Contacts of the helix formed by residues 282 - 303 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLY 5.3 1.2 - - - +
29A PHE* 4.4 16.8 - - + -
111A TYR* 3.2 33.8 - - + -
158A ALA* 5.3 0.4 - - - -
278A VAL 3.2 16.0 + - - +
279A SER* 4.3 5.2 - - - +
280A PHE 2.5 5.7 + - - -
281A CYS* 1.3 71.7 - - - +
283A ALA* 1.3 58.6 + - - +
284A ALA 2.8 4.0 - - - -
285A GLY* 2.9 20.8 + - - -
286A CYS* 3.7 9.2 + - - -
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLY 3.1 28.3 - - - +
111A TYR* 3.7 14.3 - - + +
112A LEU* 4.1 21.1 - - + -
280A PHE* 2.9 7.5 + - + +
282A ALA* 1.3 78.6 - - - +
284A ALA* 1.3 56.2 + - - +
285A GLY 3.3 0.2 - - - -
286A CYS* 3.3 10.6 + - - +
287A LEU* 3.0 25.2 + - - +
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ALA* 3.0 41.2 - - - +
157A LEU* 4.2 15.3 - - + -
280A PHE* 2.8 28.6 + - + +
281A CYS* 3.5 19.5 - - - +
282A ALA 2.8 0.4 - - - -
283A ALA* 1.3 77.6 - - - +
285A GLY* 1.3 62.1 + - - +
287A LEU* 3.3 13.1 + - + -
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Residues in contact with GLY 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY 4.4 2.4 - - - +
25A GLY* 4.7 12.1 - - - +
154A ALA 4.7 1.3 - - - -
155A THR* 4.3 11.8 - - - +
158A ALA* 3.9 15.9 - - - +
281A CYS 3.8 2.8 + - - -
282A ALA 2.9 10.6 + - - -
284A ALA* 1.3 78.4 - - - +
286A CYS* 1.3 60.9 + - - +
288A GLY* 3.8 1.0 + - - -
289A SER* 3.0 25.5 + - - -
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Residues in contact with CYS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY 4.6 1.8 - - - -
26A SER* 4.4 15.0 - - - -
104A MET* 3.0 39.5 - - + -
105A VAL* 6.1 0.7 - - + -
107A ILE* 5.0 3.8 - - - -
108A GLY* 4.3 17.5 - - - -
111A TYR* 5.3 3.8 - - - -
136A PHE* 4.4 2.8 - - - -
282A ALA 3.9 13.0 - - - -
283A ALA* 3.3 7.3 + - - +
284A ALA 3.2 0.6 - - - -
285A GLY* 1.3 78.3 - - - +
287A LEU* 1.3 62.2 + - - +
288A GLY 3.4 0.2 - - - -
289A SER* 3.7 8.3 - - - -
290A LEU* 3.5 23.0 + - + +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 2.6 47.6 - - + -
139A LEU* 6.0 0.2 - - + -
150A VAL* 3.5 28.0 - - + +
154A ALA* 3.8 12.1 - - + -
157A LEU* 6.0 4.0 - - + -
280A PHE* 6.2 4.5 - - + -
283A ALA 3.0 11.6 + - - +
284A ALA* 3.3 17.8 + - + +
286A CYS* 1.3 78.1 - - - +
288A GLY* 1.3 59.4 + - - +
291A GLY 4.3 0.9 + - - -
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Residues in contact with GLY 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE* 5.1 0.3 - - - +
150A VAL* 4.8 1.1 - - - -
151A GLN* 2.4 57.7 - - - +
154A ALA* 3.4 14.2 - - - +
155A THR* 4.4 0.7 - - - -
284A ALA 3.6 1.8 + - - -
285A GLY 3.8 1.3 + - - -
287A LEU* 1.3 79.7 - - - +
289A SER* 1.3 63.1 + - - +
291A GLY* 3.2 4.9 + - - -
292A GLY 3.2 4.5 + - - -
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Residues in contact with SER 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY 4.1 11.9 - - - -
22A ASN* 4.4 5.8 + - - +
26A SER* 5.2 6.2 - - - -
104A MET* 3.5 19.7 - - - +
151A GLN* 3.4 8.7 - - - +
285A GLY 3.0 20.6 + - - -
286A CYS* 3.7 10.1 - - - -
287A LEU 3.5 0.2 - - - -
288A GLY* 1.3 72.9 - - - +
290A LEU* 1.3 57.3 + - - +
291A GLY 2.6 14.2 + - - -
