Contacts of the helix formed by residues 193 - 213 (chain B) in PDB entry 3NUI
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 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B TYR* 3.5 5.2 - - - -
191B GLY 3.8 4.0 + - - +
192B GLU* 1.3 76.2 - - - +
194B GLU* 1.3 60.8 + - - +
195B GLU* 3.5 15.4 + - - +
196B GLN* 2.9 44.5 + - - +
197B PHE* 2.9 27.4 + - - +
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Residues in contact with GLU 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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184B TYR* 3.3 44.1 + - + +
193B THR* 1.3 72.8 - - - +
195B GLU* 1.3 62.0 + - - +
197B PHE* 3.3 2.8 + - - +
198B VAL* 3.0 23.6 + - - +
235B ALA* 3.4 15.7 - - + +
236B LYS* 2.9 59.6 + - + +
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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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193B THR* 3.2 12.7 + - - +
194B GLU* 1.3 80.9 - - + +
196B GLN* 1.3 62.5 + - + +
198B VAL* 3.4 7.4 + - - +
199B ALA* 3.0 22.4 + - - +
236B LYS 5.6 1.6 - - - -
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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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191B GLY 4.2 2.8 - - - +
192B GLU* 3.6 18.6 - - + +
193B THR* 2.9 46.2 + - - +
195B GLU* 1.3 80.6 - - + +
197B PHE* 1.3 59.1 + - - +
199B ALA* 3.2 8.0 + - - +
200B ARG* 2.8 28.9 + - - +
203B ARG* 4.3 5.2 + - - +
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Residues in contact with PHE 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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180B THR* 5.1 0.2 - - + -
181B CYS 4.0 9.4 - - - -
182B PRO 3.8 11.0 - - - -
183B HIS 3.9 15.9 - - - -
184B TYR* 3.6 37.2 - + + -
187B TYR* 3.8 18.2 - - + -
188B GLY* 3.8 6.1 - - - -
192B GLU* 3.5 13.1 + - - -
193B THR 2.9 12.4 + - - +
194B GLU 3.4 7.2 - - - +
196B GLN* 1.3 76.7 - - - +
198B VAL* 1.3 56.9 + - - +
200B ARG* 3.1 30.6 + - - +
201B LEU* 2.9 59.7 + - + +
235B ALA* 3.8 21.1 - - + -
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Residues in contact with VAL 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 GLU 3.0 13.1 + - - +
195B GLU* 3.7 8.7 - - - +
197B PHE* 1.3 76.7 - - + +
199B ALA* 1.3 57.3 + - - +
201B LEU* 3.2 8.7 + - + +
202B ALA* 2.9 26.5 + - - +
235B ALA* 3.6 24.2 - - + +
236B LYS 3.3 24.5 - - - +
237B GLY 3.9 10.1 - - - +
238B TYR* 4.1 13.5 - - + +
241B ALA* 3.5 28.7 - - + -
242B ILE* 5.7 1.2 - - + +
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Residues in contact with ALA 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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195B GLU 3.0 14.9 + - - +
196B GLN* 3.2 10.7 + - - +
198B VAL* 1.3 77.1 - - - +
200B ARG* 1.3 56.9 + - - +
202B ALA* 3.3 9.4 + - - +
203B ARG* 3.0 39.8 + - - +
241B ALA* 5.8 0.9 - - - -
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Residues in contact with ARG 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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180B THR* 5.8 3.8 + - - +
187B TYR* 3.0 24.9 + - - +
189B GLU* 3.5 29.3 + - - +
192B GLU* 2.8 38.6 + - - +
196B GLN 2.8 14.9 + - - +
197B PHE* 3.1 21.2 + - - +
199B ALA* 1.3 71.4 - - - +
201B LEU* 1.3 68.9 + - + +
203B ARG* 3.2 39.6 + - - +
204B GLU* 2.9 26.4 + - + +
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Residues in contact with LEU 201 (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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180B THR* 4.1 29.8 - - + +
181B CYS 4.5 0.2 - - - +
182B PRO* 3.7 27.8 - - + -
197B PHE* 2.9 56.1 + - + +
198B VAL* 3.2 8.9 + - + +
200B ARG* 1.3 88.0 - - - +
202B ALA* 1.3 63.6 + - - +
204B GLU* 3.4 13.1 - - + +
205B LEU* 3.0 23.4 + - - +
238B TYR* 4.1 18.4 - - + -
242B ILE* 4.6 4.3 - - - +
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Residues in contact with ALA 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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198B VAL 2.9 16.4 + - - +
199B ALA* 3.3 12.8 + - - +
201B LEU* 1.3 71.6 - - - +
203B ARG* 1.3 63.1 + - - +
205B LEU* 3.3 5.1 + - - +
206B GLU* 3.0 21.6 + - - +
241B ALA* 4.5 16.6 - - + +
242B ILE* 4.5 5.7 - - - +
245B ILE* 3.6 29.2 - - + +
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Residues in contact with ARG 203 (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 GLU* 5.1 1.4 + - - -
196B GLN* 4.3 7.1 + - - +
