Contacts of the helix formed by residues 181 - 200 (chain B) in PDB entry 2QKB
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 THR 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B CYS* 3.8 11.2 - - - +
151B ASN* 3.7 7.2 - - - -
158B ALA* 4.2 2.3 - - - +
176B LEU* 4.6 0.8 - - - +
179B ARG* 3.2 45.1 + - + +
180B GLN* 1.3 78.1 - - - +
182B ASN* 1.3 63.4 + - - +
184B ARG* 2.9 19.4 + - - +
185B ALA* 3.3 20.4 + - - +
24D A 3.1 26.0 - - - +
25D T 2.7 14.4 + - - -
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Residues in contact with ASN 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLY* 5.3 0.2 - - - -
147B CYS 5.2 0.7 - - - +
148B CYS* 4.0 6.7 - - - +
151B ASN* 3.3 11.8 + - - +
181B THR* 1.3 70.7 - - - +
183B GLN* 1.3 73.0 + - - +
185B ALA* 3.2 4.7 + - - +
186B GLU* 3.0 33.1 + - - +
18C U 2.8 31.4 + - - +
19C C 3.4 38.0 + - - +
23D A 3.9 1.8 - - - -
24D A 3.2 41.0 + - - +
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Residues in contact with GLN 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B THR* 3.4 0.6 + - - -
182B ASN* 1.3 91.3 + - - +
184B ARG* 1.3 64.7 + - - +
186B GLU* 3.4 6.0 + - - +
187B ILE* 3.0 30.9 + - - +
211B SER* 4.5 5.7 + - - -
213B PHE* 3.2 56.5 - - + +
240B ASN* 4.0 2.5 - - - +
17C U 5.0 1.2 + - - +
18C U 4.6 3.5 + - - -
24D A 3.5 27.3 + - + +
25D T 3.1 44.4 + - - +
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Residues in contact with ARG 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 3.9 14.3 - - + +
177B PRO 2.8 29.9 + - - -
178B GLY* 3.7 1.8 - - - -
179B ARG* 3.1 37.6 + - - +
181B THR* 2.9 19.8 + - - +
183B GLN* 1.3 79.9 - - - +
185B ALA* 1.3 57.9 + - - +
187B ILE* 3.8 1.7 - - - -
188B HIS* 2.9 65.3 + - - +
240B ASN* 3.6 8.5 - - - +
242B GLU* 5.3 4.0 + - - -
243B ASP* 2.8 32.8 + - - +
9004B EDO 3.5 25.4 - - - -
25D T 4.0 1.1 - - - +
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Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLY* 3.8 9.0 - - - -
147B CYS 3.9 10.8 - - - +
158B ALA* 4.3 1.8 - - + -
159B GLY 3.4 23.8 - - - +
160B ILE* 3.5 9.5 - - + +
176B LEU* 3.7 15.2 - - + +
181B THR 3.3 14.9 + - - +
182B ASN 3.2 5.1 + - - +
184B ARG* 1.3 76.4 - - - +
186B GLU* 1.3 61.3 + - - +
189B ALA* 2.8 32.7 + - - +
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Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B THR* 4.8 2.8 + - - -
145B ASP* 3.3 16.4 - - - +
146B GLY* 3.0 39.2 + - - +
182B ASN 3.0 21.8 + - - +
183B GLN* 3.9 6.3 - - - +
185B ALA* 1.3 78.6 - - - +
187B ILE* 1.3 60.9 + - - +
189B ALA* 3.4 4.0 + - - +
190B ALA* 3.3 17.3 + - - +
209B THR* 3.8 6.2 + - - -
210B ASN* 3.8 4.1 - - - +
211B SER* 3.3 37.6 - - - +
214B THR* 3.7 5.6 + - - +
18C U 3.1 25.3 + - - +
19C C 3.4 9.2 - - - +
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Residues in contact with ILE 187 (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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183B GLN 3.0 19.7 + - - +
184B ARG 3.9 2.9 - - - +
186B GLU* 1.3 73.1 - - - +
188B HIS* 1.3 63.3 + - - +
190B ALA* 3.1 7.4 + - - +
191B CYS* 2.9 25.8 + - - -
213B PHE* 3.7 12.8 - - + -
214B THR* 3.3 23.8 - - - +
240B ASN* 4.2 5.8 - - + -
243B ASP* 3.8 40.4 - - + +
244B PHE* 3.4 36.3 - - + -
247B LEU* 4.1 17.7 - - + +
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Residues in contact with HIS 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ILE* 3.5 19.8 - - + +
176B LEU* 4.0 9.8 - - + +
177B PRO* 6.1 0.9 - - + -
184B ARG* 2.9 48.5 + - - +
187B ILE* 1.3 75.0 - - + +
189B ALA* 1.3 60.6 + - - +
190B ALA 3.2 0.2 - - - -
191B CYS* 3.5 18.8 - - + +
192B LYS* 2.8 28.8 + - - +
243B ASP* 2.9 48.6 + - + +
246B ALA* 4.9 8.1 - - + +
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B THR* 3.9 4.7 - - - +
145B ASP 3.3 38.4 - - - +
160B ILE* 3.6 18.8 - - + +
161B GLY 4.3 1.8 - - - +
162B VAL* 3.9 4.4 - - - +
185B ALA 2.8 18.8 + - - +
186B GLU 3.5 6.5 - - - +
188B HIS* 1.3 77.4 - - - +
190B ALA* 1.3 63.3 + - - +
192B LYS* 3.3 3.1 + - - +
193B ALA* 3.0 22.7 + - - +
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B THR* 4.1 15.8 + - - +
186B GLU 3.3 8.3 + - - +
187B ILE 3.1 10.1 + - - +
189B ALA* 1.3 76.8 - - - +
191B CYS* 1.3 66.8 + - - +
193B ALA* 3.2 3.1 + - - +
194B ILE* 3.0 26.3 + - - +
207B LEU* 4.1 3.3 - - + +
209B THR* 6.0 0.4 - - + -
214B THR* 4.4 3.4 - - + -
247B LEU* 4.2 9.6 - - + -
258B TRP* 3.7 36.3 - - + -
