Contacts of the helix formed by residues 180 - 200 (chain B) in PDB entry 3Q37
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 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ALA* 1.3 77.7 - - - +
181B PRO* 1.3 75.3 - - + +
182B GLN* 3.5 15.0 + - - +
183B GLN* 2.9 41.1 + - - +
184B ALA* 3.0 21.1 + - - +
223B LEU* 5.0 1.1 - - - -
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Residues in contact with PRO 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ALA 4.4 2.2 - - - +
180B THR* 1.3 88.1 - - + +
182B GLN* 1.3 69.2 + - - +
184B ALA* 3.3 2.6 + - - +
185B GLN* 2.9 30.0 + - - +
222B THR* 4.0 30.5 - - - +
223B LEU* 3.9 20.9 - - + -
225B GLN* 4.8 1.8 - - - +
226B MET* 3.8 28.0 - - + +
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Residues in contact with GLN 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B THR* 3.2 17.9 + - - +
181B PRO* 1.3 90.6 - - - +
183B GLN* 1.3 60.3 + - + +
185B GLN* 3.4 2.9 + - - +
186B GLU* 2.9 29.6 + - - +
225B GLN* 5.2 2.8 + - - -
226B MET* 4.2 23.8 - - + +
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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
----------------------------------------------------------
135B ARG* 3.8 26.9 + - - +
167B TYR* 5.0 0.8 - - - -
171B TRP* 3.4 25.3 - - + -
179B ALA* 3.4 9.3 - - + -
180B THR* 2.9 45.9 + - - +
182B GLN* 1.3 75.7 - - + +
184B ALA* 1.3 63.2 + - - +
186B GLU* 3.5 17.1 + - - +
187B VAL* 3.5 18.0 + - - +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TYR* 4.8 7.0 - - - -
179B ALA* 5.0 1.9 - - - +
180B THR 3.0 12.2 + - - +
181B PRO 3.6 7.6 - - - +
183B GLN* 1.3 74.6 - - - +
185B GLN* 1.3 65.7 + - - +
187B VAL* 3.1 4.5 + - - +
188B HIS* 2.9 29.9 + - + -
211B TYR* 3.6 38.4 - - + -
223B LEU* 4.1 4.5 - - + -
229B ILE* 4.0 13.0 - - + -
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Residues in contact with GLN 185 (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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181B PRO 2.9 20.4 + - - +
182B GLN* 3.8 3.8 - - - +
184B ALA* 1.3 74.0 - - - +
186B GLU* 1.3 59.6 + - - +
188B HIS* 4.3 3.4 - - - -
189B GLU* 2.8 41.5 + - + +
226B MET* 3.5 28.8 - - + +
227B ARG* 3.4 17.9 + - - +
228B ASP* 2.8 54.0 + - - +
229B ILE* 4.2 3.3 + - - +
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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
----------------------------------------------------------
135B ARG* 4.3 16.8 + - - -
182B GLN 2.9 17.3 + - - +
183B GLN* 3.6 10.2 - - - +
184B ALA 3.1 0.4 - - - -
185B GLN* 1.3 78.3 - - - +
187B VAL* 1.3 65.0 + - + +
189B GLU* 4.0 10.3 - - - +
190B LEU* 3.2 22.2 + - - +
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ARG* 4.6 4.9 - - - +
140B THR* 4.0 18.4 - - + -
144B VAL* 4.4 14.8 - - + -
167B TYR* 3.6 61.7 - - + +
183B GLN 3.5 9.8 + - - +
184B ALA 3.1 3.0 + - - +
186B GLU* 1.3 79.1 - - + +
188B HIS* 1.3 65.5 + - - +
190B LEU* 3.2 7.6 + - + +
191B LEU* 2.9 33.8 + - + +
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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
----------------------------------------------------------
167B TYR* 3.9 21.0 - + + +
184B ALA* 2.9 32.4 + - + +
185B GLN* 3.8 5.4 - - - +
187B VAL* 1.3 76.0 - - - +
189B GLU* 1.3 62.1 + - - +
191B LEU* 3.3 9.0 + - - +
192B ARG* 3.0 23.9 + - - +
209B ILE* 3.2 34.3 - - + +
210B LEU 3.4 21.0 + - - -
211B TYR* 3.5 22.3 - - - +
228B ASP* 3.1 35.0 + - + +
229B ILE* 3.5 17.9 - - + +
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLN* 2.8 34.1 + - - +
186B GLU* 4.0 9.4 - - - +
188B HIS* 1.3 76.9 - - - +
190B LEU* 1.3 58.5 + - - +
192B ARG* 3.3 1.6 + - + +
193B ARG* 2.6 84.9 + - + +
228B ASP* 3.8 18.3 - - - +
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B THR* 5.9 1.1 - - + -
141B ALA* 3.8 33.0 - - + -
144B VAL* 3.9 11.7 - - + -
145B LEU* 3.6 38.3 - - + +
186B GLU* 3.2 16.5 + - + +
187B VAL* 3.2 8.4 + - + +
189B GLU* 1.3 79.6 - - - +
191B LEU* 1.3 63.7 + - - +
193B ARG* 4.0 5.6 - - - +
194B TRP* 3.2 22.2 + - - +
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 4.2 22.0 - - + -
144B VAL* 4.1 23.1 - - + +
145B LEU* 4.0 16.2 - - + -
