Contacts of the helix formed by residues 269 - 284 (chain O) in PDB entry 5L4K
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 LEU 269 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245O VAL* 4.5 16.2 - - + -
248O PHE* 3.6 31.4 - - + -
249O GLN* 4.9 6.5 - - + +
252O LYS* 4.8 10.3 - - - +
265O GLU* 3.5 17.7 + - + +
266O ALA* 4.5 5.8 - - - +
267O GLN 3.2 0.6 - - - -
268O LEU* 1.3 74.8 - - - +
270O ARG* 1.3 60.2 + - - +
272O ILE* 4.3 3.8 - - + +
273O GLN* 3.1 45.4 + - + +
301O LYS 6.0 2.0 - - - +
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Residues in contact with ARG 270 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266O ALA 3.9 8.7 + - - +
267O GLN* 3.0 16.4 + - + +
269O LEU* 1.3 78.9 - - - +
271O LYS* 1.3 58.1 + - - +
273O GLN* 3.0 32.1 + - - +
274O LEU* 3.0 32.6 + - + +
302O ILE* 5.9 0.2 - - - +
306O GLU* 3.6 32.8 + - - +
310O LEU* 4.4 9.2 - - + +
313O LYS* 3.5 43.3 - - + +
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Residues in contact with LYS 271 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204O GLY 3.2 19.8 + - - -
205O LEU 3.7 13.2 - - - +
207O GLY 2.6 28.8 + - - +
208O GLU* 4.3 0.9 - - - +
209O GLY 4.4 1.5 - - - +
210O VAL* 3.1 35.5 + - - +
211O PHE* 4.0 22.4 - - + -
213O PHE* 4.0 8.0 - - - -
240O PHE* 4.1 18.4 - - + -
267O GLN* 3.1 14.8 + - + +
268O LEU* 4.1 6.5 - - + -
270O ARG* 1.3 79.1 - - - +
272O ILE* 1.3 63.0 + - - +
274O LEU* 4.0 7.2 - - - +
275O LEU* 3.3 25.6 + - + +
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Residues in contact with ILE 272 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239O ALA 4.6 5.6 - - - +
240O PHE* 3.4 36.8 - - + +
243O GLY* 4.5 6.5 - - - -
244O ASN 3.7 23.3 - - - +
245O VAL* 4.0 18.2 - - + -
248O PHE* 3.2 45.8 - - + -
268O LEU 3.2 20.0 + - - +
269O LEU* 4.9 2.9 - - + +
270O ARG 3.3 0.2 - - - -
271O LYS* 1.3 75.2 - - - +
273O GLN* 1.3 67.6 + - - +
274O LEU 3.0 1.3 - - - -
275O LEU* 3.0 6.9 + - - +
276O CYS* 2.9 20.8 + - - +
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Residues in contact with GLN 273 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245O VAL* 4.3 15.8 - - + +
269O LEU* 3.1 33.0 + - + +
270O ARG* 3.0 33.8 + - - +
272O ILE* 1.3 78.6 - - - +
274O LEU* 1.3 62.8 + - - +
276O CYS* 3.2 15.0 + - - +
277O LEU 3.5 3.8 + - - -
300O ALA* 3.4 25.1 + - + +
301O LYS 5.0 1.6 - - - -
302O ILE* 3.1 38.6 - - - +
306O GLU* 4.5 0.8 - - - +
310O LEU* 4.0 29.4 - - + +
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Residues in contact with LEU 274 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211O PHE* 3.9 19.1 - - + -
270O ARG* 3.0 19.6 + - + +
271O LYS* 4.0 7.9 - - - +
272O ILE 3.0 0.2 - - - -
273O GLN* 1.3 76.1 - - - +
275O LEU* 1.3 60.2 + - + +
276O CYS 3.1 0.7 + - - -
277O LEU* 3.2 9.9 + - + +
278O MET* 3.0 25.2 + - - +
310O LEU* 3.5 38.4 - - + +
313O LYS* 4.2 11.7 - - + -
314O ALA* 3.9 20.9 - - + +
317O VAL* 4.6 8.3 - - + -
319O LEU* 3.8 27.8 - - + -
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Residues in contact with LEU 275 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211O PHE* 3.7 37.9 - - + +
213O PHE* 3.8 24.2 - - + -
240O PHE* 3.6 29.6 - - + +
241O ASN 6.0 0.9 - - - +
243O GLY* 3.9 8.8 + - - +
271O LYS* 3.3 18.1 + - + +
272O ILE* 3.0 8.1 + - - +
274O LEU* 1.3 75.8 - - + +
276O CYS* 1.3 57.3 + - - +
278O MET* 3.4 33.4 - - + +
279O GLU* 2.9 29.8 + - - +
319O LEU* 5.0 2.2 - - + -
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Residues in contact with CYS 276 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243O GLY* 3.3 30.7 - - - +
245O VAL* 4.3 6.5 - - + -
272O ILE 2.9 9.6 + - - +
273O GLN* 3.4 11.0 - - - +
274O LEU 3.1 0.6 - - - -
275O LEU* 1.3 73.9 - - - +
277O LEU* 1.3 61.6 + - - +
