Contacts of the helix formed by residues 182 - 200 (chain B) in PDB entry 2HQR
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 ASN 182 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLU* 3.1 10.7 + - - -
180B THR* 5.4 0.2 + - - -
181B PRO* 1.3 92.1 + - - +
183B VAL* 1.3 63.0 + - - +
184B ILE* 3.3 4.7 - - - +
185B GLU* 3.4 40.7 + - - +
186B VAL* 4.4 6.4 + - - +
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU* 4.0 23.8 - - + -
172B ILE* 6.5 0.2 - - + -
173B TRP 4.6 5.4 - - - +
174B GLU* 4.1 3.1 + - + -
179B VAL* 3.8 35.4 - - + -
180B THR* 3.7 18.2 - - - +
181B PRO 3.3 0.8 + - - -
182B ASN* 1.3 73.6 - - - +
184B ILE* 1.3 78.5 + - + +
185B GLU 3.1 2.6 + - - -
186B VAL* 3.5 11.9 + - + +
187B ALA* 2.9 36.8 + - + +
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Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LYS* 3.7 61.5 - - + +
168B LEU* 3.8 31.9 - - + -
169B LEU* 3.8 28.7 - - + +
172B ILE* 5.7 2.7 - - + -
182B ASN* 3.3 2.0 - - - -
183B VAL* 1.3 86.2 - - + +
185B GLU* 1.3 63.5 + - + +
187B ALA* 4.3 5.8 - - + -
188B ILE* 2.9 33.3 + - + +
212B TYR* 5.5 1.3 - - + -
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Residues in contact with GLU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LYS* 5.1 15.3 - - + +
182B ASN* 3.4 36.8 + - + +
183B VAL 3.1 0.6 + - - -
184B ILE* 1.3 83.0 - - + +
186B VAL* 1.3 68.4 + - + +
188B ILE* 3.3 16.2 - - - +
189B ASN* 3.3 18.1 + - - +
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Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B THR* 5.3 5.8 - - - +
182B ASN 4.5 3.1 - - - +
183B VAL* 3.6 22.4 - - + +
185B GLU* 1.3 83.9 - - + +
187B ALA* 1.3 66.8 + - - +
189B ASN* 4.9 3.4 - - - +
190B GLN* 3.0 47.9 + - - +
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Residues in contact with ALA 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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168B LEU* 6.5 0.9 - - + -
183B VAL* 2.9 33.5 + - + +
184B ILE* 4.2 6.5 - - + +
186B VAL* 1.3 82.1 - - + +
188B ILE* 1.3 56.6 + - - +
190B GLN* 4.9 2.0 - - - -
191B ILE* 2.8 47.4 + - + +
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Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LYS* 6.0 1.1 - - - -
168B LEU* 4.3 20.4 - - + +
184B ILE* 2.9 33.8 + - + +
185B GLU* 3.3 8.5 - - - +
187B ALA* 1.3 75.6 - - - +
189B ASN* 1.3 84.9 + - - +
190B GLN 3.1 1.8 - - - -
191B ILE* 4.4 11.0 - - + -
192B ARG* 3.1 67.6 + - + +
204B VAL* 5.9 0.2 - - + -
212B TYR* 3.7 36.3 - - + +
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Residues in contact with ASN 189 (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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185B GLU* 3.3 20.1 + - - +
186B VAL* 4.4 3.1 - - - +
188B ILE* 1.3 89.5 - - - +
190B GLN* 1.3 63.3 + - + +
192B ARG* 3.9 8.6 + - - +
193B GLN* 3.3 22.2 + - - +
212B TYR* 4.8 5.1 + - - -
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Residues in contact with GLN 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B VAL* 3.0 39.1 + - - +
187B ALA* 4.3 1.8 - - - +
188B ILE 3.1 0.4 - - - -
189B ASN* 1.3 78.2 - - + +
191B ILE* 1.3 69.1 + - + +
192B ARG 3.0 1.3 - - - -
193B GLN* 2.8 13.3 + - - +
194B LYS* 2.7 48.5 + - + +
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Residues in contact with ILE 191 (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 PRO 5.5 1.6 - - - +
151B VAL* 3.6 43.3 - - + -
152B LEU* 5.5 6.5 - - + -
168B LEU* 6.2 1.3 - - + -
187B ALA* 2.8 37.8 + - + +
188B ILE* 4.0 12.8 - - + +
190B GLN* 1.3 77.3 - - + +
192B ARG* 1.3 60.7 + - + +
194B LYS* 3.4 17.2 - - - +
195B MET* 2.7 56.4 + - + +
