Contacts of the helix formed by residues 264 - 279 (chain A) in PDB entry 3SN6
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 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A TYR 3.6 24.5 - - - +
254A ASN 3.0 9.2 + - - -
263A THR* 1.3 83.9 - - - +
265A ARG* 1.3 60.7 + - - +
266A LEU* 3.1 2.9 + - - +
267A GLN* 2.9 39.0 + - + +
268A GLU* 3.5 11.6 + - - +
311A TYR* 3.4 37.1 + - + +
312A PHE* 3.7 8.8 - - - -
46N GLU* 4.8 5.4 - - - +
61N THR* 3.9 18.5 - - + +
62N GLY 4.9 0.2 - - - +
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Residues in contact with ARG 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA* 5.3 7.6 - - + +
49A GLY* 5.0 8.8 + - - -
50A GLU* 3.6 33.1 - - - +
252A SER* 3.1 23.8 + - - -
255A MET* 3.3 39.2 + - - +
263A THR* 4.0 21.1 - - + -
264A ASN* 1.3 73.4 - - - +
266A LEU* 1.3 60.5 + - - +
267A GLN 3.3 0.2 - - - -
268A GLU* 3.4 13.6 + - + +
269A ALA* 2.9 26.9 + - - +
293A LYS* 6.1 1.0 - - - +
43N LYS* 4.6 12.2 - - - +
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL* 5.2 1.3 - - + -
249A ALA 4.4 11.9 - - - +
250A SER* 4.9 1.6 - - - +
252A SER* 3.1 17.2 + - - +
253A TYR* 3.6 27.4 - - + +
264A ASN* 3.1 1.9 - - - +
265A ARG* 1.3 76.3 - - - +
267A GLN* 1.3 59.8 + - - +
269A ALA* 3.3 5.2 + - + +
270A LEU* 2.9 29.5 + - + +
308A ILE* 6.0 1.3 - - + -
312A PHE* 3.5 31.0 - - + -
340A PHE* 6.2 0.9 - - + -
341A ILE* 4.0 30.5 - - + -
344A GLU* 6.1 1.3 - - + -
345A PHE* 3.7 31.2 - - + -
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Residues in contact with GLN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ASN* 2.9 35.1 + - - +
266A LEU* 1.3 73.5 - - - +
268A GLU* 1.3 64.9 + - - +
270A LEU* 3.3 25.6 + - - +
271A ASN* 2.9 51.8 + - - +
312A PHE* 3.8 12.1 - - + -
47N TRP* 3.6 31.3 - - + +
60N TYR 5.5 0.9 - - - -
61N THR* 4.4 11.9 - - + -
62N GLY 5.1 3.8 + - - -
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Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA* 5.9 4.3 - - + -
263A THR* 4.2 4.7 - - + +
264A ASN* 3.5 16.1 - - - +
265A ARG* 3.5 17.5 - - + +
266A LEU 3.2 0.8 - - - -
267A GLN* 1.3 83.0 - - - +
269A ALA* 1.3 57.0 + - - +
271A ASN* 3.1 9.6 + - - +
272A LEU* 2.9 28.7 + - - +
45N LEU 4.8 5.0 - - - +
46N GLU* 3.5 16.5 - - - +
47N TRP* 3.1 42.9 + - - +
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA* 4.9 11.6 - - + +
246A PHE* 3.5 8.6 - - - -
248A VAL* 3.4 34.8 - - + -
252A SER* 5.6 1.1 - - - +
265A ARG 2.9 14.6 + - - +
266A LEU* 3.3 11.6 + - - +
268A GLU* 1.3 76.2 - - - +
270A LEU* 1.3 56.5 + - - +
272A LEU* 3.3 5.9 + - - -
273A PHE* 2.9 29.3 + - - +
345A PHE* 4.1 7.2 - - + -
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Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LEU* 2.9 20.3 + - + +
267A GLN* 3.5 33.0 - - - +
269A ALA* 1.3 75.8 - - - +
271A ASN* 1.3 57.9 + - - +
273A PHE* 3.2 2.8 + - - +
274A LYS* 2.9 29.5 + - - +
312A PHE* 3.7 22.2 - - + -
344A GLU* 3.7 32.8 - - + +
345A PHE* 3.4 43.5 - - + -
348A ILE* 4.0 11.9 - - + +
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Residues in contact with ASN 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A GLN* 2.9 36.2 + - - +
268A GLU* 3.2 14.3 + - - +
270A LEU* 1.3 74.6 - - - +
272A LEU* 1.3 66.7 + - - +
274A LYS* 3.2 15.4 + - - +
275A SER* 2.9 28.9 + - - +
47N TRP* 3.2 52.6 - - - +
50N ASP* 5.5 1.2 - - - +
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 4.4 7.4 - - + -
47A GLY 5.5 0.2 - - - -
48A ALA* 5.2 10.8 - - + +