292A GLY* 2.6 17.5 + - - -
293A TRP* 3.0 24.6 + - - -
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASN* 3.1 42.7 + - + +
104A MET* 3.8 22.4 - - + -
105A VAL* 3.2 36.3 - - + -
133A LEU* 3.6 19.5 - - + -
136A PHE* 4.0 23.8 - - + -
286A CYS* 3.5 16.9 + - + +
288A GLY 3.5 0.6 - - - -
289A SER* 1.3 78.7 + - - +
291A GLY* 1.3 52.9 - - - +
293A TRP* 3.9 3.4 - - + +
294A THR* 2.7 40.8 + - + +
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Residues in contact with GLY 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 4.1 12.0 - - - -
140A ASN* 3.3 9.6 + - - -
147A ILE* 3.5 34.1 - - - -
288A GLY 3.2 4.5 + - - -
289A SER 2.6 5.9 + - - -
290A LEU* 1.3 73.5 - - - +
292A GLY* 1.3 64.2 + - - -
294A THR* 3.1 5.7 + - - -
295A LEU* 2.9 19.6 + - - +
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Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET* 3.7 24.0 - - - -
22A ASN* 4.1 7.4 - - - -
147A ILE* 4.3 1.2 - - - +
151A GLN* 3.0 23.2 + - - -
288A GLY 3.2 0.2 + - - -
289A SER 2.6 10.8 + - - -
291A GLY* 1.3 70.3 - - - -
293A TRP* 1.3 56.3 + - - -
295A LEU* 3.0 23.8 + - - +
296A LEU* 3.1 12.0 + - - +
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Residues in contact with TRP 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASN* 2.9 43.9 + - + +
93A TYR* 4.2 9.9 - + - -
96A ALA 4.1 7.0 - - - -
97A CYS* 3.3 59.2 - - + +
100A GLY* 6.4 0.2 - - - -
101A ASN* 3.8 18.2 - - - +
104A MET* 6.3 1.3 - - + -
205A ILE* 4.4 16.2 - - + -
206A GLY* 4.4 15.7 - - - -
208A GLU* 3.6 21.1 - - - -
289A SER* 3.0 22.7 + - - +
290A LEU* 4.0 7.0 - - + +
292A GLY* 1.3 73.6 - - - +
294A THR* 1.3 66.0 + - - +
296A LEU* 3.2 16.9 + - + +
297A ALA 3.2 14.7 + - - -
361A THR* 5.1 3.8 - - + -
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Residues in contact with THR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A CYS 6.0 0.9 - - - -
98A TRP* 6.5 0.7 - - - +
101A ASN* 3.0 22.0 - - - +
133A LEU 5.9 0.4 - - - +
136A PHE* 4.5 10.2 + - + -
137A VAL* 5.0 6.9 + - + +
140A ASN* 3.1 23.7 + - - +
290A LEU* 2.7 25.3 + - + +
291A GLY* 3.1 2.0 + - - -
293A TRP* 1.3 75.8 - - - +
295A LEU* 1.3 66.0 + - - +
297A ALA* 2.9 19.3 + - - +
298A GLY* 3.0 10.9 + - - -
327A LEU* 4.7 11.0 - - - +
330A VAL* 5.2 10.2 - - + +
334A MET* 4.7 14.1 - - + -
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET* 3.5 32.5 - - + -
140A ASN* 3.5 23.6 - - - +
144A PRO* 4.4 20.0 - - + -
147A ILE* 4.0 7.9 - - + -
148A THR* 4.9 4.0 - - + -
213A ALA* 5.6 6.1 - - + -
216A VAL* 5.1 7.9 - - + -
291A GLY 2.9 9.3 + - - +
292A GLY* 3.0 13.2 - - - +
294A THR* 1.3 82.9 + - - +
296A LEU* 1.3 58.8 + - + +
298A GLY* 3.3 2.5 + - - -
299A GLN* 3.1 43.6 + - + +
327A LEU* 5.4 3.4 - - + -
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 4.1 17.3 - - - -
22A ASN* 4.0 8.3 - - - +
93A TYR* 4.1 14.6 - - - +
97A CYS* 4.8 6.7 - - - -
208A GLU* 5.3 0.7 - - + -
209A SER* 3.1 44.0 - - - +
212A VAL* 3.6 23.6 - - + +
213A ALA* 4.9 6.1 - - + +
292A GLY 3.3 17.0 - - - +
293A TRP* 3.7 16.2 - - + +
294A THR 3.1 0.8 - - - -
295A LEU* 1.3 82.1 - - + +
297A ALA* 1.3 55.5 + - - +
298A GLY 3.1 5.2 - - - -
299A GLN* 4.3 2.5 - - + +