148B LEU* 3.9 23.5 - - + +
165B ILE* 4.3 8.3 - - + -
167B TYR* 4.3 8.1 - - + -
187B VAL* 2.9 34.6 + - + +
188B HIS 3.6 6.1 - - - +
189B GLU 3.2 0.2 - - - -
190B LEU* 1.3 77.4 - - + +
192B ARG* 1.3 61.1 + - - +
194B TRP* 3.2 5.2 + - - +
195B VAL* 3.1 26.6 + - + +
209B ILE* 4.0 28.5 - - + -
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Residues in contact with ARG 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 5.4 1.3 - - - +
188B HIS 3.0 14.7 + - - +
189B GLU 3.9 2.9 - - - +
191B LEU* 1.3 76.5 - - - +
193B ARG* 1.3 58.9 + - - +
195B VAL* 3.2 7.4 + - - +
196B ARG* 2.8 47.3 + - - +
204B ALA* 2.8 42.5 + - + +
205B ALA* 4.3 7.6 + - - +
207B LEU* 2.8 26.7 + - + +
209B ILE* 3.6 18.2 - - + +
227B ARG 5.2 0.4 + - - -
228B ASP* 2.7 49.6 + - - +
230B ASN* 2.7 30.3 + - - +
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Residues in contact with ARG 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLU* 2.6 57.0 + - + +
190B LEU* 4.0 6.0 - - - +
192B ARG* 1.3 74.5 - - - +
194B TRP* 1.3 64.4 + - - +
196B ARG* 3.2 33.0 + - - +
197B SER* 3.0 24.6 + - - -
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Residues in contact with TRP 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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145B LEU* 3.7 37.3 - - + +
148B LEU* 3.6 22.9 - - + -
149B ALA* 3.7 29.4 - - + +
152B ALA* 3.5 32.5 - - + -
160B TRP* 5.2 3.4 - + - -
190B LEU 3.2 14.7 + - - +
191B LEU 3.5 8.1 - - - +
193B ARG* 1.3 76.9 - - - +
195B VAL* 1.3 74.1 + - + +
197B SER* 2.6 23.0 + - - -
198B LYS* 3.1 55.5 + - + +
199B LEU* 5.6 1.3 - - + -
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Residues in contact with VAL 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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148B LEU* 3.9 19.1 - - + -
160B TRP* 4.3 12.3 - - + -
165B ILE* 5.8 0.2 - - + -
191B LEU* 3.1 15.0 + - + +
192B ARG 3.5 7.6 - - - +
194B TRP* 1.3 85.7 - - + +
196B ARG* 1.3 58.1 + - - +
198B LYS* 3.1 0.7 + - - -
199B LEU* 2.8 50.3 + - + +
203B ILE* 4.0 16.6 - - + -
204B ALA* 4.0 13.5 - - + +
207B LEU* 3.8 26.9 - - + -
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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
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192B ARG* 2.8 51.7 + - - +
193B ARG* 3.2 37.7 + - - +
195B VAL* 1.3 72.4 - - - +
197B SER* 1.3 59.7 + - - +
200B GLY* 3.0 35.3 + - - +
201B THR* 4.3 16.1 + - - +
204B ALA* 3.6 20.4 - - + +
228B ASP* 4.9 1.8 + - - -
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Residues in contact with SER 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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193B ARG 3.0 12.2 + - - -
194B TRP* 2.6 25.3 + - - -
196B ARG* 1.3 77.9 - - - +
198B LYS* 1.3 80.7 + - - +
200B GLY 4.8 0.4 + - - -
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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 TRP* 3.1 61.4 + - + +
195B VAL 4.0 1.3 - - - +
197B SER* 1.3 99.8 + - - +
199B LEU* 1.3 68.1 + - + +
200B GLY 3.8 0.4 - - - -
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Residues in contact with LEU 199 (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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152B ALA* 5.7 0.7 - - + -
156B SER* 4.9 0.9 - - - -
157B LYS* 3.9 38.4 + - + +
160B TRP* 3.0 57.2 - - + +
194B TRP* 5.6 1.8 - - + -
195B VAL* 2.8 24.4 + - + +
198B LYS* 1.3 83.6 - - + +
200B GLY* 1.3 59.7 + - - +
203B ILE* 3.8 30.4 - - + +
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Residues in contact with GLY 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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195B VAL 3.7 0.2 + - - -
196B ARG* 3.0 21.0 + - - -
197B SER 4.8 0.2 - - - -
199B LEU* 1.3 80.9 - - - +
201B THR* 1.3 65.9 + - - -
202B ASP 3.4 2.7 - - - -
203B ILE 3.7 0.3 + - - -
204B ALA* 3.3 25.3 + - - +
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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
------------------------------------------------------------
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