Contacts of the helix formed by residues 281 - 297 (chain Q) 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 GLY 281 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248Q ILE* 5.5 6.5 - - - +
279Q TYR 4.2 0.8 - - - -
280Q ALA* 1.3 73.9 - - - +
282Q ARG* 1.3 65.4 + - - -
283Q GLN* 3.3 3.4 - - - -
284Q THR* 3.5 7.3 + - - -
285Q GLU* 3.0 34.2 + - - +
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Residues in contact with ARG 282 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281Q GLY* 1.3 72.1 - - - -
283Q GLN* 1.3 67.2 + - + +
285Q GLU* 3.1 15.7 + - - +
286Q ALA* 3.0 22.0 + - - +
308Q ASP 3.9 15.2 + - - -
309Q TYR* 3.4 36.9 - - - +
311Q ALA* 5.3 4.4 - - - +
312Q GLU* 3.0 39.7 + - - +
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Residues in contact with GLN 283 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248Q ILE* 3.7 42.1 - - + +
249Q THR* 4.2 15.6 + - - +
252Q LYS* 3.8 40.3 + - + +
281Q GLY* 3.3 1.5 - - - -
282Q ARG* 1.3 78.6 - - + +
284Q THR* 1.3 62.6 + - - +
286Q ALA* 3.4 15.3 + - - +
287Q LEU* 3.7 10.6 + - - +
312Q GLU* 3.9 24.5 - - + +
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Residues in contact with THR 284 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248Q ILE* 4.9 5.9 - - - +
251Q LEU* 5.0 10.1 - - + +
252Q LYS* 6.4 0.9 - - - +
255Q LEU* 4.5 8.5 - - + +
271Q VAL* 4.3 20.2 - - + -
276Q ALA* 5.4 1.1 - - + -
279Q TYR 3.6 14.9 + - - +
280Q ALA* 4.4 9.0 - - + -
281Q GLY 3.5 22.7 + - - -
282Q ARG 3.3 0.4 - - - -
283Q GLN* 1.3 79.6 - - - +
285Q GLU* 1.3 57.8 + - - +
287Q LEU* 3.0 11.0 + - - +
288Q LYS* 2.9 46.5 + - + +
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Residues in contact with GLU 285 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280Q ALA* 4.9 6.2 - - + +
281Q GLY* 3.0 23.7 + - - +
282Q ARG* 3.1 22.8 + - - +
284Q THR* 1.3 74.1 - - + +
286Q ALA* 1.3 63.4 + - - +
288Q LYS* 4.2 29.7 + - + +
289Q CYS* 4.0 10.6 + - - +
309Q TYR* 3.4 27.7 + - + +
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Residues in contact with ALA 286 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252Q LYS* 5.7 0.2 - - - -
282Q ARG 3.0 10.5 + - - +
283Q GLN 3.5 11.4 - - - +
284Q THR 3.1 0.4 - - - -
285Q GLU* 1.3 75.7 - - - +
287Q LEU* 1.3 61.9 + - + +
289Q CYS* 3.2 5.4 + - - +
290Q VAL* 3.0 30.1 + - - +
305Q ALA* 5.5 0.2 - - - +
309Q TYR* 4.2 23.1 - - + -
312Q GLU* 4.4 5.8 - - + -
313Q LEU* 3.8 32.3 - - + -
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Residues in contact with LEU 287 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252Q LYS* 2.7 52.0 - - + +
255Q LEU* 3.8 28.5 - - + -
256Q LEU* 4.0 24.2 - - + +
259Q ILE* 4.7 4.8 - - + +
267Q VAL* 4.8 1.3 - - - -
283Q GLN 3.7 9.8 + - - +
284Q THR* 3.0 6.5 + - - +
286Q ALA* 1.3 73.9 - - - +
288Q LYS* 1.3 67.6 + - - +
290Q VAL* 4.3 12.8 - - + +
291Q ALA* 2.8 28.2 + - - +
313Q LEU* 4.4 19.1 - - + -
319Q ILE* 5.8 1.6 - - + -
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Residues in contact with LYS 288 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255Q LEU* 5.2 0.7 - - + -
267Q VAL* 4.5 8.9 - - + +
271Q VAL* 4.2 26.5 - - + +
284Q THR* 2.9 39.4 + - + +
285Q GLU* 4.2 24.6 + - + +
287Q LEU* 1.3 75.5 - - - +
289Q CYS* 1.3 57.0 + - - +
291Q ALA* 3.5 5.9 - - - +
292Q GLN* 3.0 27.2 + - - +
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Residues in contact with CYS 289 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285Q GLU 4.0 11.3 + - - +
286Q ALA 3.2 9.1 + - - +
287Q LEU 3.0 0.6 - - - -
288Q LYS* 1.3 75.9 - - - +
290Q VAL* 1.3 67.0 + - - +
291Q ALA 3.1 1.1 - - - -
