Contacts of the helix formed by residues 190 - 207 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLU* 4.0 15.3 - - - +
127B PRO 5.2 0.2 - - - +
128B VAL 3.7 22.2 - - - +
130B SER* 4.1 3.6 - - - +
148B ARG* 3.5 48.2 - - + +
186B ALA* 4.4 5.8 - - + -
187B ASN* 3.5 36.8 - - + +
188B PRO 3.1 1.2 - - - -
189B ASN* 1.3 79.9 - - + +
191B SER* 1.3 68.3 + - - +
192B THR* 3.4 22.0 - - - +
193B THR* 3.1 18.7 + - - +
194B ILE* 3.3 13.6 + - - +
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Residues in contact with SER 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B SER* 3.2 18.8 + - - -
147B ASP 4.6 0.5 + - - -
148B ARG* 3.5 8.1 - - - +
149B GLU* 3.1 40.4 + - - +
162B ASN* 5.2 1.6 + - - +
190B ILE* 1.3 73.4 - - - +
192B THR* 1.3 59.5 + - - +
194B ILE* 3.3 9.6 + - - +
195B GLY* 2.9 26.3 + - - -
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Residues in contact with THR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ASP* 3.2 49.0 + - - +
148B ARG* 4.0 7.2 + - + +
162B ASN* 3.7 28.7 - - - +
186B ALA* 6.1 0.3 - - - +
190B ILE* 3.4 14.1 - - - +
191B SER* 1.3 78.7 + - - +
193B THR* 1.3 60.1 + - - +
195B GLY 3.5 0.7 + - - -
196B ARG* 2.9 48.0 + - - +
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Residues in contact with THR 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 3.7 38.1 - - + +
186B ALA* 3.7 21.7 - - - +
187B ASN 2.8 29.3 + - - +
188B PRO* 3.8 14.6 - - + -
190B ILE* 3.1 10.9 + - - +
192B THR* 1.3 77.9 + - - +
194B ILE* 1.3 60.8 + - + +
196B ARG* 3.2 3.5 + - - +
197B LYS* 2.8 29.1 + - + +
218B TYR* 4.5 2.5 - - + -
250B THR* 6.0 0.2 - - - -
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PRO* 3.3 36.6 - - + +
189B ASN 5.6 0.2 - - - -
190B ILE 3.3 8.3 + - - +
191B SER* 3.3 11.3 + - - +
193B THR* 1.3 74.1 - - + +
195B GLY* 1.3 66.7 + - - +
197B LYS* 3.4 13.2 + - + +
198B ASN* 2.9 47.8 + - - +
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Residues in contact with GLY 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ASN* 3.9 18.4 - - - -
163B GLU* 3.2 15.9 - - - -
191B SER 2.9 16.7 + - - -
192B THR 3.8 1.8 - - - -
194B ILE* 1.3 77.6 - - - +
196B ARG* 1.3 60.2 + - - +
198B ASN* 3.3 9.2 + - - +
199B GLY 3.1 17.0 + - - -
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Residues in contact with ARG 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ASP* 4.3 5.9 + - - -
160B VAL* 4.6 2.2 - - - +
162B ASN* 2.7 39.2 + - - +
166B ALA* 3.0 28.8 - - + +
183B LEU* 4.9 1.2 - - - +
185B LEU* 4.2 14.4 - - + -
192B THR* 2.9 37.0 + - - +
193B THR* 3.8 3.8 - - - +
195B GLY* 1.3 73.0 - - - +
197B LYS* 1.3 66.2 + - - +
199B GLY 3.2 0.3 + - - -
200B TYR* 3.1 11.4 + - - +
250B THR* 2.7 42.3 + - + -
251B ASN* 4.4 7.9 - - - +
278B PHE* 3.7 31.6 - - + +
279B ASP* 5.4 0.4 + - - -
296B GLN* 3.6 28.7 + - - +
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Residues in contact with LYS 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 4.5 5.6 - - + -
185B LEU* 3.8 22.7 - - + +
193B THR* 2.8 18.6 + - + +
194B ILE* 3.7 14.8 - - + +
195B GLY 3.4 0.2 - - - -
196B ARG* 1.3 76.1 - - - +
198B ASN* 1.3 64.3 + - - +
200B TYR* 3.4 3.3 + - - +
201B ASN* 3.0 40.8 + - - +
216B ILE* 4.2 21.3 - - + -
218B TYR* 2.7 32.2 + - + +
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Residues in contact with ASN 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLU* 3.6 22.7 + - - +
194B ILE* 2.9 39.0 + - - +
195B GLY* 3.6 7.9 - - - +
196B ARG 3.3 0.2 - - - -
197B LYS* 1.3 79.4 - - - +
199B GLY* 1.3 62.3 + - - +
201B ASN* 3.8 13.6 + - - +
202B LYS* 3.1 24.6 + - - +
