Contacts of the helix formed by residues 260 - 281 (chain A) in PDB entry 1V72
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 ASP 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A LEU 4.9 1.2 + - - -
258A THR 3.0 2.8 + - - +
259A ASP* 1.3 77.6 - - - +
261A LEU* 1.3 65.3 + - - +
262A TRP* 3.3 16.5 + - - +
263A LEU* 3.2 27.2 + - + +
264A ARG* 3.0 27.4 + - + +
267A ARG* 5.2 3.8 - - - +
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Residues in contact with LEU 261 (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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21A SER* 4.1 15.7 - - - +
23A GLU* 4.1 34.5 - - + +
24A VAL* 4.6 5.2 - - + -
255A ALA 3.4 22.0 - - - +
256A TYR* 3.7 11.8 + - + +
258A THR 2.9 15.5 + - - +
259A ASP 3.0 1.4 + - - -
260A ASP* 1.3 76.0 - - - +
262A TRP* 1.3 59.1 + - - +
264A ARG* 3.2 32.3 + - - +
265A ASN* 2.8 54.2 + - - +
268A LYS* 6.2 0.4 - - - +
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Residues in contact with TRP 262 (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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55A ILE* 3.9 34.0 - - + +
183A PHE* 4.2 7.0 - + - -
184A ALA* 4.2 13.5 - - + -
187A LEU* 3.8 28.3 - - + -
194A PRO* 4.1 7.0 - - + -
208A PHE* 3.6 34.3 - + - -
213A ASN* 2.9 24.4 + - - +
256A TYR* 3.0 59.5 + + + +
257A LEU* 3.8 22.5 - - + +
260A ASP* 4.0 16.4 + - - +
261A LEU* 1.3 74.4 - - - +
263A LEU* 1.3 93.8 + - + +
265A ASN* 3.3 2.0 + - - -
266A ALA* 3.0 10.4 + - - +
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Residues in contact with LEU 263 (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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184A ALA* 5.2 2.0 - - + -
187A LEU* 3.6 31.2 - - + -
188A VAL* 3.9 16.1 - - + +
260A ASP* 3.2 28.8 + - + +
262A TRP* 1.3 102.0 - - + +
264A ARG* 1.3 61.4 + - - +
266A ALA* 3.1 3.8 + - - +
267A ARG* 2.8 62.1 + - - +
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Residues in contact with ARG 264 (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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23A GLU* 4.5 10.7 + - - -
259A ASP* 3.1 38.3 + - - +
260A ASP* 3.0 15.1 + - + +
261A LEU* 3.6 37.7 - - - +
263A LEU* 1.3 75.2 - - - +
265A ASN* 1.3 63.6 + - - +
267A ARG* 3.2 21.2 + - - +
268A LYS* 3.0 49.1 + - - +
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Residues in contact with ASN 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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21A SER* 2.9 28.2 + - - -
213A ASN* 3.3 31.0 + - - +
214A GLY* 4.1 2.0 - - - -
256A TYR* 5.0 2.4 - - - -
261A LEU* 2.8 39.3 + - - +
262A TRP* 3.5 4.9 - - - +
264A ARG* 1.3 78.1 - - - +
266A ALA* 1.3 61.1 + - - +
268A LYS* 3.4 15.6 + - - +
269A ALA* 3.1 17.8 + - - +
332A PHE* 3.5 32.7 - - + +
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Residues in contact with ALA 266 (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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184A ALA* 3.6 41.1 - - + +
185A ASN* 4.0 8.3 - - - +
188A VAL* 3.9 9.4 - - + -
213A ASN* 3.3 8.2 + - - +
262A TRP 3.0 13.5 + - - +
263A LEU 3.1 7.4 + - - +
265A ASN* 1.3 74.6 - - - +
267A ARG* 1.3 66.5 + - - +
269A ALA* 3.2 1.1 + - - +
270A ASN* 2.9 29.6 + - - -