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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
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188B ILE* 3.1 44.1 + - + +
189B ASN* 4.0 8.7 - - - +
190B GLN 3.0 0.8 - - - -
191B ILE* 1.3 76.9 - - + +
193B GLN* 1.3 63.0 + - - +
194B LYS 2.9 5.9 + - - -
195B MET* 3.1 16.3 + - + -
196B ASP* 3.2 21.1 + - + +
204B VAL* 1.9 75.8 + - + +
205B GLU 5.5 0.4 - - - -
206B THR* 6.0 0.2 - - - -
212B TYR* 3.0 41.2 - - - +
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Residues in contact with GLN 193 (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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189B ASN 3.3 15.6 + - - +
190B GLN* 2.8 11.9 + - - +
192B ARG* 1.3 79.5 - - - +
194B LYS* 1.3 61.6 + - + +
196B ASP* 5.7 0.4 - - - -
197B LYS* 3.4 37.9 - - - +
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Residues in contact with LYS 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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148B PRO* 5.6 8.1 - - - +
190B GLN* 2.7 45.4 + - + +
191B ILE* 3.4 15.6 - - - +
193B GLN* 1.3 85.6 - - + +
195B MET* 1.3 53.1 + - - +
197B LYS* 4.8 1.6 - - - -
198B PRO* 2.7 32.8 - - - +
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Residues in contact with MET 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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152B LEU* 4.3 16.4 - - + -
155B LEU* 4.1 32.3 - - + -
191B ILE* 2.7 42.0 + - + +
192B ARG* 4.0 6.3 - - + +
194B LYS* 1.3 74.6 - - - +
196B ASP* 1.3 69.1 + - - +
197B LYS 2.9 3.0 + - - -
198B PRO* 3.1 12.9 - - - +
199B LEU* 3.1 38.7 + - + +
201B ILE 5.7 2.9 - - - +
203B THR* 4.3 17.7 - - - -
204B VAL* 5.2 13.5 - - + -
214B PHE* 4.9 5.6 - - + -
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Residues in contact with ASP 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 3.2 13.3 + - - +
193B GLN* 5.7 0.2 - - - -
195B MET* 1.3 81.9 - - - +
197B LYS* 1.3 57.6 + - + +
200B GLY* 2.7 37.6 + - - +
201B ILE 3.4 30.3 - - - -
202B SER* 3.5 13.5 + - - -
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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
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192B ARG 4.6 1.0 + - - -
193B GLN* 3.4 33.4 + - + +
194B LYS* 4.4 1.8 - - - +
195B MET 2.9 2.6 + - - +
196B ASP* 1.3 82.4 - - - +
198B PRO* 1.3 72.1 - - + +
200B GLY* 3.5 5.7 + - - -
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Residues in contact with PRO 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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137B TYR* 5.6 6.7 - - + -
138B LYS* 2.2 45.2 + - - -
140B ARG* 5.6 5.4 - - - +
194B LYS* 2.7 29.8 - - - +
195B MET* 3.1 15.3 - - - +
197B LYS* 1.3 92.0 - - + +
199B LEU* 1.3 60.1 - - + +
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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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126B LEU* 3.7 33.8 - - + +
137B TYR* 3.5 48.0 - - + +
138B LYS* 3.3 13.1 + - - +
195B MET* 3.1 36.1 + - + +
198B PRO* 1.3 88.7 - - + +
200B GLY* 1.3 59.7 + - - +
201B ILE* 3.0 30.4 + - + +
203B THR* 5.9 4.3 - - + +
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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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196B ASP* 2.7 32.2 + - - +
197B LYS 4.0 4.3 - - - -
198B PRO 3.5 1.0 - - - -
199B LEU* 1.3 74.0 - - - +
201B ILE* 1.3 67.9 + - - +
202B SER 4.1 0.5 + - - -
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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
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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