Contacts of the helix formed by residues 237 - 249 (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 GLY 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B VAL* 3.9 5.0 - - - +
235B ALA 3.2 0.6 + - - -
236B LYS* 1.3 72.3 - - - +
238B TYR* 1.3 64.3 + - - +
240B GLN* 3.4 25.6 + - - +
241B ALA* 3.0 23.6 + - - +
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Residues in contact with TYR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ARG* 3.3 47.8 + - - +
179B LEU* 5.0 4.7 - - - +
180B THR 4.7 2.2 + - - -
182B PRO* 3.5 26.2 - - + -
198B VAL* 4.1 15.3 - - + -
201B LEU* 4.1 21.1 - - + -
220B PHE* 4.3 2.4 - - - -
234B PRO* 3.9 15.5 - - + -
235B ALA 3.0 19.9 + - - +
236B LYS 3.3 0.6 + - - -
237B GLY* 1.3 78.5 - - - +
239B PHE* 1.3 79.3 + + + +
240B GLN* 4.0 0.2 + - - -
241B ALA* 3.0 4.5 + - - +
242B ILE* 2.9 67.4 + - + +
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Residues in contact with PHE 239 (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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146B ARG* 4.4 1.8 - - - -
220B PHE* 4.7 2.0 - + - -
222B ALA* 4.2 17.7 - - + -
223B GLU 4.3 5.6 - - - -
224B PRO* 3.7 35.0 - - + -
234B PRO* 3.8 17.5 - - + -
237B GLY 3.6 0.2 - - - -
238B TYR* 1.3 103.1 - + + +
240B GLN* 1.3 70.2 + - - +
242B ILE* 3.9 9.0 - - + -
243B LEU* 2.9 55.7 + - + +
274B TYR* 3.8 21.3 - + + +
276B PHE* 3.7 38.1 - + + -
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Residues in contact with GLN 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B GLY* 3.4 29.0 + - - +
238B TYR 3.2 0.4 + - - -
239B PHE* 1.3 83.9 + - - +
241B ALA* 1.3 54.7 + - - +
243B LEU* 5.3 0.2 - - - -
244B PRO* 3.2 23.4 - - - +
274B TYR* 2.8 32.3 + - - +
275B ASP* 3.8 21.1 + - - +
276B PHE* 5.2 0.6 - - - +
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Residues in contact with ALA 241 (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* 3.5 33.0 - - + +
199B ALA* 5.8 0.4 - - - -
202B ALA* 4.5 13.5 - - + +
237B GLY 3.0 5.8 + - - +
238B TYR 3.0 3.3 + - - +
240B GLN* 1.3 78.8 - - - +
242B ILE* 1.3 64.8 + - + +
243B LEU 3.6 0.2 - - - -
244B PRO* 3.6 8.2 - - - +
245B ILE* 3.5 18.7 - - - +
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Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 6.2 0.4 - - + -
198B VAL* 5.7 0.7 - - + +
201B LEU 4.6 4.5 - - - +
202B ALA* 4.5 17.5 - - - +
205B LEU* 3.7 20.6 - - + -
220B PHE* 3.4 39.7 - - + -
238B TYR* 2.9 62.9 + - + +
239B PHE* 3.9 14.6 - - + -
241B ALA* 1.3 76.2 - - + +
243B LEU* 1.3 69.0 + - + +
244B PRO 3.4 0.2 - - - -
245B ILE* 3.1 6.9 + - - +
246B LEU* 3.1 30.2 + - + +
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Residues in contact with LEU 243 (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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220B PHE* 5.4 0.4 - - + -
239B PHE* 2.9 53.9 + - + +
240B GLN* 5.3 0.2 - - - -
242B ILE* 1.3 80.6 - - + +
244B PRO* 1.4 67.7 - - + +
246B LEU* 3.1 8.3 + - + +
247B ARG* 2.9 58.2 + - + +
253B VAL* 4.1 24.9 - - + -
276B PHE* 4.1 26.5 - - + -
277B THR 4.6 3.4 - - - +
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Residues in contact with PRO 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B GLN* 3.2 26.5 - - - +
241B ALA 3.6 6.3 - - - +
242B ILE 3.6 2.9 - - - -
243B LEU* 1.4 92.6 - - + +
245B ILE* 1.3 62.5 + - + +
247B ARG* 3.4 7.9 + - + +
248B LYS* 3.1 25.7 + - - +
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Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ALA* 3.6 39.7 - - + +
205B LEU* 3.8 24.0 - - + -
206B GLU* 3.7 36.1 - - + +
209B ILE* 4.1 10.3 - - + -
241B ALA 3.5 19.5 - - - +
242B ILE* 3.1 6.2 + - - +
243B LEU 3.1 0.4 - - - -
244B PRO* 1.3 80.4 - - + +
246B LEU* 1.3 62.9 + - - +
248B LYS* 3.1 13.0 + - - +
249B TYR* 3.0 27.1 - - + -
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Residues in contact with LEU 246 (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* 3.9 27.6 - - + -
205B LEU* 4.0 16.6 - - + -
209B ILE* 4.4 0.9 - - + -
220B PHE* 3.6 46.2 - - + -
242B ILE* 3.1 29.9 + - + +
243B LEU* 3.7 9.2 - - + +
245B ILE* 1.3 74.9 - - - +
247B ARG* 1.3 58.8 + - - +
249B TYR* 3.0 19.6 + - - +
250B ASP 3.4 9.5 + - - -
251B ILE* 3.9 25.8 + - + +
253B VAL* 4.2 20.2 - - + -
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Residues in contact with ARG 247 (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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243B LEU* 2.9 35.4 + - + +
244B PRO* 3.6 8.7 - - + +
246B LEU* 1.3 74.2 - - - +
248B LYS* 1.3 61.9 + - - +
249B TYR 3.1 2.8 + - - -
250B ASP* 4.0 10.2 + - - +
251B ILE 4.4 4.6 + - - -
253B VAL* 3.5 19.0 - - - +
277B THR 3.0 26.7 + - - -
278B PRO 4.1 1.8 - - - -
279B ASP* 2.7 44.1 + - - -
302B GLU* 5.0 1.2 + - - -
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Residues in contact with LYS 248 (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* 2.9 31.3 + - - -
210B GLN* 6.0 0.4 - - - +
244B PRO 3.1 22.3 + - - +
245B ILE* 3.1 9.5 + - + +
247B ARG* 1.3 76.6 - - - +
249B TYR* 1.3 85.0 + - + +
250B ASP* 5.1 1.7 - - - +
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Residues in contact with TYR 249 (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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140B LYS* 4.9 1.7 + - - -
206B GLU* 3.0 24.2 + - - -
209B ILE* 3.8 27.4 - - + -
210B GLN* 3.9 17.5 + - + +
214B ALA* 3.6 26.7 - - + +
245B ILE* 3.0 31.6 - - + -
246B LEU 3.0 2.9 + - - +
248B LYS* 1.3 109.4 + - + +
250B ASP* 1.3 76.9 + - - +
251B ILE* 3.4 21.2 - - + +
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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