Contacts of the helix formed by residues 182 - 201 (chain A) in PDB entry 4QNR
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 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU 3.3 13.9 + - - -
10A GLY* 3.5 1.2 - - - -
12A ALA* 4.0 9.0 - - + -
14A SER* 4.0 6.7 - - - +
15A PHE* 3.4 37.8 - - - +
40A THR* 4.9 8.9 + - - +
177A PRO* 3.6 39.6 + - + +
178A PRO 3.5 11.2 - - - +
179A LEU* 2.8 17.9 + - + +
181A GLU* 1.3 81.7 - - - +
183A GLU* 1.3 54.2 + - - +
184A SER* 3.2 4.3 - - - -
185A ASP* 2.8 61.8 + - + +
186A ILE* 3.5 3.1 + - - +
189A MET* 3.2 30.2 - - - +
226A ILE* 4.7 10.8 - - - +
301A ATP 5.2 2.2 + - - -
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LEU 4.2 0.2 - - - -
180A ARG* 3.1 22.5 - - - +
181A GLU* 3.3 16.8 - - - +
182A ARG* 1.3 72.1 - - - +
184A SER* 1.3 61.7 + - - +
186A ILE* 3.2 32.0 + - + +
187A MET* 4.3 1.2 + - - +
218A LEU* 3.7 22.2 - - + +
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Residues in contact with SER 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU* 5.2 3.2 - - - +
12A ALA* 4.0 22.9 + - - +
183A GLU* 1.3 78.0 - - - +
185A ASP* 1.3 65.4 + - - +
186A ILE 3.3 0.6 + - - -
187A MET* 4.2 3.5 + - - +
188A LEU* 4.0 15.2 + - - +
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Residues in contact with ASP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLY* 3.4 13.2 - - - -
11A GLU* 3.0 21.8 + - - +
12A ALA* 3.1 24.7 + - - +
179A LEU* 4.6 3.4 - - + -
182A ARG* 2.8 49.2 + - + +
184A SER* 1.3 80.4 + - - +
186A ILE* 1.3 59.6 + - - +
187A MET 3.4 0.2 - - - -
188A LEU* 3.8 12.1 - - - +
189A MET* 2.8 40.9 + - + +
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Residues in contact with ILE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LEU* 3.6 43.1 - - + +
180A ARG* 4.6 4.9 - - - -
182A ARG 4.1 0.2 - - - +
183A GLU* 3.2 23.7 + - + +
185A ASP* 1.3 77.3 - - - +
187A MET* 1.3 60.5 + - - +
190A ALA* 2.9 31.2 + - + +
217A LEU* 3.9 31.6 - - + +
218A LEU* 3.9 24.2 - - + +
220A TYR 5.2 0.4 - - - +
222A TRP* 4.0 23.8 - - + +
229A LEU* 3.9 12.9 - - + +
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Residues in contact with MET 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLU 4.3 1.6 + - - +
184A SER 4.2 5.5 + - - +
186A ILE* 1.3 78.0 - - - +
188A LEU* 1.3 65.7 + - - +
190A ALA* 3.8 1.0 - - + +
191A GLU* 3.0 26.6 + - + +
209A PHE* 3.4 35.4 - - + -
214A ARG* 3.8 44.6 - - + +
217A LEU* 3.7 32.8 - - + -
218A LEU* 4.2 24.9 - - + -
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 5.9 5.4 - - + -
10A GLY* 4.6 10.1 - - - +
11A GLU* 3.8 42.0 - - + +
184A SER 4.0 12.7 + - - +
185A ASP* 3.4 17.6 + - - +
186A ILE 3.3 0.2 - - - -
187A MET* 1.3 78.9 - - - +
189A MET* 1.3 64.7 + - + +
191A GLU* 3.7 5.4 - - + +
192A TYR* 3.2 21.2 + - + +
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Residues in contact with MET 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.4 39.3 - - + +
10A GLY 5.2 0.7 - - - +
179A LEU* 4.2 6.3 - - - -
182A ARG* 3.2 37.9 - - - +
185A ASP* 2.8 27.4 + - + +
188A LEU* 1.3 73.7 - - + +
190A ALA* 1.3 61.2 + - - +
192A TYR* 3.2 7.5 + - - +
193A PHE* 2.9 42.6 + - + -
226A ILE* 3.5 39.5 - - + -
229A LEU* 3.6 13.0 - - + -
301A ATP 4.6 5.6 - - + +
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Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ILE 2.9 19.4 + - - +
187A MET* 3.8 6.1 - - - +
189A MET* 1.3 76.6 - - - +
191A GLU* 1.3 57.2 + - - +
193A PHE* 3.4 0.8 + - - -
194A ALA* 2.9 30.5 + - - +
209A PHE* 3.8 19.5 - - + -
217A LEU* 4.1 15.0 - - + -
229A LEU* 4.0 8.7 - - + +
233A VAL* 3.5 25.2 - - + +
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Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A MET* 3.0 18.1 + - + +
188A LEU* 3.7 6.3 - - + +
190A ALA* 1.3 77.8 - - - +
192A TYR* 1.3 62.7 + - - +
194A ALA* 3.3 3.2 + - - +
