Contacts of the helix formed by residues 281 - 299 (chain S) 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 ASN 281 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93S PHE* 5.3 12.1 - - - -
96S ARG* 5.6 4.8 - - - +
245S ASP* 4.7 4.6 + - - +
280S ALA* 1.3 74.1 - - - +
282S ASN* 1.3 79.2 + - - +
283S ASN* 3.1 19.8 + - - +
284S GLU* 2.6 37.5 + - + +
285S TRP* 3.2 8.7 + - - +
15Y GLU* 3.9 11.9 - - - +
16Y ASP 2.8 34.2 + - - +
17Y ASP* 5.2 3.3 + - - +
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Residues in contact with ASN 282 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385R ARG* 3.2 41.7 + - - +
389R MET* 3.8 24.1 - - + +
280S ALA 3.5 3.8 + - - +
281S ASN* 1.3 79.0 + - - +
283S ASN* 1.3 57.8 + - - +
285S TRP* 2.6 30.1 + - - +
286S ALA* 2.8 14.2 + - - +
315S LYS* 4.0 18.3 + - + +
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Residues in contact with ASN 283 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281S ASN* 3.1 14.1 + - - +
282S ASN* 1.3 78.1 - - - +
284S GLU* 1.3 63.5 + - - +
286S ALA* 3.2 5.0 + - - +
287S ARG* 3.0 29.3 + - - +
315S LYS 5.3 1.5 + - - -
317S PRO* 4.2 17.2 - - - +
16Y ASP* 4.1 15.0 - - + -
17Y ASP* 3.6 31.3 + - - +
18Y GLU 2.9 25.5 - - - +
19Y PHE* 3.3 27.2 - - + -
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Residues in contact with GLU 284 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245S ASP* 4.4 5.4 - - - +
248S ALA* 4.6 5.9 - - + +
249S THR* 2.6 29.1 + - - +
252S ASN* 3.3 27.8 + - - +
276S PHE* 4.5 2.5 - - - -
280S ALA* 3.4 14.2 - - + +
281S ASN* 2.6 42.4 + - + +
283S ASN* 1.3 75.9 - - - +
285S TRP* 1.3 60.5 + - - +
287S ARG* 3.3 3.9 + - - +
288S TYR* 3.0 22.2 + - - +
15Y GLU* 2.7 27.2 + - - -
16Y ASP* 3.8 18.7 - - + +
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Residues in contact with TRP 285 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276S PHE* 4.0 16.6 - + + -
277S PRO 3.1 25.1 - - - -
278S GLU* 2.9 39.0 - - - -
280S ALA* 3.6 30.5 - - + -
281S ASN 3.2 6.8 + - - +
282S ASN* 2.6 18.8 + - - +
284S GLU* 1.3 72.9 - - - +
286S ALA* 1.3 56.0 + - - +
288S TYR* 3.5 11.7 + + - +
289S LEU* 2.9 66.8 + - + +
315S LYS* 3.8 25.4 - - + +
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Residues in contact with ALA 286 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282S ASN 2.8 9.7 + - - +
283S ASN* 3.6 9.0 - - - +
285S TRP* 1.3 73.2 - - - +
287S ARG* 1.3 67.4 + - - +
289S LEU* 3.2 6.3 + - - +
290S TYR* 2.9 19.1 + - - +
312S ALA* 4.3 7.3 - - - +
315S LYS* 4.3 22.6 - - + +
316S ALA* 4.3 11.2 - - - +
324S PHE* 3.5 25.2 - - + -
19Y PHE* 4.5 7.4 - - + -
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Residues in contact with ARG 287 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212S TYR* 3.4 44.5 + - - -
249S THR* 4.3 9.1 - - - +
252S ASN* 3.7 24.7 - - - +
253S LEU* 4.6 6.4 - - - +
283S ASN* 3.0 18.1 + - - +
284S GLU* 3.5 5.8 - - - +
286S ALA* 1.3 74.8 - - - +
288S TYR* 1.3 64.6 + - - +
290S TYR* 2.9 13.6 + - - +
