Contacts of the helix formed by residues 282 - 303 (chain B) in PDB entry 3LRB
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 ALA 282 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLY 5.3 1.4 - - - +
29B PHE* 4.4 17.3 - - + -
111B TYR* 3.2 35.3 - - + -
278B VAL* 3.2 16.2 + - + +
279B SER* 4.3 3.1 - - - +
280B PHE 2.5 6.0 + - - +
281B CYS* 1.3 73.2 - - - +
283B ALA* 1.3 61.8 + - - +
284B ALA 2.8 4.9 + - - -
285B GLY* 3.0 14.6 + - - -
286B CYS* 3.7 9.5 + - - -
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Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLY 3.1 27.8 - - - +
111B TYR* 3.7 14.6 - - + +
112B LEU* 4.1 21.1 - - + -
280B PHE* 2.9 8.0 + - + +
282B ALA* 1.3 79.0 - - - +
284B ALA* 1.3 57.2 + - - +
286B CYS* 3.3 10.7 + - - +
287B LEU* 3.0 25.1 + - - +
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Residues in contact with ALA 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ALA* 3.0 41.5 - - + +
157B LEU* 4.2 14.4 - - + -
280B PHE* 2.9 21.1 + - + +
281B CYS* 3.5 26.0 - - - +
282B ALA 2.8 0.6 - - - -
283B ALA* 1.3 80.1 - - - +
285B GLY* 1.3 60.2 + - - +
287B LEU* 3.3 12.9 + - + -
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Residues in contact with GLY 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY 4.4 2.8 - - - +
25B GLY* 4.7 12.8 - - - +
154B ALA 4.8 1.3 - - - -
155B THR* 4.3 11.7 - - - +
158B ALA* 4.0 15.5 - - - +
281B CYS 3.8 3.0 + - - -
282B ALA 3.0 11.2 + - - -
284B ALA* 1.3 78.4 - - - +
286B CYS* 1.3 60.8 + - - +
288B GLY* 3.8 0.9 + - - -
289B SER* 3.0 26.6 + - - -
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Residues in contact with CYS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLY 4.6 1.8 - - - -
26B SER* 4.3 15.9 - - - -
104B MET* 3.0 39.0 - - + -
105B VAL* 6.0 1.1 - - + +
107B ILE* 5.0 3.8 - - - -
108B GLY* 4.3 17.7 - - - -
111B TYR* 5.3 3.6 - - - -
136B PHE* 4.4 2.9 - - - -
282B ALA 3.9 12.8 - - - -
283B ALA* 3.3 7.1 + - - +
284B ALA 3.2 0.4 - - - -
285B GLY* 1.3 78.7 - - - +
287B LEU* 1.3 61.9 + - - +
288B GLY 3.4 0.4 - - - -
289B SER* 3.7 8.3 - - - -
290B LEU* 3.6 22.4 + - + +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 2.6 48.3 - - + -
139B LEU* 6.0 0.2 - - + -
150B VAL* 3.5 27.6 - - + +
154B ALA* 3.8 12.3 - - + -
157B LEU* 6.1 4.0 - - + -
280B PHE* 6.1 4.9 - - + -
283B ALA 3.0 12.3 + - - +
284B ALA* 3.3 16.1 + - + +
286B CYS* 1.3 78.7 - - - +
288B GLY* 1.3 60.5 + - - +
291B GLY 4.4 0.7 + - - -
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Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 5.1 0.2 - - - +
150B VAL* 4.8 0.9 - - - -
151B GLN* 2.4 58.0 - - - +
154B ALA* 3.4 14.6 - - - +
155B THR* 4.4 1.1 - - - -
284B ALA 3.6 1.8 + - - -
285B GLY 4.2 0.7 - - - -
287B LEU* 1.3 79.5 - - - +
289B SER* 1.3 63.2 + - - +
291B GLY* 3.2 4.9 + - - -
292B GLY 3.2 5.0 + - - -
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Residues in contact with SER 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY 4.1 12.3 - - - -
22B ASN* 4.4 7.1 + - - +
26B SER* 5.2 6.2 + - - -
104B MET* 3.4 19.8 - - - +
151B GLN* 3.3 8.3 - - - +
285B GLY 3.0 21.3 + - - -
286B CYS* 3.7 10.5 - - - -
287B LEU 3.5 0.2 - - - -
288B GLY* 1.3 72.7 - - - +
290B LEU* 1.3 56.9 + - - +
