Contacts of the helix formed by residues 276 - 290 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A PHE 2.8 29.2 + - - -
275A LEU 3.4 30.3 - - - -
276A SER* 3.9 5.4 - - - +
275B LEU* 1.3 77.7 - - - +
277B TRP* 1.3 65.1 + - - +
278B ASN* 3.5 0.7 + - - -
279B GLN* 2.9 38.7 + - - +
280B GLN* 3.0 20.6 + - - -
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Residues in contact with TRP 277 (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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276B SER* 1.3 74.0 - - - +
278B ASN* 1.3 71.8 + - - +
280B GLN* 3.2 21.2 + - + +
281B VAL* 3.0 46.2 + - + +
306B GLN* 3.3 75.6 - - + +
307B ALA* 4.2 4.5 - - - -
309B ALA* 6.1 0.4 - - + -
310B LEU* 3.8 29.6 - - + -
388B LEU* 6.2 0.4 - - + -
389B PRO* 5.0 15.7 + - + +
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Residues in contact with ASN 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ASN 4.8 1.4 + - - -
273A PHE* 3.2 40.7 + - - +
276B SER* 3.2 0.8 - - - -
277B TRP* 1.3 90.7 - - - +
279B GLN* 1.3 57.1 + - - +
281B VAL* 3.3 8.7 + - - +
282B THR* 3.0 30.3 + - - -
389B PRO* 5.8 3.5 - - - +
408B ASN* 2.9 34.2 + - - +
409B PRO 4.0 0.7 - - - +
410B THR* 3.4 13.4 - - - +
411B GLY* 3.7 19.0 - - - +
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Residues in contact with GLN 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ASP 5.2 0.2 + - - -
235A SER* 6.0 0.4 - - - +
274A GLY* 2.9 31.1 + - - +
279A GLN* 5.2 0.3 - - - +
236B TRP* 3.5 47.8 - - + +
239B ILE* 4.4 5.9 - - - +
274B GLY 4.1 2.6 - - - +
275B LEU* 3.6 17.2 - - + -
276B SER* 2.9 34.8 + - - +
278B ASN* 1.3 77.0 - - - +
280B GLN* 1.3 55.6 + - - +
282B THR* 3.3 5.2 + - - -
283B GLN* 3.1 26.3 + - - +
410B THR* 3.3 31.8 + - - +
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Residues in contact with GLN 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ILE* 3.4 26.9 - - + +
271B GLY* 3.0 29.0 + - - -
272B ASN 5.6 2.0 - - - +
275B LEU* 3.3 35.3 + - + -
276B SER 3.0 27.3 + - - +
277B TRP* 3.2 22.6 + - + +
279B GLN* 1.3 74.3 - - - +
281B VAL* 1.3 64.7 + - - +
283B GLN 3.3 1.1 + - - +
284B MET 3.1 18.2 + - - -
307B ALA* 4.2 6.6 - - - +
310B LEU* 3.4 17.0 - - + +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B TRP* 3.0 51.8 + - + +
278B ASN* 3.6 10.1 - - - +
280B GLN* 1.3 74.4 - - - +
282B THR* 1.3 63.8 + - - +
284B MET* 3.3 2.1 + - - +
285B ALA* 3.0 23.4 + - + +
310B LEU* 3.8 14.1 - - + -
388B LEU* 3.8 30.1 - - + -
389B PRO* 4.4 15.0 - - + -
411B GLY* 5.8 0.2 - - - -
412B THR* 3.8 20.4 - - - +
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Residues in contact with THR 282 (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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236B TRP* 3.8 24.0 - - + -
239B ILE* 4.9 0.9 - - + -
243B LEU* 4.4 15.9 - - + -
278B ASN 3.0 8.4 + - - -
279B GLN 3.5 9.0 - - - -
280B GLN 3.2 0.4 - - - -
281B VAL* 1.3 76.6 - - - +
283B GLN* 1.3 63.2 + - - +
286B LEU* 3.0 27.4 + - + +
354B ILE* 4.2 8.3 - - + -
410B THR 2.8 23.9 + - - -
411B GLY 3.2 4.9 + - - -
412B THR* 2.7 28.6 + - - +
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Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE* 3.1 20.4 - - - +
239B ILE* 3.8 23.6 - - + +
267B MET 2.9 26.5 + - - -
268B LEU* 3.6 10.9 - - + +
269B VAL* 3.0 28.7 + - - +
270B ILE* 3.7 13.2 + - + +
275B LEU* 4.4 0.2 - - - +
279B GLN 3.1 8.7 + - - +
280B GLN* 3.3 6.5 + - - +
282B THR* 1.3 73.0 - - - +
284B MET* 1.3 67.5 + - - +