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Residues in contact with ARG 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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188A VAL* 4.0 26.7 - - + +
260A ASP* 5.1 4.2 + - - +
263A LEU* 2.8 52.5 + - - +
264A ARG* 3.5 21.0 - - - +
266A ALA* 1.3 77.6 - - - +
268A LYS* 1.3 57.7 + - + +
270A ASN* 3.4 3.1 + - - +
271A ALA* 2.8 33.3 + - - +
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Residues in contact with LYS 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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261A LEU* 6.2 0.2 - - - +
264A ARG* 3.0 40.9 + - - +
265A ASN* 3.7 19.3 + - - +
266A ALA 3.2 0.2 - - - -
267A ARG* 1.3 78.2 - - + +
269A ALA* 1.3 61.4 + - - +
271A ALA* 3.5 6.9 + - - +
272A ALA* 3.0 23.9 + - - +
331A SER 4.4 1.8 - - - -
332A PHE 3.8 19.9 + - - +
334A THR 4.3 8.2 - - - +
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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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185A ASN* 3.7 15.0 - - - +
213A ASN* 5.1 2.0 - - - +
265A ASN 3.1 12.0 + - - +
266A ALA* 3.2 7.4 + - - +
268A LYS* 1.3 74.7 - - - +
270A ASN* 1.3 66.3 + - - +
272A ALA* 3.3 7.5 + - - +
273A ALA 3.3 1.9 + - - -
295A ASN* 3.8 13.0 - - + +
330A THR* 2.7 22.3 + - - -
331A SER* 3.4 33.6 + - - -
332A PHE 3.7 2.2 - - - +
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Residues in contact with ASN 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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185A ASN* 2.8 54.9 + - - +
188A VAL* 3.4 11.9 - - + +
189A SER* 4.0 3.6 - - - -
266A ALA 2.9 12.6 + - - +
267A ARG* 3.9 3.4 - - - +
269A ALA* 1.3 76.1 - - - +
271A ALA* 1.3 62.9 + - - +
273A ALA 3.3 1.6 + - - -
274A GLN* 3.0 24.5 + - - +
293A GLU 4.0 5.0 - - - +
294A ALA* 3.4 37.3 - - - +
295A ASN* 3.4 1.6 - - - +
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Residues in contact with ALA 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 ARG 2.8 20.2 + - - +
268A LYS* 3.7 8.3 - - - +
270A ASN* 1.3 77.4 - - - +
272A ALA* 1.3 57.0 + - - +
274A GLN* 3.5 7.0 + - - +
275A ARG* 3.0 28.8 + - - +
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Residues in contact with ALA 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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268A LYS 3.0 17.5 + - - +
269A ALA 3.5 5.8 - - - +
270A ASN 3.2 0.4 - - - -
271A ALA* 1.3 75.4 - - - +
273A ALA* 1.3 64.1 + - - +
275A ARG* 3.3 7.2 + - - +
276A LEU* 3.0 18.5 + - - +
330A THR* 3.8 7.6 - - - -
334A THR* 3.7 37.2 - - + +
335A THR 5.0 1.8 - - - +
336A ALA* 6.2 0.7 - - - +
339A VAL* 3.5 17.1 - - + +
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Residues in contact with ALA 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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269A ALA 3.3 2.0 + - - -
270A ASN 3.3 1.7 + - - +
272A ALA* 1.3 79.5 - - - +
274A GLN* 1.3 57.6 + - - +
276A LEU* 3.1 8.6 + - - +
277A ALA* 2.9 28.8 + - - +
292A THR* 3.8 12.6 - - + -
294A ALA 3.5 24.0 - - - +
295A ASN* 3.9 11.0 - - - +
296A ILE 4.2 0.7 - - - +
297A LEU* 3.7 9.9 - - + +
328A PHE 5.9 0.4 - - - +
330A THR* 3.6 21.2 + - + +