291S TYR* 3.0 34.9 + - + +
324S PHE* 3.9 10.2 - - + -
16Y ASP* 2.9 42.8 + - - +
18Y GLU 3.7 12.3 + - - -
19Y PHE* 3.7 13.2 - - + -
21Y GLU* 3.4 26.6 + - - +
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Residues in contact with TYR 288 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251S LEU* 4.7 4.5 - - + -
252S ASN* 3.8 4.9 + - - +
255S LEU* 3.7 28.0 - - + -
271S VAL* 3.6 31.5 + - + +
274S SER 5.2 1.4 + - - -
276S PHE* 3.3 64.9 + + + +
284S GLU 3.0 10.0 + - - +
285S TRP* 3.9 9.2 - - - +
287S ARG* 1.3 78.8 - - - +
289S LEU* 1.3 70.4 + - + +
291S TYR* 4.6 5.2 - - - -
292S THR* 2.9 46.1 + - + +
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Residues in contact with LEU 289 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285S TRP* 2.9 55.5 + - + +
286S ALA* 3.9 3.4 - - - +
287S ARG 3.2 0.2 - - - -
288S TYR* 1.3 81.9 - - + +
290S TYR* 1.3 62.5 + - - +
292S THR* 3.8 7.6 - - + -
293S GLY* 3.7 7.4 + - - -
308S THR* 3.3 39.4 - - + +
309S MET* 4.4 1.4 + - - -
311S ASN* 4.3 21.8 - - + +
312S ALA* 4.0 21.4 - - + +
315S LYS* 4.5 14.4 - - + +
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Residues in contact with TYR 290 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286S ALA 2.9 13.4 + - - +
287S ARG 3.5 5.8 - - - +
289S LEU* 1.3 77.5 - - - +
291S TYR* 1.3 83.3 + + - +
293S GLY 3.6 0.7 + - - -
294S ARG* 2.9 53.3 + - + +
309S MET* 4.4 11.8 - - - +
312S ALA* 4.1 5.1 - - + +
324S PHE* 3.9 14.4 - + + -
327S THR* 3.7 20.8 + - + -
328S VAL* 3.8 29.2 - - + -
331S LEU* 3.8 23.8 - - + +
22Y PHE* 3.7 31.8 - + - -
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Residues in contact with TYR 291 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252S ASN* 4.2 18.2 - - + -
255S LEU* 4.2 26.0 - - + -
256S ARG* 3.5 38.6 + - + +
259S LEU* 3.5 28.9 - - + +
287S ARG* 3.0 38.2 + - + +
288S TYR* 4.0 5.6 - - - +
290S TYR* 1.3 100.4 - + - +
292S THR* 1.3 66.6 + - - +
293S GLY 3.0 1.3 - - - -
294S ARG* 3.0 8.5 + - + +
295S ILE* 2.9 28.1 + - + +
21Y GLU* 4.0 15.2 + - - -
22Y PHE* 4.3 7.7 - + - -
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Residues in contact with THR 292 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255S LEU* 5.7 0.2 - - - +
271S VAL* 3.5 24.4 - - - +
288S TYR* 2.9 39.5 + - + +
289S LEU* 3.8 7.4 - - + -
291S TYR* 1.3 76.6 - - - +
293S GLY* 1.3 59.4 + - - +
295S ILE* 3.5 11.7 + - - +
296S LYS* 3.0 38.7 + - + +
308S THR* 3.7 24.9 - - + +
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Residues in contact with GLY 293 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289S LEU 3.7 8.5 + - - -
290S TYR 3.6 4.2 + - - -
291S TYR 3.0 0.6 - - - -
292S THR* 1.3 82.3 - - - +
294S ARG* 1.3 66.2 + - - +
296S LYS* 3.3 6.9 + - - +
297S ALA* 2.9 24.3 + - - +
305S ALA* 4.1 7.2 - - - +
308S THR* 4.6 12.3 - - - -
309S MET* 4.1 13.9 - - - -
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Residues in contact with ARG 294 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259S LEU* 5.0 16.4 - - + -