287B TRP* 2.9 62.6 + - + +
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Residues in contact with MET 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B TYR* 3.9 8.3 - - - +
268B LEU* 4.0 24.2 - - - -
270B ILE* 3.8 14.7 - - + +
280B GLN 3.1 16.0 + - - +
281B VAL 3.3 2.9 + - - +
283B GLN* 1.3 77.2 - - - +
285B ALA* 1.3 63.1 + - - +
287B TRP* 3.9 2.1 - - - +
288B ALA* 3.1 22.4 + - + +
294B LEU* 4.5 12.0 - - + +
310B LEU* 3.6 42.2 - - + +
311B LEU* 3.7 20.4 - - - +
313B ASP 5.1 0.2 - - - +
316B VAL* 3.9 22.8 - - + +
317B ILE* 4.1 17.0 - - + +
388B LEU* 4.6 0.9 - - + -
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B VAL* 3.0 18.4 + - + +
282B THR 3.8 3.4 - - - +
284B MET* 1.3 76.7 - - - +
286B LEU* 1.3 60.9 + - + +
288B ALA* 3.2 6.6 + - - +
289B ILE* 3.0 29.8 + - - +
316B VAL* 4.7 0.2 - - - -
388B LEU* 4.1 17.6 - - + +
412B THR* 3.9 25.4 - - + -
414B LEU* 4.3 21.0 - - + +
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU* 3.8 25.4 - - + -
282B THR* 3.0 21.9 + - + +
285B ALA* 1.3 81.1 - - + +
287B TRP* 1.3 67.5 + - + +
289B ILE* 3.4 5.5 + - + +
290B MET* 2.9 34.2 + - - +
340B TRP* 3.4 54.3 - - + -
352B ALA* 3.9 17.3 - - + -
354B ILE* 3.7 24.2 - - + -
412B THR* 4.0 7.2 - - + +
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Residues in contact with TRP 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE* 4.3 4.5 - - + -
239B ILE* 4.4 13.0 - - + -
242B ILE* 4.0 23.6 - - + -
243B LEU* 4.0 13.9 - - + -
265B PRO* 3.6 29.1 - - + +
266B ASP 2.8 24.1 + - - -
268B LEU* 3.7 20.8 - - + +
283B GLN* 2.9 60.5 + - + +
284B MET 3.9 3.1 - - - +
286B LEU* 1.3 76.5 - - + +
288B ALA* 1.3 62.2 + - - +
290B MET* 3.4 19.5 + - + -
291B ALA 3.5 1.4 + - - -
292B ALA* 3.2 32.7 + - + +
293B PRO 4.0 8.5 - - - -
294B LEU* 3.9 12.1 - - + -
320B ASN* 3.1 17.4 + - - -
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Residues in contact with ALA 288 (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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284B MET 3.1 13.9 + - - +
285B ALA 3.3 9.4 - - - +
286B LEU 3.2 0.2 - - - -
287B TRP* 1.3 75.4 - - - +
289B ILE* 1.3 62.2 + - - +
291B ALA 3.3 3.3 + - - -
294B LEU* 5.0 1.2 - - + +
316B VAL* 3.7 32.8 - - + +
319B ILE* 3.9 13.5 - - + +
320B ASN* 3.7 13.3 - - + +
342B ARG* 2.9 29.1 + - - -
414B LEU* 5.1 3.4 - - + -
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Residues in contact with ILE 289 (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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285B ALA 3.0 17.7 + - - +
286B LEU* 3.4 11.2 + - + +
288B ALA* 1.3 77.1 - - + +
290B MET* 1.3 60.1 + - - +
291B ALA 3.2 0.2 - - - -
319B ILE* 4.6 0.6 - - - +
328B GLY* 2.8 37.9 + - - -
340B TRP* 4.0 33.0 - - + +
341B GLU* 4.1 4.9 - - - +
342B ARG* 3.4 16.6 - - + +
350B ALA* 3.6 42.2 - - + +
352B ALA* 3.9 28.3 - - + +
414B LEU* 4.3 5.4 - - + -
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Residues in contact with MET 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE* 5.2 0.7 - - + -
243B LEU* 4.1 15.0 - - + -
246B THR* 3.8 29.8 - - - -
263B ASN* 4.9 2.1 - - - +
265B PRO* 3.7 25.4 - - + -
286B LEU* 2.9 17.3 + - - +
287B TRP* 3.4 43.9 + - + +
288B ALA 3.2 0.6 - - - -
289B ILE* 1.3 75.5 - - + +
291B ALA* 1.3 67.7 + - - +
292B ALA* 3.2 5.7 + - + +
327B GLN* 3.1 39.1 + - + +
328B GLY 4.4 1.1 - - - +
340B TRP* 3.9 20.0 - - + -
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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