Contacts of the helix formed by residues 276 - 290 (chain A) in PDB entry 3LX9
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 SER 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A LEU* 1.3 78.0 - - - +
277A TRP* 1.3 66.1 + - - +
278A ASN 3.6 0.3 + - - -
279A GLN* 2.8 37.2 + - - +
280A GLN* 3.0 20.5 + - - +
273B PHE 2.7 29.2 + - - -
275B LEU 3.4 31.9 - - - -
276B SER* 3.9 4.6 - - - +
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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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276A SER* 1.3 73.3 - - - +
278A ASN* 1.3 70.9 + - - +
280A GLN* 3.1 24.0 + - - +
281A VAL* 3.0 48.7 + - + +
306A GLN* 3.4 48.9 - - + -
307A ALA* 4.1 5.4 - - + -
310A LEU* 3.8 27.8 - - + -
388A LEU* 6.4 0.4 - - + -
389A PRO* 5.0 15.2 + - + +
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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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276A SER 3.3 0.6 - - - -
277A TRP* 1.3 88.3 - - - +
279A GLN* 1.3 57.1 + - - +
281A VAL* 3.5 7.6 + - - +
282A THR* 2.9 30.5 + - - -
389A PRO* 5.6 4.3 - - - +
408A ASN* 2.8 35.9 + - - +
409A PRO 3.9 9.2 - - - +
410A THR* 3.2 5.6 - - - +
411A GLY* 3.6 18.5 - - - +
272B ASN 5.2 0.6 + - - -
273B PHE* 3.5 39.0 + - - +
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Residues in contact with GLN 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TRP* 3.6 49.0 - - + +
239A ILE* 5.1 1.0 - - - +
274A GLY 4.0 2.8 - - - +
275A LEU* 3.4 19.9 - - + +
276A SER* 2.8 34.7 + - - +
278A ASN* 1.3 73.4 - - - +
280A GLN* 1.3 61.1 + - - +
282A THR* 3.5 5.2 + - - -
283A GLN* 3.1 25.6 + - - +
410A THR* 3.3 26.1 + - - +
234B ASP 5.3 0.2 + - - -
235B SER* 5.9 0.2 - - - +
274B GLY* 2.7 36.4 + - - +
279B GLN* 5.2 0.3 - - - +
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Residues in contact with GLN 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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270A ILE* 3.2 32.7 - - + +
271A GLY* 3.1 27.8 + - - -
272A ASN 5.7 0.4 - - - -
275A LEU* 3.4 40.6 + - + -
276A SER 3.0 19.3 + - - +
277A TRP* 3.1 24.3 + - + +
279A GLN* 1.3 74.9 - - - +
281A VAL* 1.3 65.0 + - - +
283A GLN* 3.2 1.7 + - - +
284A MET 3.1 18.5 + - - -
307A ALA* 4.3 5.4 - - - +
310A LEU* 3.6 10.5 - - + +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TRP* 3.0 50.4 + - + +
278A ASN* 3.6 11.2 - - - +
280A GLN* 1.3 73.5 - - - +
282A THR* 1.3 65.6 + - - +
284A MET* 3.3 2.3 + - - +
285A ALA* 2.9 23.3 + - + +
310A LEU* 3.9 14.8 - - + -
388A LEU* 3.9 24.7 - - + +
389A PRO* 4.4 15.3 - - + -
412A THR* 3.7 27.1 - - - +
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Residues in contact with THR 282 (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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236A TRP* 3.9 23.6 - - + -
239A ILE* 4.9 0.4 - - + -
243A LEU* 4.2 17.5 - - + -
278A ASN 2.9 8.0 + - - -
279A GLN* 3.5 9.4 - - - -
280A GLN 3.2 0.4 - - - -
281A VAL* 1.3 76.4 - - - +
283A GLN* 1.3 63.5 + - - +
286A LEU* 3.0 28.2 + - + +
354A ILE* 4.3 6.3 - - + -
410A THR 2.7 24.4 + - - -
411A GLY 3.3 4.3 - - - -
412A THR* 2.9 28.2 + - - +
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Residues in contact with GLN 283 (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 ILE* 3.3 6.1 - - - +
239A ILE* 3.3 33.2 - - + +
267A MET 3.0 25.9 + - - -
268A LEU* 3.6 14.6 - - + +
269A VAL* 2.9 28.7 + - - +
270A ILE* 3.7 12.5 + - + +
275A LEU* 4.3 1.9 - - + +
279A GLN 3.1 14.9 + - - +
280A GLN* 3.2 7.4 + - - +
282A THR* 1.3 76.2 - - - +
284A MET* 1.3 64.6 + - - +
286A LEU* 5.0 0.2 - - - -
287A TRP* 3.0 57.5 + - + +
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Residues in contact with MET 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TYR* 3.9 7.2 - - - +
