Contacts of the helix formed by residues 190 - 207 (chain A) in PDB entry 2QU7
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 ILE 190 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU* 4.2 14.6 - - - +
128A VAL 3.6 22.0 - - - +
129A LYS* 5.2 0.2 - - - +
130A SER* 4.1 3.1 - - - +
148A ARG* 3.5 44.0 - - + +
186A ALA* 4.3 9.9 - - + -
187A ASN* 3.4 36.3 - - + +
188A PRO 3.1 1.9 - - - -
189A ASN* 1.3 81.2 - - - +
191A SER* 1.3 65.8 + - - +
192A THR* 3.3 23.8 - - - +
193A THR* 3.1 17.2 + - - +
194A ILE* 3.3 13.8 + - - +
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Residues in contact with SER 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A SER* 3.5 10.8 + - - -
147A ASP 4.5 0.3 + - - -
148A ARG* 3.5 9.0 - - - +
149A GLU* 3.0 56.1 + - - +
162A ASN* 5.2 2.1 + - - -
190A ILE* 1.3 73.0 - - - +
192A THR* 1.3 61.0 + - - +
194A ILE* 3.5 9.0 + - - +
195A GLY* 3.0 24.9 + - - -
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Residues in contact with THR 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASP* 3.3 45.2 + - - +
148A ARG* 4.1 9.3 + - + -
162A ASN* 3.7 28.6 - - - +
186A ALA* 5.9 0.5 - - - +
190A ILE* 3.3 15.5 - - - +
191A SER* 1.3 78.7 + - - +
193A THR* 1.3 60.0 + - - +
195A GLY* 3.5 0.7 + - - -
196A ARG* 2.9 48.2 + - - +
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Residues in contact with THR 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 3.8 27.2 - - + +
186A ALA* 3.5 39.7 + - - +
187A ASN 2.9 23.7 + - - +
188A PRO* 3.9 11.0 - - + -
190A ILE* 3.1 9.7 + - - +
192A THR* 1.3 77.4 + - - +
194A ILE* 1.3 63.2 + - + +
196A ARG* 3.1 6.1 + - - +
197A LYS* 2.9 29.1 + - + +
218A TYR* 4.4 3.1 - - + -
250A THR* 6.0 0.2 - - - -
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Residues in contact with ILE 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PRO* 3.3 37.9 - - + +
190A ILE 3.3 7.7 + - - +
191A SER* 3.9 8.3 - - - +
192A THR 3.4 0.4 - - - -
193A THR* 1.3 77.3 - - + +
195A GLY* 1.3 63.3 + - - +
197A LYS* 3.4 15.9 + - + +
198A ASN* 2.9 46.0 + - - +
218A TYR* 6.2 0.4 - - + -
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Residues in contact with GLY 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A CL 4.6 8.5 - - - -
162A ASN* 3.9 10.8 - - - -
163A GLU* 3.2 29.5 - - - -
191A SER 3.0 16.7 + - - -
192A THR 3.8 1.6 - - - -
194A ILE* 1.3 76.4 - - - +
196A ARG* 1.3 61.3 + - - +
198A ASN* 3.3 10.5 + - - +
199A GLY 3.2 8.5 + - - -
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Residues in contact with ARG 196 (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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147A ASP* 4.3 5.7 + - - -
160A VAL* 4.7 1.4 - - - +
162A ASN* 2.8 41.2 + - + +
166A ALA* 3.0 30.6 - - + +
183A LEU* 5.0 0.4 - - - +
185A LEU* 4.1 14.1 - - + -
192A THR* 2.9 38.9 + - - +
193A THR* 3.1 3.6 + - - +
195A GLY* 1.3 72.2 - - - +
197A LYS* 1.3 67.0 + - - +
199A GLY 3.2 0.7 + - - -
200A TYR* 3.1 10.9 + - - +
250A THR* 2.7 42.6 + - + -
251A ASN* 4.4 7.1 - - - +
278A PHE* 3.6 29.3 - - + +
279A ASP* 5.1 0.2 + - - -
296A GLN* 3.4 28.5 + - - +
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Residues in contact with LYS 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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183A LEU* 4.3 14.1 - - + -
185A LEU* 3.8 17.2 - - + +
193A THR* 2.9 17.9 + - + +
194A ILE* 3.7 17.6 - - + +
196A ARG* 1.3 76.3 - - - +
198A ASN* 1.3 65.5 + - - +
200A TYR* 3.2 2.8 + - - +
201A ASN* 3.0 44.7 + - - +
211A VAL* 6.4 0.4 - - - -
216A ILE* 4.6 12.3 - - + -
218A TYR* 2.9 29.7 + - + +
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Residues in contact with ASN 198 (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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163A GLU* 3.8 23.3 + - - +
194A ILE* 2.9 40.2 + - - +
195A GLY* 3.6 8.3 - - - +
196A ARG 3.3 0.2 - - - -
197A LYS* 1.3 79.9 - - - +
199A GLY* 1.3 57.5 + - - +
201A ASN* 3.5 15.5 + - - +
202A LYS* 3.1 27.9 + - - +