231A ARG* 3.5 56.8 - - + +
235A ILE* 5.5 1.6 - - + -
246A PHE* 4.0 21.8 - - + -
268A GLU 2.9 12.1 + - - +
269A ALA* 3.3 9.2 + - - +
271A ASN* 1.3 75.7 - - - +
273A PHE* 1.3 57.9 + - - +
275A SER* 3.4 7.9 + - - -
276A ILE* 2.9 50.3 + - + +
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Residues in contact with PHE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A PHE* 3.4 35.2 - + + -
269A ALA 2.9 9.3 + - - +
270A LEU 3.4 7.9 - - - +
271A ASN 3.1 0.2 - - - -
272A LEU* 1.3 74.1 - - - +
274A LYS* 1.3 68.0 + - - +
276A ILE* 3.1 7.7 + - + +
277A TRP* 2.8 37.3 + + - +
287A VAL* 3.4 35.2 - - + -
289A LEU* 5.6 0.7 - - + -
345A PHE* 3.6 32.8 - + + -
348A ILE* 3.7 28.5 - - + -
349A SER* 3.3 23.3 - - - -
359A CYS* 4.0 11.4 - - - -
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Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A LEU 2.9 16.7 + - - +
271A ASN* 3.7 13.9 + - - +
273A PHE* 1.3 76.1 - - - +
275A SER* 1.3 58.0 + - - +
277A TRP* 3.2 1.2 + - - +
278A ASN* 2.9 52.3 + - - +
348A ILE* 3.8 39.3 - - + -
33N LYS* 4.4 16.5 - - - +
47N TRP* 5.9 0.6 - - - -
50N ASP* 3.7 15.3 + - - -
57N SER* 5.7 2.4 + - - -
59N SER* 3.7 21.8 + - - -
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Residues in contact with SER 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ASN* 2.9 19.1 + - - +
272A LEU* 3.6 11.3 - - - -
274A LYS* 1.3 76.3 - - - +
276A ILE* 1.3 64.4 + - - +
278A ASN* 3.3 4.3 + - - +
279A ASN* 3.1 26.2 + - - +
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Residues in contact with ILE 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 4.1 29.4 - - + -
231A ARG* 6.0 0.2 - - - -
235A ILE* 3.6 24.9 - - + -
244A ILE* 3.9 22.9 - - + -
246A PHE* 5.2 6.5 - - + -
272A LEU* 2.9 35.4 + - + +
273A PHE* 3.5 7.0 - - - +
275A SER* 1.3 76.1 - - - +
277A TRP* 1.3 62.6 + - + +
278A ASN 3.4 0.2 + - - -
279A ASN* 3.5 3.2 + - - -
282A LEU* 3.3 42.5 - - + +
285A ILE 6.1 0.4 - - - +
287A VAL* 4.4 16.2 - - + -
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Residues in contact with TRP 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A PHE* 2.8 34.8 + + + +
274A LYS* 3.6 8.1 - - - +
275A SER 3.2 0.2 - - - -
276A ILE* 1.3 77.5 - - - +
278A ASN* 1.3 66.6 + - - +
279A ASN 3.8 0.2 + - - -
282A LEU 5.3 0.2 - - - -
283A ARG* 4.4 9.5 - - - +
285A ILE 4.0 1.1 - - - -
287A VAL* 3.7 38.4 - - + -
348A ILE* 3.8 21.1 - - + -
349A SER* 3.4 33.6 + - - +
352A SER* 3.5 21.7 + - - -
357A HIS* 3.0 65.9 + + - -
358A TYR 3.4 27.4 - - - -
359A CYS* 3.7 2.7 - - + -
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Residues in contact with ASN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LYS* 2.9 41.1 + - - +
275A SER* 3.8 4.0 - - - +
277A TRP* 1.3 92.4 - - - +
279A ASN* 1.3 62.1 + - - +
280A ARG 3.5 1.9 + - - -
283A ARG* 4.0 14.7 + - - -
348A ILE* 5.4 0.9 - - - +
352A SER* 4.5 6.8 + - - -
33N LYS* 5.8 2.8 - - - +
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Residues in contact with ASN 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ARG* 5.7 1.4 + - - +
235A ILE* 5.2 10.8 - - + +
236A GLN* 5.5 2.9 - - - +
275A SER 3.1 16.6 + - - +
276A ILE* 3.8 8.3 - - - +
277A TRP 3.5 2.0 - - - -
278A ASN* 1.3 76.5 - - - +
280A ARG* 1.3 60.8 + - - +
281A TRP* 2.7 43.5 + - - +
282A LEU* 3.1 22.8 + - + +
283A ARG* 2.9 30.9 + - - +
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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