291B GLY 2.6 1.6 + - - -
292B GLY* 2.5 30.3 + - - -
293B TRP* 3.0 22.3 + - - +
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASN* 3.1 42.5 + - + +
104B MET* 3.8 22.7 - - + -
105B VAL* 3.3 36.1 - - + -
133B LEU* 3.6 19.1 - - + -
136B PHE* 4.1 22.2 - - + -
286B CYS* 3.6 16.5 + - + +
288B GLY 3.5 0.8 - - - -
289B SER* 1.3 80.1 + - - +
291B GLY* 1.3 51.8 + - - +
293B TRP* 3.8 3.6 - - + +
294B THR* 2.8 40.8 + - + +
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Residues in contact with GLY 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 4.1 13.9 - - - -
140B ASN* 3.3 10.3 + - - -
147B ILE* 3.5 32.3 - - - -
287B LEU 4.4 0.2 + - - -
288B GLY 3.2 4.3 + - - -
289B SER 2.6 5.5 + - - -
290B LEU* 1.3 75.2 - - - +
292B GLY* 1.3 65.4 + - - -
293B TRP 3.2 0.2 + - - -
294B THR* 3.2 3.1 + - - -
295B LEU* 2.9 19.4 + - - +
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Residues in contact with GLY 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MET* 3.7 24.0 - - - -
22B ASN* 4.1 8.5 - - - -
147B ILE* 4.3 1.2 - - - +
151B GLN* 3.0 24.1 + - - -
289B SER 2.5 11.0 + - - -
291B GLY* 1.3 69.9 - - - -
293B TRP* 1.3 56.1 + - - -
295B LEU* 2.9 24.2 + - - +
296B LEU* 3.1 12.3 + - - +
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Residues in contact with TRP 293 (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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22B ASN* 2.9 44.7 + - + +
93B TYR* 4.3 7.2 - + - -
96B ALA 4.1 7.2 - - - -
97B CYS* 3.3 57.8 - - + +
100B GLY* 6.4 0.2 - - - -
101B ASN* 3.8 18.4 - - - +
104B MET* 6.3 1.3 - - + -
205B ILE* 4.5 15.9 - - + -
206B GLY* 4.4 16.4 - - - -
208B GLU* 3.5 24.2 - - - -
289B SER* 3.0 22.7 + - - +
290B LEU* 4.0 6.7 - - + +
292B GLY* 1.3 74.3 - - - +
294B THR* 1.3 65.1 + - - +
296B LEU* 3.2 16.4 + - + +
297B ALA 3.2 14.9 + - - -
361B THR* 5.0 4.0 - - + -
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Residues in contact with THR 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B CYS 6.0 0.7 - - - -
98B TRP* 6.4 0.9 - - - +
101B ASN* 3.0 22.9 - - - +
133B LEU 5.8 0.7 - - - +
136B PHE* 4.5 10.9 + - + -
137B VAL* 4.9 7.2 + - - +
140B ASN* 3.2 23.1 + - - +
290B LEU* 2.8 26.0 + - + +
291B GLY* 3.2 2.0 + - - -
293B TRP* 1.3 72.4 - - - +
295B LEU* 1.3 68.8 + - - +
297B ALA* 2.9 18.9 + - - +
298B GLY* 3.0 10.9 + - - -
327B LEU* 4.6 10.7 - - - +
330B VAL* 5.1 12.0 - - + +
334B MET* 4.6 14.1 - - + -
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Residues in contact with LEU 295 (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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18B MET* 3.5 33.2 - - + -
140B ASN* 3.5 22.9 - - - +
144B PRO* 4.4 20.4 - - + -
147B ILE* 4.0 9.0 - - + -
148B THR* 5.0 3.8 - - + -
213B ALA* 5.6 6.1 - - + -
216B VAL* 5.1 7.4 - - + -
291B GLY 2.9 12.6 + - - +
292B GLY* 3.0 13.9 - - - +
294B THR* 1.3 78.8 + - - +
296B LEU* 1.3 59.0 + - + +
298B GLY* 3.2 3.2 + - - -
299B GLN* 3.1 41.8 + - + +
327B LEU* 5.3 3.4 - - + -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MET* 4.0 18.2 - - - -
22B ASN* 4.0 8.1 - - - +
93B TYR* 4.1 16.2 - - + +
97B CYS* 4.7 7.2 - - - -
208B GLU* 5.2 1.1 - - + -
209B SER* 3.1 42.8 - - - +