199B ALA* 3.0 23.0 + - - +
200B ARG* 3.2 53.9 + - - +
202B ALA* 1.3 72.7 - - - +
204B GLU* 1.3 68.2 + - - +
206B GLU* 3.2 7.6 + - - +
207B GLU* 2.9 45.5 + - - +
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Residues in contact with GLU 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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178B HIS 5.1 2.1 - - - +
179B LEU* 3.4 16.2 - - + +
180B THR* 2.6 53.3 + - - +
200B ARG* 2.9 13.3 + - + +
201B LEU* 3.3 17.7 + - + +
203B ARG* 1.3 76.9 - - - +
205B LEU* 1.3 51.9 + - - +
207B GLU* 3.6 8.8 - - - +
208B THR* 2.7 51.0 + - - +
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Residues in contact with LEU 205 (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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144B LEU* 4.1 11.0 - - + -
179B LEU* 3.8 37.9 - - + -
201B LEU 3.0 13.4 + - - +
202B ALA* 3.5 9.0 - - - +
204B GLU* 1.3 74.8 - - - +
206B GLU* 1.3 58.8 + - - +
208B THR* 3.3 0.7 + - - -
209B ILE* 2.9 48.7 + - + +
242B ILE* 3.7 39.5 - - + +
245B ILE* 3.8 20.4 - - + -
246B LEU* 4.0 14.4 - - + -
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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
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202B ALA 3.0 16.9 + - - +
203B ARG* 3.6 9.6 - - - +
205B LEU* 1.3 79.0 - - - +
207B GLU* 1.3 60.2 + - + +
209B ILE* 3.9 2.6 - - - +
210B GLN* 3.0 49.4 + - - +
245B ILE* 3.7 30.8 - - + +
248B LYS* 2.9 31.7 + - - -
249B TYR* 3.0 22.6 + - - -
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Residues in contact with GLU 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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203B ARG* 2.9 40.1 + - - +
204B GLU* 3.6 7.0 - - - +
206B GLU* 1.3 78.3 - - + +
208B THR* 1.3 54.0 + - - +
210B GLN* 3.4 10.9 + - - +
211B ARG* 2.8 45.3 + - - +
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Residues in contact with THR 208 (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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144B LEU* 4.1 14.1 - - + -
177B VAL* 3.5 33.2 - - + -
178B HIS 5.1 3.8 + - - +
179B LEU* 4.1 12.4 - - + +
204B GLU* 2.7 36.5 + - - +
205B LEU* 3.6 3.8 - - - -
207B GLU* 1.3 70.0 - - - +
209B ILE* 1.3 60.2 + - + +
211B ARG* 3.2 26.9 + - - +
212B GLU* 2.9 33.7 + - + +
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Residues in contact with ILE 209 (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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144B LEU* 4.5 2.5 - - + -
205B LEU* 2.9 47.5 + - + +
206B GLU* 3.9 3.8 - - - +
208B THR* 1.3 74.3 - - - +
210B GLN* 1.3 57.9 + - - +
213B GLY* 2.8 30.8 + - - -
214B ALA* 3.6 17.2 + - + +
217B ILE* 4.1 13.7 - - + -
245B ILE* 4.1 16.4 - - + +
246B LEU* 4.4 4.0 - - + -
249B TYR* 3.8 41.5 - - + -
251B ILE* 3.7 26.7 - - + -
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Residues in contact with GLN 210 (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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206B GLU* 3.0 38.9 + - - +
207B GLU* 4.0 10.2 + - - +
209B ILE* 1.3 78.3 - - - +
211B ARG* 1.3 63.5 + - - +
213B GLY* 3.5 7.5 + - - -
248B LYS* 6.0 0.2 - - - +
249B TYR* 3.9 21.1 + - + +
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Residues in contact with ARG 211 (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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177B VAL* 5.4 1.8 - - - +
178B HIS 5.8 1.0 + - - -
207B GLU* 2.8 40.4 + - - +
208B THR* 3.2 32.2 + - - +
210B GLN* 1.3 74.7 - - - +
212B GLU* 1.3 76.4 + - - +
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Residues in contact with GLU 212 (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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142B LYS* 2.6 43.9 + - + +
177B VAL* 3.9 37.1 - - + +
208B THR* 2.9 24.7 + - + +
211B ARG* 1.3 88.6 + - + +
213B GLY* 1.3 59.0 + - - +
216B THR* 2.8 21.9 + - - +
217B ILE* 3.9 17.5 - - + -
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Residues in contact with GLY 213 (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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209B ILE 2.8 13.2 + - - -
210B GLN* 3.5 6.4 + - - -
211B ARG 3.3 2.6 - - - -
212B GLU* 1.3 75.2 - - - +
214B ALA* 1.3 66.2 + - - -
215B ASP* 3.0 3.8 - - - -
216B THR* 2.8 26.1 + - - -
217B ILE* 3.7 7.7 - - - +
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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