 2.9 28.8 + - - +
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Residues in contact with TYR 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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198N ARG 4.2 5.8 - - - +
199N ARG* 3.3 16.3 + - - +
200N ARG 3.1 0.8 - - - -
201N PRO* 1.3 80.7 - - - +
203N ASN* 1.3 57.1 + - - +
205N ASP* 3.3 5.8 + - - +
206N ALA* 2.9 27.3 + - - +
287O MET 6.4 0.2 - - - -
288O LYS* 5.6 13.7 - - + -
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Residues in contact with ASN 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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199N ARG 3.2 10.2 + - - +
200N ARG* 3.7 7.9 - - - +
202N TYR* 1.3 75.8 - - - +
204N ASP* 1.3 61.4 + - - +
206N ALA* 3.2 8.9 + - - +
207N ASP* 2.9 29.1 + - - +
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Residues in contact with ASP 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 ARG 2.9 16.5 + - - +
201N PRO* 3.7 10.8 - - + +
203N ASN* 1.3 76.6 - - - +
205N ASP* 1.3 57.9 + - - +
207N ASP* 3.3 5.8 + - - +
208N ILE* 2.9 29.3 + - - +
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Residues in contact with ASP 205 (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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856 U 4.5 4.5 + - - +
201N PRO 2.9 18.5 + - - +
202N TYR* 3.8 5.6 - - - +
204N ASP* 1.3 75.5 - - - +
206N ALA* 1.3 58.9 + - - +
208N ILE* 3.8 6.5 - - - +
209N ASP* 2.9 28.9 + - - +
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Residues in contact with ALA 206 (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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202N TYR 2.9 17.4 + - - +
203N ASN* 3.5 9.9 - - - +
204N ASP 3.2 0.4 - - - -
205N ASP* 1.3 75.0 - - - +
207N ASP* 1.3 59.3 + - - +
209N ASP* 3.4 5.9 + - - +
210N TYR* 2.9 28.1 + - - +
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Residues in contact with ASP 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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203N ASN 2.9 15.6 + - - +
204N ASP* 3.8 6.5 - - - +
206N ALA* 1.3 73.2 - - - +
208N ILE* 1.3 65.5 + - - +
210N TYR* 3.2 18.4 + - - +
211N ILE* 3.6 8.8 + - - +
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Residues in contact with ILE 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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846 A 3.6 4.7 + - - -
856 U 3.3 31.9 + - - +
204N ASP 2.9 18.7 + - - +
205N ASP* 4.1 4.7 - - - +
207N ASP* 1.3 77.1 - - - +
209N ASP* 1.3 60.5 + - - +
211N ILE* 3.3 23.4 + - - +
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Residues in contact with ASP 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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846 A 3.3 31.0 + - + +
856 U 4.1 0.6 + - - -
205N ASP 2.9 20.8 + - - +
206N ALA* 3.7 7.2 - - - +
207N ASP 3.3 0.2 - - - -
208N ILE* 1.3 72.3 - - - +
210N TYR* 1.3 60.2 + - - +
211N ILE 3.1 10.3 + - - +
212N ASN* 5.1 3.6 - - - +
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Residues in contact with TYR 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 ALA 2.9 16.6 + - - +
207N ASP* 3.5 11.7 - - - +
208N ILE 3.2 0.6 - - - -
209N ASP* 1.3 75.9 - - - +
211N ILE* 1.3 57.1 + - - +
212N ASN* 3.7 3.7 + - - +
213N GLU 5.8 0.2 - - - +
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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