212B VAL* 3.7 20.9 - - + -
213B ALA* 5.0 5.8 - - + +
292B GLY 3.3 17.3 - - - +
293B TRP* 3.7 17.9 - - + +
294B THR 3.1 0.4 - - - -
295B LEU* 1.3 82.6 - - + +
297B ALA* 1.3 54.9 + - - +
298B GLY 3.0 5.4 - - - -
299B GLN* 4.3 2.9 - - + +
300B THR* 2.8 34.0 + - - -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TRP* 2.9 31.8 - - + +
97B CYS* 3.7 27.3 - - + +
98B TRP* 4.2 10.8 - - + +
293B TRP 3.2 6.8 + - - +
294B THR* 2.9 12.7 + - - +
296B LEU* 1.3 73.7 - - - +
298B GLY* 1.3 61.5 + - - +
300B THR 4.4 1.6 - - - +
301B ALA* 3.7 1.2 - - - +
302B LYS* 2.8 21.5 + - - -
330B VAL* 4.7 11.2 - - + -
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Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B THR 3.0 11.1 + - - -
295B LEU 3.2 4.5 + - - -
296B LEU 3.0 0.2 - - - -
297B ALA* 1.3 79.7 - - - +
299B GLN* 1.3 59.7 + - - +
302B LYS* 2.9 50.2 + - - +
323B PRO* 4.6 11.4 - - - -
327B LEU* 4.7 9.9 - - - -
330B VAL* 5.6 0.9 - - - -
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Residues in contact with GLN 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PRO* 6.2 0.2 - - - +
71B GLY* 4.6 2.7 - - - +
144B PRO* 5.3 0.8 - - - +
212B VAL 3.7 20.4 - - - +
213B ALA* 4.2 14.3 + - - +
215B GLY* 5.1 1.6 - - - -
216B VAL* 2.8 39.2 - - - +
295B LEU* 3.1 27.5 + - + +
296B LEU* 3.9 5.6 - - + +
298B GLY* 1.3 73.6 - - - +
300B THR* 1.3 53.2 + - - +
301B ALA 2.5 20.0 + - - -
302B LYS* 5.4 2.4 - - - +
303B ALA* 2.9 31.2 + - - +
323B PRO* 5.8 4.4 - - - +
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Residues in contact with THR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLY* 2.7 25.6 + - - -
72B GLY 4.3 13.0 - - - +
73B SER* 5.7 0.9 - - - -
74B TYR* 4.5 11.4 - - + -
90B ASN* 2.1 36.6 - - - +
93B TYR* 3.1 37.1 - - + -
94B TRP* 3.9 7.6 - - - +
212B VAL* 3.0 16.1 - - - +
296B LEU 2.8 17.4 + - - -
297B ALA* 5.4 0.7 - - - -
299B GLN* 1.3 66.9 - - - +
301B ALA* 1.3 54.2 + - - +
303B ALA* 4.6 5.2 - - - -
304B ALA* 5.2 1.1 - - - -
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ASN* 3.5 6.7 - - - -
94B TRP* 3.5 24.5 - - + -
297B ALA 3.7 1.1 - - - +
299B GLN 2.5 8.1 + - - -
300B THR* 1.3 77.5 - - - +
302B LYS* 1.3 66.9 + - + +
303B ALA* 2.7 5.2 + - - +
304B ALA 3.1 3.2 + - - +
305B ALA* 2.7 35.7 + - - +
310B PHE* 3.2 29.3 - - + -
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Residues in contact with LYS 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TRP* 3.1 18.4 - - - +
297B ALA 2.8 22.2 + - - -
298B GLY* 2.9 27.2 + - - +
299B GLN* 4.4 4.5 - - - +
301B ALA* 1.3 77.9 - - - +
303B ALA* 1.3 61.0 + - - +
305B ALA* 3.5 7.8 - - - +
306B ASP* 3.3 14.6 + - - +
314B PHE* 3.0 62.6 - - + +
315B ALA* 4.1 4.6 + - - +
317B VAL* 6.1 1.1 - - + -
323B PRO* 3.5 24.0 - - + -
326B GLY* 3.4 15.9 - - - -
330B VAL* 4.2 7.5 - - - +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PRO* 3.5 32.8 - - + +
71B GLY* 4.6 3.1 - - - -
74B TYR* 5.0 2.9 - - + -
299B GLN* 2.9 24.2 + - - +
300B THR* 4.6 1.3 - - - -
301B ALA 2.7 1.8 - - - +
302B LYS* 1.3 74.4 - - - +
304B ALA* 1.3 53.3 + - - +
305B ALA 2.5 2.9 + - - -
306B ASP* 2.3 45.4 + - - +
307B ASP* 3.5 6.6 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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