268A LEU* 4.2 10.5 - - - -
270A ILE* 3.7 9.4 - - + +
280A GLN 3.1 15.6 + - - +
281A VAL 3.8 1.8 - - - +
283A GLN* 1.3 76.3 - - - +
285A ALA* 1.3 61.7 + - - +
287A TRP* 4.1 4.0 - - - +
288A ALA* 3.3 21.3 + - - +
294A LEU* 4.5 11.8 - - + +
310A LEU* 3.6 38.4 - - + +
311A LEU* 3.5 45.8 - - - +
313A ASP 5.0 0.2 - - - +
316A VAL* 3.8 22.5 - - + +
317A ILE* 4.1 16.6 - - + -
388A LEU* 4.7 0.4 - - + -
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Residues in contact with ALA 285 (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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281A VAL 2.9 17.7 + - - +
282A THR 3.8 1.6 - - - +
284A MET* 1.3 77.0 - - - +
286A LEU* 1.3 59.8 + - + +
288A ALA* 3.3 7.0 + - - +
289A ILE* 3.0 29.1 + - - +
316A VAL* 4.7 0.2 - - - -
388A LEU* 4.0 14.5 - - + +
412A THR* 3.8 28.3 - - + -
414A LEU* 4.2 23.9 - - + +
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Residues in contact with LEU 286 (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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243A LEU* 3.7 28.5 - - + -
282A THR* 3.0 21.3 + - + +
285A ALA* 1.3 77.5 - - + +
287A TRP* 1.3 64.0 + - + +
289A ILE* 3.3 5.3 + - + +
290A MET* 2.8 35.8 + - - +
340A TRP* 3.3 54.1 - - + -
352A ALA* 4.1 6.1 - - + -
354A ILE* 3.7 24.7 - - + -
412A THR* 3.9 21.3 - - + +
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Residues in contact with TRP 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE* 4.0 6.3 - - + -
239A ILE* 4.1 16.8 - - + -
242A ILE* 3.9 21.1 - - + -
243A LEU* 4.0 14.6 - - + -
265A PRO* 3.6 28.7 - - + +
266A ASP 2.8 22.3 + - - -
268A LEU* 3.5 26.9 - - + +
283A GLN* 3.0 64.6 + - + +
284A MET* 4.1 3.1 - - - +
286A LEU* 1.3 79.8 - - + +
288A ALA* 1.3 58.4 + - - +
290A MET* 3.4 19.7 - - + -
291A ALA 3.5 1.2 + - - -
292A ALA* 3.2 34.7 + - + +
293A PRO 4.0 7.9 - - - -
294A LEU* 4.0 7.9 - - + -
320A ASN* 3.1 17.4 + - - -
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Residues in contact with ALA 288 (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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284A MET 3.3 13.3 + - - +
285A ALA 3.3 9.8 + - - +
286A LEU 3.2 0.8 - - - -
287A TRP* 1.3 75.6 - - - +
289A ILE* 1.3 62.7 + - - +
291A ALA 3.3 2.6 + - - -
294A LEU* 5.1 1.0 - - + +
316A VAL* 3.7 32.8 - - + +
319A ILE* 4.0 10.8 - - + +
320A ASN* 3.7 16.0 - - + +
342A ARG* 2.9 29.8 + - - -
414A LEU* 5.1 2.9 - - + -
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Residues in contact with ILE 289 (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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285A ALA 3.0 18.0 + - - +
286A LEU* 3.3 10.7 + - - +
288A ALA* 1.3 77.4 - - + +
290A MET* 1.3 53.1 + - - +
291A ALA 3.4 1.0 + - - -
319A ILE* 5.3 0.2 - - + -
328A GLY* 2.8 45.2 + - - -
340A TRP* 3.9 33.0 - - + -
341A GLU* 4.2 4.0 - - - +
342A ARG* 3.4 15.2 - - + +
350A ALA* 3.7 42.6 - - + +
352A ALA* 3.9 27.8 - - + +
414A LEU* 4.2 7.0 - - + -
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Residues in contact with MET 290 (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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242A ILE* 5.2 0.9 - - + -
243A LEU* 4.1 13.9 - - + -
246A THR* 3.8 31.0 - - + -
263A ASN* 5.0 1.7 - - - +
265A PRO* 3.8 20.2 - - + -
286A LEU* 2.8 20.7 + - - +
287A TRP* 3.4 48.0 - - + +
288A ALA 3.2 0.6 - - - -
289A ILE* 1.3 73.1 - - + +
291A ALA* 1.3 71.5 + - - +
292A ALA* 4.2 5.7 - - + +
327A GLN* 3.0 35.9 - - - +
328A GLY 4.5 1.1 - - - +
340A TRP* 4.0 19.7 - - + -
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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