Contacts of the helix formed by residues 241 - 256 (chain B) in PDB entry 3ONW
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 241 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A VAL* 5.4 1.6 - - - +
229B ASP 6.1 0.9 - - - +
230B TYR 5.4 1.8 + - - +
232B LEU 4.7 13.9 - - - +
233B VAL 5.8 0.2 - - - -
234B LEU* 3.6 19.0 - - + +
240B MET* 1.3 78.9 - - - +
242B ARG* 1.3 58.6 + - - +
243B MET* 3.5 6.6 + - - +
244B HIS* 2.8 48.3 + - - +
245B GLU* 3.0 10.4 + - - +
285B ILE 4.3 5.3 + - - -
286B CYS* 3.2 40.5 + - - +
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Residues in contact with ARG 242 (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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2B SO4 2.7 48.3 + - - +
147B LEU* 3.3 26.5 - - - +
229B ASP* 4.5 22.4 + - + +
232B LEU* 3.8 30.5 + - + +
233B VAL 3.3 25.3 + - - -
234B LEU* 5.1 0.2 - - - +
235B ALA* 3.6 19.0 - - - +
241B ASN* 1.3 73.2 - - - +
243B MET* 1.3 62.7 + - - +
245B GLU* 3.2 22.3 + - - +
246B SER* 3.0 22.7 + - - -
507D VAL* 6.1 0.2 - - - +
510D SER* 5.2 8.1 - - - +
511D GLY* 4.7 5.1 - - - +
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Residues in contact with MET 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B VAL* 3.9 14.4 - - - -
226B ALA 4.0 8.7 - - - +
227B LEU* 3.6 26.0 - - - +
229B ASP* 4.6 7.2 + - - +
230B TYR* 3.7 25.6 - - + +
241B ASN* 3.3 1.5 + - - +
242B ARG* 1.3 79.8 - - - +
244B HIS* 1.3 56.5 + - - +
246B SER* 3.3 6.5 + - - -
247B MET* 2.9 27.4 + - - +
286B CYS* 3.5 22.7 - - - -
287B TYR* 3.4 23.3 - - + +
303B ILE* 4.2 17.7 - - + -
307B PHE* 3.8 23.6 - - + -
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Residues in contact with HIS 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLU* 2.9 39.9 + - - -
240B MET* 3.5 25.6 - - + +
241B ASN* 2.8 36.5 + - - +
243B MET* 1.3 75.0 - - - +
245B GLU* 1.3 58.8 + - - +
247B MET* 3.3 18.7 + - + +
248B LYS* 2.9 29.8 + - - +
286B CYS* 3.3 26.6 - - - -
287B TYR* 3.7 17.7 - + - -
288B PRO* 5.5 0.4 - - + -
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Residues in contact with GLU 245 (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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2B SO4 4.2 6.2 + - - -
238B GLU* 2.9 44.9 - - - +
240B MET* 3.5 18.2 - - + +
241B ASN 3.0 7.7 + - - +
242B ARG* 3.2 31.4 + - - +
244B HIS* 1.3 73.7 - - - +
246B SER* 1.3 63.6 + - - +
248B LYS* 3.2 6.9 + - - +
249B LEU* 3.0 22.7 + - - +
503D LEU* 4.8 2.5 - - + +
506D ARG* 4.5 11.6 + - - +
507D VAL* 4.1 29.5 - - + +
510D SER* 5.2 5.8 - - - -
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Residues in contact with SER 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA* 5.1 14.6 + - - -
223B PHE* 3.4 24.1 - - - -
224B CYS 4.6 2.4 + - - -
225B VAL* 3.6 19.7 - - - +
242B ARG 3.0 12.2 + - - -
243B MET* 3.5 11.2 - - - -
245B GLU* 1.3 76.0 - - - +
247B MET* 1.3 56.9 + - - +
249B LEU* 3.3 5.9 + - - -
250B PHE* 3.0 28.2 + - - +
307B PHE* 3.7 4.3 - - - -
507D VAL* 4.7 6.4 - - - +
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Residues in contact with MET 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLU* 4.3 2.7 - - - +
243B MET 2.9 18.6 + - - +
244B HIS* 3.5 31.2 - - + +
246B SER* 1.3 77.1 - - - +
248B LYS* 1.3 57.3 + - - +
250B PHE* 3.2 0.3 + - - +
251B ASP* 2.8 32.1 + - - +
287B TYR* 3.3 30.1 - - - -
306B GLN* 4.0 33.7 - - + +
307B PHE* 3.6 30.0 - - + -
310B LEU* 3.4 22.1 - - + +
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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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234A LEU* 5.6 1.2 - - - +
239A GLU 5.1 8.3 + - - -
239B GLU* 4.4 8.1 + - - -
240B MET* 4.0 29.1 - - + +
244B HIS 2.9 15.9 + - - +
245B GLU* 3.2 11.0 + - - +
247B MET* 1.3 73.0 - - - +
249B LEU* 1.3 61.9 + - - +
251B ASP* 3.4 7.1 + - + +
252B SER* 3.1 22.3 + - - -
503D LEU* 4.0 27.4 - - + -
506D ARG* 5.4 5.8 - - - +