195A ILE* 3.0 38.0 + - + +
206A PHE* 4.9 6.5 - - + -
209A PHE* 3.9 15.0 - - + -
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Residues in contact with TYR 192 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ASN* 5.9 5.8 - - + +
9A LEU* 3.4 45.8 - - + -
188A LEU 3.2 11.3 + - - +
189A MET 3.2 7.5 + - - +
191A GLU* 1.3 80.4 - - - +
193A PHE* 1.3 78.3 + + - +
195A ILE* 3.4 9.5 + - + +
196A GLN* 3.1 28.8 + - + +
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Residues in contact with PHE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.3 10.5 - - + -
189A MET* 2.9 33.6 + - + +
190A ALA* 3.9 3.6 - - - +
192A TYR* 1.3 98.0 - + - +
194A ALA* 1.3 63.7 + - - +
196A GLN* 3.4 6.9 + - + +
197A MET* 3.1 22.7 + - - +
226A ILE* 3.8 28.5 - - + -
229A LEU* 4.1 9.9 - - + -
230A LYS* 3.6 60.6 - - + +
233A VAL* 3.9 13.6 - - + +
234A GLU* 4.5 4.8 - - + +
301A ATP 4.3 13.7 - + - -
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ALA 2.9 19.0 + - - +
191A GLU 3.6 4.3 - - - +
192A TYR 3.2 0.4 - - - -
193A PHE* 1.3 74.5 - - - +
195A ILE* 1.3 60.3 + - - +
197A MET* 3.2 4.0 + - - +
198A CYS* 2.9 33.7 + - - -
206A PHE* 3.6 36.3 - - + -
209A PHE* 4.0 2.0 - - + -
233A VAL* 3.5 17.0 - - + +
237A VAL* 3.8 8.5 - - + +
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Residues in contact with ILE 195 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A GLU* 3.0 29.3 + - + +
192A TYR* 3.7 7.4 - - - +
194A ALA* 1.3 76.6 - - - +
196A GLN* 1.3 64.0 + - - +
198A CYS* 3.1 9.8 + - - +
199A ARG* 3.1 43.3 + - + +
206A PHE* 4.0 22.2 - - + +
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Residues in contact with GLN 196 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A TYR* 3.1 24.7 + - + +
193A PHE* 3.7 11.9 - - + +
194A ALA 3.3 0.2 - - - -
195A ILE* 1.3 76.0 - - - +
197A MET* 1.3 62.9 + - - +
199A ARG* 3.2 10.4 + - - +
200A GLU* 3.1 21.1 + - - +
230A LYS* 6.5 0.9 - - - -
234A GLU* 5.4 5.4 - - - +
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Residues in contact with MET 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A PHE 3.1 14.7 + - - +
194A ALA* 3.2 7.6 + - - +
196A GLN* 1.3 73.8 - - - +
198A CYS* 1.3 66.7 + - - +
200A GLU* 3.1 26.9 + - + +
201A ILE* 3.0 43.5 + - + +
234A GLU* 3.6 56.5 + - + +
237A VAL* 3.8 17.5 - - + -
238A TYR* 3.9 14.6 - - + +
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Residues in contact with CYS 198 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A ALA 2.9 18.6 + - - -
195A ILE* 3.1 10.3 + - - +
197A MET* 1.3 76.5 - - - +
199A ARG* 1.3 75.2 + - - +
201A ILE* 3.6 6.5 - - - -
202A LYS 2.8 24.3 + - - -
203A LEU* 2.9 31.3 + - + +
205A LEU 4.2 1.1 - - - -
206A PHE* 3.7 38.8 - - - +
207A PRO* 4.8 0.7 - - - -
237A VAL* 4.0 13.2 - - - -
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Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ILE* 3.1 38.5 + - + +
196A GLN* 3.5 11.0 - - - +
197A MET 3.2 0.2 - - - -
198A CYS* 1.3 88.3 - - - +
200A GLU* 1.3 62.5 + - - +
202A LYS* 3.3 21.1 + - - +
203A LEU 3.1 24.9 + - - -
204A PRO 3.4 18.3 + - - -
205A LEU* 3.8 7.5 - - - +
206A PHE 4.5 1.2 - - - +
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Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A GLN 3.1 12.1 + - - +
197A MET* 3.1 30.8 + - - +
199A ARG* 1.3 79.0 - - - +
201A ILE* 1.3 61.2 - - + +
202A LYS* 3.8 9.0 + - - +
234A GLU* 4.7 7.4 - - - +
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Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A MET* 3.0 39.5 + - + +
198A CYS 4.0 4.0 - - - +
200A GLU* 1.3 81.4 - - + +
202A LYS* 1.3 69.7 + - - +
203A LEU* 3.4 30.9 + - + +
237A VAL* 4.1 17.0 - - + +
238A TYR* 4.1 26.0 - - + +
241A GLY* 4.8 5.8 - - - -
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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