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Residues in contact with GLN 274 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A ASN 3.0 17.7 + - - +
271A ALA* 3.8 7.9 - - - +
273A ALA* 1.3 76.6 - - - +
275A ARG* 1.3 61.7 + - - +
277A ALA* 3.4 12.1 + - - +
278A GLN* 3.0 29.5 + - + +
291A GLY 4.0 8.0 + - - +
292A THR* 3.2 25.1 - - - +
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Residues in contact with ARG 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 ALA 3.0 18.4 + - - +
272A ALA* 3.4 7.9 - - - +
274A GLN* 1.3 77.8 - - - +
276A LEU* 1.3 56.8 + - - +
278A GLN* 3.3 6.9 + - - +
279A GLY* 3.0 24.9 + - - -
336A ALA* 3.5 33.1 - - - +
339A VAL* 3.8 15.7 - - + -
340A ASP* 2.8 39.1 + - - +
343A LEU* 4.0 5.1 - - + +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PHE* 5.3 1.8 - - + -
272A ALA 3.0 13.1 + - - +
273A ALA* 3.1 11.6 + - - +
275A ARG* 1.3 77.2 - - - +
277A ALA* 1.3 57.4 + - - +
279A GLY 3.3 0.3 + - - -
280A LEU* 2.9 46.1 + - + +
297A LEU* 3.7 19.3 - - + -
328A PHE* 3.7 34.1 - - + +
330A THR* 5.2 8.1 - - + -
339A VAL* 3.7 14.5 - - + +
342A LEU* 3.6 28.9 - - + -
343A LEU* 3.6 23.9 - - + +
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Residues in contact with ALA 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 ALA 2.9 12.9 + - - +
274A GLN* 3.8 13.2 - - - +
276A LEU* 1.3 76.2 - - - +
278A GLN* 1.3 63.1 + - - +
280A LEU* 3.4 4.4 + - - +
281A GLU* 3.1 32.8 + - + +
288A VAL* 4.0 10.7 - - + +
292A THR* 3.8 18.2 - - - +
297A LEU* 3.4 21.3 - - + +
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Residues in contact with GLN 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 GLN* 3.0 22.7 + - + +
275A ARG* 3.7 6.7 - - - +
277A ALA* 1.3 77.5 - - - +
279A GLY* 1.3 59.9 + - - +
281A GLU* 3.9 25.2 + - - +
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Residues in contact with GLY 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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275A ARG 3.0 10.3 + - - -
276A LEU 3.3 0.2 + - - -
278A GLN* 1.3 77.0 - - - +
280A LEU* 1.3 63.9 + - - +
281A GLU 3.7 2.3 + - - +
283A LEU* 3.6 7.1 - - - +
343A LEU* 3.4 28.7 - - - -
347A ARG* 3.0 28.6 + - - -
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Residues in contact with LEU 280 (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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276A LEU* 2.9 43.6 + - + +
277A ALA 3.4 0.2 + - - -
279A GLY* 1.3 78.3 - - - +
281A GLU* 1.3 61.8 + - - +
282A GLY 3.1 2.9 + - - -
283A LEU* 3.3 16.8 + - + +
286A VAL* 3.7 23.7 - - + +
288A VAL* 3.7 18.3 - - + +
297A LEU* 3.8 24.2 - - + -
299A CYS* 4.2 15.3 - - - -
301A LEU* 5.5 1.1 - - + -
328A PHE* 4.9 4.7 - - + -
343A LEU* 3.8 15.5 - - + -
346A VAL* 3.8 34.3 - - + -
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Residues in contact with GLU 281 (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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277A ALA* 3.1 18.0 + - + +
278A GLN* 3.9 25.9 - - - +
279A GLY 3.5 5.1 - - - +
280A LEU* 1.3 72.5 - - - +
282A GLY* 1.1 60.8 + - - +
283A LEU* 4.7 1.6 - - - +
286A VAL 5.8 0.7 - - - -
288A VAL* 4.3 15.2 - - + +
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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