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Residues in contact with CYS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ILE* 2.9 16.0 + - - +
188B HIS* 3.5 26.2 - - + +
189B ALA 3.2 0.2 - - - -
190B ALA* 1.3 76.4 - - - +
192B LYS* 1.3 63.3 + - - +
194B ILE* 3.0 13.8 + - - +
195B GLU* 3.1 20.8 + - - +
243B ASP 4.6 3.1 - - - -
246B ALA* 4.3 3.6 - - - -
247B LEU* 3.5 47.3 - - - +
250B LEU* 3.8 18.9 - - + +
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Residues in contact with LYS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ILE* 4.5 9.2 - - + -
162B VAL* 3.6 19.7 - - + -
172B VAL* 4.2 14.1 - - + -
174B ILE* 4.3 20.2 - - + +
188B HIS 2.8 17.9 + - - +
189B ALA* 3.5 7.0 - - - +
191B CYS* 1.3 76.5 - - - +
193B ALA* 1.3 64.0 + - - +
195B GLU* 3.2 24.7 + - - +
196B GLN* 3.1 42.2 + - + +
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Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 4.3 19.7 - - + -
144B THR* 3.5 32.1 - - + -
162B VAL* 4.1 8.7 - - + +
164B TRP* 3.6 5.9 - - - -
189B ALA 3.0 7.0 + - - +
190B ALA* 3.7 5.2 - - - +
192B LYS* 1.3 77.1 - - - +
194B ILE* 1.3 59.2 + - + +
196B GLN* 3.2 15.4 + - - +
197B ALA* 2.9 25.7 + - - +
205B LEU* 5.1 1.3 - - + -
207B LEU* 4.9 2.7 - - + -
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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
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190B ALA 3.4 13.5 - - - +
191B CYS 3.0 7.8 + - - +
193B ALA* 1.3 74.7 - - - +
195B GLU* 1.3 66.1 - - - +
197B ALA* 3.3 6.6 + - - +
198B LYS* 3.2 29.5 + - - +
205B LEU* 4.1 17.3 - - + -
207B LEU* 4.4 3.6 - - + -
247B LEU* 3.7 25.1 - - + -
250B LEU* 3.5 32.3 - - + +
251B THR* 4.2 6.1 - - + -
254B MSE 4.4 12.8 - - + -
256B ILE* 3.8 19.1 - - + -
258B TRP* 4.3 10.5 - - + -
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Residues in contact with GLU 195 (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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191B CYS* 3.1 17.0 + - - +
192B LYS* 3.2 31.8 + - + +
194B ILE* 1.3 74.6 - - - +
196B GLN* 1.3 65.1 + - + +
198B LYS* 3.1 11.1 + - - +
199B THR* 3.0 20.0 + - - -
250B LEU* 4.0 30.7 - - + +
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Residues in contact with GLN 196 (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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162B VAL* 2.7 32.9 - - - +
164B TRP* 2.9 18.1 + - + -
170B LEU* 2.9 42.2 + - + +
172B VAL* 3.7 18.0 - - - +
192B LYS* 3.1 28.2 + - + +
193B ALA* 3.5 6.9 - - - +
195B GLU* 1.3 78.9 - - + +
197B ALA* 1.3 62.4 + - - +
199B THR* 3.0 26.4 + - - +
200B GLN* 3.2 9.7 + - - +
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Residues in contact with ALA 197 (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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164B TRP* 3.9 17.4 - - + -
193B ALA 2.9 13.5 + - - +
194B ILE 3.6 7.9 - - - +
195B GLU 3.2 0.2 - - - -
196B GLN* 1.3 74.8 - - - +
198B LYS* 1.3 58.8 + - - +
200B GLN* 3.0 14.6 + - - -
202B ILE* 2.9 42.7 + - + +
205B LEU* 4.1 11.9 - - + -
254B MSE 4.0 17.9 - - + -
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Residues in contact with LYS 198 (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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194B ILE* 3.2 14.1 + - + +
195B GLU* 3.1 12.4 + - - +
197B ALA* 1.3 74.5 - - - +
199B THR* 1.3 65.6 + - - +
200B GLN 3.0 2.0 - - - -
201B ASN* 3.1 14.4 + - - +
202B ILE 4.4 4.3 - - - +
249B ARG 4.7 0.4 + - - -
250B LEU* 3.1 41.1 + - + +
252B GLN* 3.3 22.8 + - - +
253B GLY 5.6 0.2 - - - -
254B MSE 3.7 27.8 - - - -
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Residues in contact with THR 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 4.1 17.7 - - + -
195B GLU 3.0 10.7 + - - -
196B GLN* 3.0 16.5 + - - +
198B LYS* 1.3 78.5 - - - +
200B GLN* 1.3 70.2 + - + +
201B ASN 3.4 0.6 + - - -
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Residues in contact with GLN 200 (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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164B TRP* 3.8 26.7 - - - -
168B HIS* 3.3 26.3 + - - -
170B LEU* 3.4 30.4 - - + +
196B GLN 3.2 7.5 + - - +
197B ALA 3.0 8.5 + - - +
199B THR* 1.3 80.9 - - + +
201B ASN* 1.3 68.7 + - - +
202B ILE* 3.2 19.5 + - + +
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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