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Residues in contact with LEU 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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40B GLY* 5.0 2.7 - - - +
223B PHE* 3.7 24.9 - - + -
245B GLU 3.0 13.8 + - - +
246B SER* 3.7 8.1 - - - +
248B LYS* 1.3 76.5 - - - +
250B PHE* 1.3 61.5 + - - +
252B SER* 3.3 1.9 + - - -
253B ILE* 3.1 36.4 + - + +
500D LEU* 4.1 6.7 - - + -
503D LEU* 3.7 28.0 - - + +
504D LEU* 3.8 36.3 - - + +
507D VAL* 3.9 28.9 - - + -
508D GLN* 4.9 7.2 - - - +
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Residues in contact with PHE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B PHE* 3.8 38.3 - + + -
246B SER 3.0 17.2 + - - +
247B MET 3.7 3.4 - - - +
249B LEU* 1.3 75.5 - - - +
251B ASP* 1.3 60.8 + - - +
253B ILE* 4.7 3.8 - - + -
254B CYS* 2.9 47.7 + - + +
264B ILE* 3.6 24.2 - - + -
266B LEU* 4.4 12.8 - - + -
307B PHE* 3.3 48.5 - + + -
308B GLU* 4.6 1.6 - - - -
310B LEU* 4.3 5.4 - - + -
311B ASN 5.4 0.7 - - - -
319B ILE* 3.8 37.2 - - + -
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Residues in contact with ASP 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLU* 5.4 3.5 - - - +
247B MET 2.8 20.4 + - - +
248B LYS* 3.6 9.1 - - + +
250B PHE* 1.3 75.3 - - - +
252B SER* 1.3 61.5 + - - +
254B CYS* 4.8 0.4 - - - -
255B ASN* 2.4 59.2 + - - +
310B LEU* 3.6 33.2 - - + +
312B LYS* 3.8 14.2 + - - -
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Residues in contact with SER 252 (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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248B LYS* 3.1 14.1 + - - -
249B LEU 3.6 7.6 - - - -
250B PHE 3.2 0.4 - - - -
251B ASP* 1.3 77.9 - - - +
253B ILE* 1.3 61.7 + - - +
255B ASN* 5.3 0.2 - - - -
256B ASN* 3.1 30.9 + - - +
496D ASP 5.0 5.5 + - - -
500D LEU* 3.6 26.7 - - - +
503D LEU* 4.2 12.1 - - - +
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Residues in contact with ILE 253 (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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39B LEU* 3.5 27.1 - - + -
215B PHE* 5.5 1.1 - - + -
221B ILE* 3.9 28.5 - - + -
223B PHE* 3.9 14.6 - - + -
249B LEU* 3.1 37.8 + - + +
250B PHE* 4.0 4.7 - - + +
252B SER* 1.3 74.9 - - - +
254B CYS* 1.3 63.7 + - + +
255B ASN 3.4 0.3 + - - -
256B ASN 3.6 2.1 + - - -
259B PHE* 3.2 39.1 - - + +
264B ILE* 4.0 15.3 - - + +
317B LYS* 5.4 0.2 - - - -
500D LEU* 3.9 16.8 - - + -
504D LEU* 4.6 2.0 - - + -
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Residues in contact with CYS 254 (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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250B PHE* 2.9 37.1 + - + +
251B ASP* 4.4 1.3 - - - +
253B ILE* 1.3 80.2 - - - +
255B ASN* 1.3 62.0 + - - +
256B ASN 3.8 1.6 + - - +
264B ILE* 4.8 8.3 - - + -
310B LEU 5.8 0.2 - - - -
311B ASN* 3.6 35.2 - - - +
313B ARG* 4.1 4.7 + - - -
317B LYS* 3.6 23.3 - - - +
319B ILE* 3.5 30.1 - - + -
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Residues in contact with ASN 255 (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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251B ASP* 2.4 48.9 + - - +
252B SER* 3.9 1.1 - - - +
254B CYS* 1.3 78.3 - - - +
256B ASN* 1.3 58.0 + - - +
257B LYS 3.3 1.2 + - - -
310B LEU 2.9 18.9 + - - -
311B ASN* 3.7 5.6 - - - +
312B LYS* 2.7 49.6 + - + +
313B ARG* 2.5 30.3 + - - +
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Residues in contact with ASN 256 (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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252B SER* 3.1 21.2 + - - +
253B ILE 3.6 0.8 + - - +
254B CYS 3.5 2.9 - - - +
255B ASN* 1.3 77.3 - - - +
257B LYS* 1.3 58.1 + - - +
258B TRP* 2.8 39.6 + - - +
259B PHE* 2.9 43.9 + - + +
260B THR* 3.8 2.4 + - - -
313B ARG* 4.1 1.8 + - - -
317B LYS* 5.9 0.5 - - - +
496D ASP* 4.6 19.2 + - - +
497D ILE* 4.0 20.1 - - - +
500D LEU* 5.2 3.8 - - + +
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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