264S TYR* 5.8 8.4 + - + -
290S TYR* 2.9 42.0 + - + +
291S TYR* 3.3 12.8 - - + +
293S GLY* 1.3 73.9 - - - +
295S ILE* 1.3 63.5 + - + +
297S ALA* 3.0 13.9 + - - +
298S ILE* 3.0 16.2 + - + +
309S MET* 4.3 1.6 - - - +
327S THR* 5.6 0.4 + - - -
331S LEU* 3.4 33.4 - - + +
389S ASP* 5.2 3.8 - - - +
390S GLY* 3.2 44.5 + - - +
391S THR* 3.5 12.5 + - - +
394S LEU* 4.9 8.6 - - - +
213T GLU* 4.8 2.8 + - - -
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Residues in contact with ILE 295 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255S LEU* 4.8 4.7 - - + -
259S LEU* 4.0 23.1 - - + -
264S TYR* 4.7 7.2 - - + +
267S ALA* 3.5 28.0 - - + -
268S GLU* 4.0 38.1 - - + +
271S VAL* 3.7 24.5 - - + -
291S TYR* 2.9 21.6 + - + +
292S THR* 3.7 6.5 - - - +
294S ARG* 1.3 75.3 - - - +
296S LYS* 1.3 67.3 + - + +
297S ALA 3.0 0.9 + - - -
298S ILE* 3.0 27.2 + - + +
299S GLN* 3.3 8.0 + - - +
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Residues in contact with LYS 296 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268S GLU* 5.9 1.7 - - - +
271S VAL* 5.6 6.1 - - - -
272S SER* 5.2 7.1 + - - -
292S THR* 3.0 33.5 + - + +
293S GLY* 3.3 6.5 + - - +
295S ILE* 1.3 77.1 - - + +
297S ALA* 1.3 63.3 + - - +
299S GLN* 3.5 21.8 - - - +
301S GLU* 3.4 45.4 + - + +
304S GLU* 3.1 36.8 + - + +
305S ALA* 4.4 16.2 - - + +
308S THR* 5.8 2.7 - - - +
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Residues in contact with ALA 297 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293S GLY 2.9 13.4 + - - +
294S ARG* 3.2 13.2 - - - +
295S ILE 3.0 0.2 - - - -
296S LYS* 1.3 78.2 - - - +
298S ILE* 1.3 64.4 + - - +
300S LEU* 3.3 10.4 + - - -
301S GLU 4.3 2.6 + - - +
302S TYR* 4.3 10.5 - - + -
305S ALA* 4.3 15.0 - - + +
309S MET* 5.2 0.4 - - + -
331S LEU* 5.0 2.7 - - + -
335S VAL* 4.5 16.6 - - + -
338S LEU* 6.3 1.1 - - + -
394S LEU* 4.0 18.5 - - + +
397S ARG* 3.8 10.2 + - - -
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Residues in contact with ILE 298 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264S TYR* 4.3 26.5 - - + -
268S GLU* 5.3 0.9 - - - +
294S ARG* 3.0 10.5 + - + +
295S ILE* 3.0 22.3 + - + +
297S ALA* 1.3 76.9 - - - +
299S GLN* 1.3 63.2 + - + +
300S LEU 3.1 3.7 + - - -
393S THR* 4.1 10.3 - - + -
394S LEU* 3.7 16.2 - - + -
397S ARG* 2.9 38.3 + - - +
209T HIS* 3.9 8.6 - - - +
210T THR* 4.3 20.0 + - + +
213T GLU* 3.0 38.8 - - + +
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Residues in contact with GLN 299 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268S GLU* 2.6 53.1 + - - +
295S ILE* 3.5 10.8 + - - +
296S LYS* 3.5 39.4 - - - +
297S ALA 3.3 0.2 - - - -
298S ILE* 1.3 78.4 - - + +
300S LEU* 1.3 68.1 + - - +
301S GLU* 3.9 16.4 + - - +
206T ALA* 3.8 31.2 - - + +
207T GLU* 5.8 1.1 - - - +
210T THR* 4.5 9.2 - - + -
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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
------------------------------------------------------------
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