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Residues in contact with GLY 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLU* 3.3 33.3 - - - +
167A TYR* 3.3 21.8 - - - -
195A GLY 3.2 10.7 + - - -
196A ARG 3.2 2.9 + - - -
198A ASN* 1.3 74.8 - - - +
200A TYR* 1.3 66.0 + - - +
202A LYS* 3.4 4.0 + - - +
203A ALA* 3.1 17.8 + - - +
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Residues in contact with TYR 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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166A ALA* 4.1 1.9 - - + +
170A THR* 3.5 38.8 - - + +
181A VAL* 2.5 42.0 + - + -
183A LEU* 3.5 44.4 - - + -
196A ARG 3.1 9.4 + - - +
197A LYS 3.2 6.9 + - - +
199A GLY* 1.3 73.4 - - - +
201A ASN* 1.3 78.3 + - - +
203A ALA* 3.2 3.8 + - - +
204A ILE* 3.0 46.1 + - + +
211A VAL* 4.6 7.9 - - + -
212A ASN 4.9 3.6 + - - -
215A LEU* 4.1 13.7 - - - +
216A ILE* 3.8 21.3 - - + -
248A VAL* 5.3 0.7 - - + -
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Residues in contact with ASN 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 LYS* 3.0 41.5 + - - +
198A ASN* 3.5 17.3 + - - +
200A TYR* 1.3 82.6 - - - +
202A LYS* 1.3 57.5 + - - +
204A ILE* 3.4 2.6 + - - +
205A SER* 2.9 35.8 + - - +
211A VAL* 3.4 37.8 - - + +
216A ILE* 4.7 1.6 - - - +
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Residues in contact with LYS 202 (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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163A GLU* 3.6 26.1 + - + +
164A GLU* 4.4 12.3 + - - +
167A TYR* 3.5 39.2 - - + -
198A ASN 3.1 11.0 + - - +
199A GLY 3.5 9.6 - - - +
201A ASN* 1.3 76.6 - - - +
203A ALA* 1.3 59.4 + - - +
205A SER* 3.5 5.3 + - - -
206A GLU* 3.0 34.0 + - - +
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Residues in contact with ALA 203 (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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167A TYR* 3.7 35.4 - - + +
170A THR* 3.7 19.5 - - + -
171A LYS* 3.8 9.4 - - + +
174A LEU* 3.8 5.2 - - + -
199A GLY 3.1 5.7 + - - +
200A TYR 3.2 6.5 + - - +
202A LYS* 1.3 75.5 - - - +
204A ILE* 1.3 65.9 + - - +
206A GLU* 3.2 3.7 + - - +
207A PHE* 3.2 29.4 + - + -
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Residues in contact with ILE 204 (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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170A THR* 4.1 4.0 - - + -
174A LEU* 4.0 28.0 - - + -
179A LYS 5.5 0.9 - - - +
181A VAL* 4.5 9.0 - - + +
200A TYR* 3.0 56.3 + - + +
201A ASN* 3.6 6.3 - - - +
203A ALA* 1.3 74.3 - - - +
205A SER* 1.3 63.3 + - - +
207A PHE* 3.1 12.3 + - - +
209A LEU* 3.1 48.8 + - + +
210A ASN 3.8 18.4 - - - +
211A VAL* 4.0 9.4 - - + +
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Residues in contact with SER 205 (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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201A ASN* 2.9 21.4 + - - +
202A LYS* 3.8 5.4 - - - -
204A ILE* 1.3 77.2 - - - +
206A GLU* 1.3 56.6 + - - +
208A ASP* 2.9 21.0 + - - +
209A LEU 3.9 10.4 + - - -
211A VAL* 4.5 9.9 - - - +
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Residues in contact with GLU 206 (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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167A TYR* 2.6 39.3 + - - -
171A LYS* 3.9 16.3 - - - +
202A LYS* 3.0 20.6 + - - +
203A ALA* 3.2 4.9 + - - +
205A SER* 1.3 76.6 - - - +
207A PHE* 1.3 69.0 + - + +
208A ASP* 3.1 3.7 + - - +
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Residues in contact with PHE 207 (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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171A LYS* 4.0 31.6 - - + -
174A LEU* 3.6 50.0 - - + -
175A GLU* 4.4 9.9 - - + -
203A ALA* 3.2 16.5 + - - +
204A ILE 3.1 9.3 + - - +
206A GLU* 1.3 85.5 - - + +
208A ASP* 1.3 69.7 + - - +
209A LEU* 3.3 21.9 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
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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