300A THR* 2.8 33.8 + - - +
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TRP* 2.9 41.6 - - + +
97A CYS* 3.6 27.1 - - + +
98A TRP* 4.2 10.3 - - + +
293A TRP 3.2 6.7 + - - +
294A THR* 2.9 12.1 + - - +
296A LEU* 1.3 73.9 - - - +
298A GLY* 1.3 61.1 + - - +
300A THR* 4.5 1.3 - - - -
301A ALA* 3.7 1.6 - - - +
302A LYS* 2.9 10.8 + - - -
330A VAL* 4.8 11.4 - - + -
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Residues in contact with GLY 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A THR 3.0 11.0 + - - -
295A LEU 3.3 4.0 + - - -
296A LEU 3.1 0.2 - - - -
297A ALA* 1.3 79.5 - - - +
299A GLN* 1.3 59.1 + - - +
302A LYS* 2.9 50.6 + - - +
323A PRO* 4.6 11.4 - - - -
327A LEU* 4.7 10.1 - - - -
330A VAL* 5.4 1.5 - - - +
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Residues in contact with GLN 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLY* 4.8 2.5 - - - +
144A PRO* 5.3 1.0 - - - +
212A VAL 3.8 20.4 - - - +
213A ALA* 4.2 14.5 + - - +
215A GLY* 5.1 1.8 - - - -
216A VAL* 2.7 39.0 - - - +
295A LEU* 3.1 28.4 + - + +
296A LEU* 3.8 5.2 - - + +
298A GLY* 1.3 73.4 - - - +
300A THR* 1.3 53.3 + - - +
301A ALA 2.5 19.2 + - - -
302A LYS* 5.4 2.4 - - - +
303A ALA* 2.8 31.3 + - - +
323A PRO* 5.8 4.6 - - - +
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Residues in contact with THR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLY* 2.8 25.1 + - - -
72A GLY 4.3 13.7 - - - +
73A SER* 5.7 0.4 - - - -
74A TYR* 4.6 10.5 - - + -
90A ASN* 2.1 37.2 - - - +
93A TYR* 3.1 37.2 - - + -
94A TRP* 3.8 7.8 - - - +
212A VAL* 3.0 15.1 - - - +
296A LEU 2.8 17.2 + - - -
297A ALA* 4.8 1.3 - - - -
299A GLN* 1.3 65.8 - - - +
301A ALA* 1.3 55.5 + - - +
303A ALA* 4.6 5.6 - - - -
304A ALA 5.2 0.4 - - - -
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASN* 3.5 6.7 - - - -
94A TRP* 3.5 24.0 - - + -
297A ALA 3.7 1.6 - - - +
299A GLN 2.5 7.7 + - - -
300A THR* 1.3 76.6 - - - +
302A LYS* 1.3 66.3 + - + +
303A ALA* 2.7 5.9 + - - +
304A ALA 3.1 3.1 + - - +
305A ALA* 2.7 35.2 + - - +
310A PHE* 3.2 29.6 - - + -
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Residues in contact with LYS 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TRP* 3.1 18.8 - - - +
297A ALA 2.9 19.6 + - - -
298A GLY* 2.9 29.7 + - - +
299A GLN* 4.4 3.8 - - - +
301A ALA* 1.3 75.7 - - - +
303A ALA* 1.3 62.6 + - - +
305A ALA* 3.5 7.0 - - - +
306A ASP* 3.3 14.4 + - - +
314A PHE* 3.0 63.4 - - + +
315A ALA* 4.1 4.6 + - - +
317A VAL* 6.1 1.3 - - + -
323A PRO* 3.6 24.5 - - + -
326A GLY* 3.4 16.2 - - - -
330A VAL* 4.1 7.3 - - - +
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PRO* 3.5 32.1 - - + +
71A GLY* 4.6 3.4 - - - -
74A TYR* 5.0 3.4 - - + -
299A GLN* 2.8 23.9 + - - +
300A THR* 4.6 1.1 - - - -
301A ALA 2.7 2.2 - - - +
302A LYS* 1.3 74.2 - - - +
304A ALA* 1.3 53.1 - - - +
305A ALA 2.5 2.6 + - - -
306A ASP* 2.3 45.6 + - - +
307A ASP* 3.5 7.2 + - - +
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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
------------------------------------------------------------
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