279O GLU* 4.7 1.3 - - - +
280O MET* 2.8 39.3 + - - +
296O ILE* 6.3 0.4 - - - -
299O SER* 3.3 43.7 - - - -
300O ALA* 4.5 4.0 - - + -
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Residues in contact with LEU 277 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273O GLN 3.5 5.4 + - - +
274O LEU* 3.2 9.7 + - + +
276O CYS* 1.3 77.2 - - - +
278O MET* 1.3 64.9 + - - +
280O MET* 3.5 6.4 - - - +
281O THR* 3.0 44.6 + - + +
291O LEU* 4.6 2.0 - - + -
296O ILE* 3.9 43.1 - - + +
300O ALA* 6.2 0.4 - - - +
310O LEU* 5.0 8.1 - - + +
311O VAL* 4.2 34.8 - - + -
314O ALA* 4.2 20.2 - - + -
320O VAL* 4.4 11.4 - - + -
331O VAL* 5.5 2.0 - - + -
333O MET* 4.9 7.0 - - - -
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Residues in contact with MET 278 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211O PHE 4.9 4.5 - - - +
212O ASN* 5.4 3.6 - - - +
274O LEU 3.0 16.3 + - - +
275O LEU* 3.4 31.9 - - + -
277O LEU* 1.3 77.0 - - - +
279O GLU* 1.3 63.7 + - - +
281O THR* 3.2 15.4 + - - -
282O PHE* 4.0 2.1 + - - +
314O ALA* 6.5 0.7 - - + -
319O LEU* 4.1 34.3 - - + +
320O VAL* 4.9 6.3 - - + -
336O VAL* 3.7 22.1 - - + +
337O GLN* 3.8 37.9 - - + +
338O PRO 4.7 5.6 - - - +
339O ARG* 4.7 20.3 + - + +
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Residues in contact with GLU 279 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241O ASN 4.4 6.7 - - - +
242O SER* 3.2 37.0 - - - +
275O LEU 2.9 21.2 + - - +
276O CYS* 4.0 2.6 - - - +
278O MET* 1.3 75.3 - - - +
280O MET* 1.3 63.5 + - - +
281O THR 3.0 1.6 - - - -
282O PHE* 2.6 45.2 + - + +
283O THR* 3.5 15.3 + - - -
339O ARG* 5.7 13.0 - - - +
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Residues in contact with MET 280 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276O CYS* 2.8 25.9 + - - +
277O LEU* 3.5 6.7 - - - +
279O GLU* 1.3 82.0 + - - +
281O THR* 1.3 60.6 + - - +
283O THR* 3.1 21.1 + - - -
284O ARG* 3.5 24.6 + - - +
291O LEU* 3.3 30.7 - - + -
295O GLU* 3.2 45.1 - - + +
296O ILE* 3.8 13.9 - - - -
299O SER* 3.8 19.7 - - - +
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Residues in contact with THR 281 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277O LEU* 3.0 18.9 + - + +
278O MET* 3.2 14.9 + - - -
279O GLU 2.8 2.6 + - - -
280O MET* 1.3 70.5 - - - +
282O PHE* 1.3 65.3 + - - +
283O THR 3.3 0.2 - - - -
284O ARG* 3.7 14.2 + - - +
289O ARG* 4.0 15.2 + - - -
291O LEU* 3.5 30.2 - - + +
333O MET* 3.3 52.0 - - + +
336O VAL* 3.6 8.9 - - - +
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Residues in contact with PHE 282 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278O MET 4.0 2.8 + - - +
279O GLU* 2.6 28.5 + - + +
281O THR* 1.3 73.7 + - - +
283O THR* 1.3 72.4 + - - +
284O ARG 3.1 11.1 - - - +
285O PRO* 4.5 2.6 - - - +
289O ARG* 4.6 7.1 + - - +
336O VAL* 5.5 5.2 - - + -
339O ARG* 2.9 43.3 - - - +
341O LEU* 5.2 2.7 - - + -
345O GLN* 4.1 22.4 - - - -
231U GLN* 5.4 7.0 - - + -
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Residues in contact with THR 283 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279O GLU* 3.5 14.9 + - - -
280O MET* 3.1 16.6 + - - -
282O PHE* 1.3 87.5 - - - +
284O ARG* 1.3 66.9 + - + +
285O PRO* 3.3 12.0 - - - +
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Residues in contact with ARG 284 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280O MET* 3.5 41.0 + - - +
281O THR* 3.7 6.1 + - - +
282O PHE 3.1 9.4 - - - +
283O THR* 1.3 78.3 - - + +
285O PRO* 1.4 64.7 - - - +
286O ALA 3.7 1.1 - - - -
288O HIS* 3.3 49.5 + - + +
289O ARG* 3.4 23.2 + - - +
290O GLN 3.9 7.2 + - - -
291O LEU* 3.6 31.7 - - - +
295O GLU* 3.3 36.0 + - - +
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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