292Q GLN* 2.9 12.2 + - - +
293Q ALA* 2.8 20.4 + - - +
301Q ASP* 3.9 13.7 - - - -
305Q ALA* 3.3 29.6 - - + -
309Q TYR* 4.9 7.4 - - + +
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Residues in contact with VAL 290 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256Q LEU* 6.5 0.9 - - + -
259Q ILE* 4.0 15.7 - - + +
286Q ALA 3.0 18.3 + - - +
287Q LEU* 3.3 12.8 + - + +
289Q CYS* 1.3 73.5 - - - +
291Q ALA* 1.3 63.7 + - - +
293Q ALA* 2.9 23.1 + - - +
294Q SER* 3.1 11.0 + - - +
302Q PHE* 4.4 23.1 - - + +
305Q ALA* 5.0 13.5 - - + +
306Q LEU* 5.7 1.1 - - + +
313Q LEU* 4.0 24.5 - - + -
323Q LEU* 5.8 2.7 - - + -
326Q LEU* 4.3 20.4 - - + -
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Residues in contact with ALA 291 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259Q ILE* 3.5 22.6 - - + +
264Q PRO* 4.3 8.5 - - - +
267Q VAL* 3.8 31.2 - - + -
268Q GLN* 6.1 2.7 - - + -
287Q LEU 2.8 18.9 + - - +
288Q LYS 3.5 4.7 - - - +
290Q VAL* 1.3 75.6 - - - +
292Q GLN* 1.3 63.1 + - - +
293Q ALA 2.8 1.9 + - - -
294Q SER* 3.0 4.0 + - - +
295Q LYS* 2.9 23.2 + - - +
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Residues in contact with GLN 292 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268Q GLN* 3.2 33.6 + - - +
288Q LYS 3.0 16.4 + - - +
289Q CYS* 2.9 20.0 + - - +
291Q ALA* 1.3 72.2 - - - +
293Q ALA* 1.3 55.1 + - - +
295Q LYS* 3.8 7.8 - - - +
296Q ASN* 3.1 62.9 + - - +
301Q ASP* 4.2 3.6 - - - +
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Residues in contact with ALA 293 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289Q CYS 2.8 9.8 + - - +
290Q VAL* 2.9 17.5 + - - +
291Q ALA 2.8 1.0 + - - -
292Q GLN* 1.3 74.0 - - - +
294Q SER* 1.3 64.8 + - - +
295Q LYS 3.0 1.5 + - - -
296Q ASN 3.4 2.3 + - - -
297Q ARG 3.0 4.0 + - - -
298Q SER* 3.0 29.5 + - - +
301Q ASP* 3.7 27.4 - - + +
302Q PHE* 4.0 25.8 - - + +
330Q LEU* 5.0 1.1 - - + -
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Residues in contact with SER 294 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259Q ILE* 3.6 32.8 - - - +
262Q ASN* 5.6 2.0 - - - -
264Q PRO* 4.3 10.5 - - - +
290Q VAL* 3.1 5.5 + - - +
291Q ALA 3.0 5.2 + - - -
293Q ALA* 1.3 77.6 - - - +
295Q LYS* 1.3 58.5 + - - +
297Q ARG* 3.4 17.2 + - - +
302Q PHE* 5.9 1.4 - - - -
326Q LEU* 4.7 5.7 - - - +
329Q ASN* 5.8 0.5 - - - +
330Q LEU* 4.1 28.6 - - - +
333Q GLN* 4.1 16.0 + - - +
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Residues in contact with LYS 295 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264Q PRO* 4.2 14.3 - - + +
265Q GLU* 3.1 39.7 + - + +
268Q GLN* 3.6 34.0 + - - +
291Q ALA 2.9 16.4 + - - +
292Q GLN* 3.7 17.0 - - - +
294Q SER* 1.3 75.7 - - - +
296Q ASN* 1.3 64.7 + - - +
297Q ARG* 3.0 10.1 + - - +
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Residues in contact with ASN 296 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292Q GLN* 3.1 43.9 + - - +
295Q LYS* 1.3 75.9 - - - +
297Q ARG* 1.3 68.7 + - - +
298Q SER* 2.9 22.8 + - - +
301Q ASP* 3.6 15.4 + - - -
337Q ARG* 3.7 12.3 + - - -
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Residues in contact with ARG 297 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398P VAL* 3.2 32.5 - - - +
293Q ALA 3.0 5.0 + - - -
294Q SER* 3.4 15.9 + - - +
295Q LYS 3.0 10.4 - - - +
296Q ASN* 1.3 78.4 + - - +
298Q SER* 1.3 56.0 + - - +
330Q LEU* 4.7 7.0 - - - -
333Q GLN* 3.7 47.4 + - - +
334Q ASN* 2.8 14.9 + - - +
336Q ILE* 4.1 10.5 - - - +
337Q ARG* 2.8 37.3 + - - +
340Q GLU* 2.8 27.1 + - - -
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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