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Residues in contact with GLY 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLU* 3.2 33.6 - - - +
167B TYR* 3.3 23.5 - - - +
195B GLY 3.1 10.9 + - - -
196B ARG 3.2 3.7 + - - -
198B ASN* 1.3 75.5 - - - +
200B TYR* 1.3 63.6 + - - +
202B LYS* 3.4 2.4 + - - +
203B ALA* 3.2 17.2 + - - +
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Residues in contact with TYR 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ALA* 3.9 2.6 - - + +
170B THR* 3.4 39.4 - - + +
181B VAL* 2.5 38.9 + - + -
183B LEU* 3.7 40.2 - - + -
196B ARG 3.1 11.7 + - - +
197B LYS 3.5 7.2 - - - +
199B GLY* 1.3 72.1 - - - +
201B ASN* 1.3 77.3 + - - +
203B ALA* 3.1 4.3 + - - +
204B ILE* 3.0 46.9 + - + +
211B VAL* 4.2 11.2 - - + +
212B ASN 5.1 1.2 + - - -
215B LEU* 4.2 15.6 - - - +
216B ILE* 4.1 21.1 - - + -
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Residues in contact with ASN 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LYS* 3.0 36.7 + - - +
198B ASN* 3.8 14.7 + - - +
199B GLY 3.4 0.2 - - - -
200B TYR* 1.3 87.1 - - - +
202B LYS* 1.3 56.8 + - - +
204B ILE* 3.3 2.8 + - - +
205B SER* 2.9 32.0 + - - -
211B VAL* 3.4 33.4 - - + +
216B ILE* 4.6 4.2 - - - +
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Residues in contact with LYS 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLU* 3.7 27.4 - - + +
164B GLU* 6.3 0.7 - - - +
167B TYR* 3.8 34.8 + - + -
198B ASN 3.1 15.8 + - - +
199B GLY 3.6 4.7 - - - +
200B TYR 3.3 0.2 - - - -
201B ASN* 1.3 77.7 - - - +
203B ALA* 1.3 62.5 + - - +
205B SER* 3.6 7.3 + - - -
206B GLU* 3.1 32.0 + - - +
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Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TYR* 3.7 25.7 - - + -
170B THR* 3.8 23.3 - - + -
171B LYS* 3.8 15.3 - - + +
174B LEU* 3.9 4.7 - - + -
199B GLY 3.2 8.7 + - - +
200B TYR 3.1 7.6 + - - +
202B LYS* 1.3 74.7 - - - +
204B ILE* 1.3 67.9 + - - +
206B GLU* 3.1 10.3 + - - +
207B PHE* 3.3 20.9 + - - -
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Residues in contact with ILE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B THR* 4.3 3.4 - - + -
174B LEU* 4.2 27.1 - - + -
179B LYS 5.0 2.7 - - - +
181B VAL* 4.7 5.6 - - + +
200B TYR* 3.0 57.2 + - + +
201B ASN 3.5 7.0 - - - +
203B ALA* 1.3 76.4 - - - +
205B SER* 1.3 60.0 + - - +
207B PHE* 3.1 8.3 + - - -
209B LEU* 3.1 57.3 + - + +
210B ASN 3.9 7.2 - - - +
211B VAL* 3.8 21.5 - - + -
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Residues in contact with SER 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ASN 2.9 18.7 + - - -
202B LYS* 3.8 8.0 + - - -
203B ALA 3.2 0.2 - - - -
204B ILE* 1.3 71.5 - - - +
206B GLU* 1.3 62.2 + - - +
207B PHE 3.1 2.2 - - - -
208B ASP* 3.0 25.1 + - - +
209B LEU 4.2 9.4 - - - -
211B VAL* 6.3 0.4 - - - -
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TYR* 2.7 38.9 + - - -
171B LYS* 3.8 14.1 + - - +
202B LYS* 3.1 23.6 + - - +
203B ALA* 3.1 7.4 + - - +
205B SER* 1.3 76.4 + - - +
207B PHE* 1.3 66.2 + - + +
208B ASP* 3.2 6.1 + - - +
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Residues in contact with PHE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LYS* 3.9 23.6 - - + -
174B LEU* 3.8 42.0 - - + -
175B GLU* 4.1 21.5 - - + -
179B LYS* 4.3 20.6 + - + -
203B ALA 3.4 13.0 - - - +
204B ILE 3.1 9.5 + - - +
205B SER 3.1 0.8 - - - -
206B GLU* 1.3 89.2 - - + +
208B ASP* 1.3 66.9 + - - +
209B LEU* 3.1 22.8 + - + +
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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
------------------------------------------------------------
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