Contacts of the helix formed by residues 13 - 42 (chain 2) in PDB entry 1CNT
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 ARG 13 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122 HIS* 1.3 75.2 - - + +
142 ARG* 1.3 66.2 + - + +
162 LEU* 3.4 4.9 + - - +
172 CYS* 3.1 31.0 + - - -
692 GLU* 2.8 38.5 + - - -
1262 LEU* 4.2 1.6 - - + +
1292 LEU* 3.7 19.7 - - + +
1302 LEU* 4.0 21.8 - - + +
1792 ILE* 2.9 28.3 + - + +
1802 SER* 3.5 17.7 - - - -
1822 HIS* 3.5 12.5 - - - +
1832 GLN* 3.8 31.9 + - - +
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Residues in contact with ARG 14 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122 HIS* 3.4 30.0 + - + +
132 ARG* 1.3 81.3 - - + +
152 ASP* 1.3 59.5 + - - +
172 CYS* 3.2 4.0 + - - +
182 SER* 2.8 33.1 + - - +
1802 SER* 3.6 34.4 + - - +
1812 SER* 3.7 6.6 - - - +
1842 THR* 2.9 33.7 + - - +
1862 ILE* 3.4 12.7 - - - +
1872 PRO* 3.1 40.8 - - - +
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Residues in contact with ASP 15 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122 HIS* 3.1 36.1 + - + +
132 ARG 3.4 0.4 - - - -
142 ARG* 1.3 74.5 - - - +
162 LEU* 1.3 64.6 + - + +
182 SER* 3.2 9.8 + - - -
192 ARG* 2.9 33.2 + - + +
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Residues in contact with LEU 16 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122 HIS 3.5 19.9 + - - +
132 ARG 3.4 4.4 + - - +
142 ARG 3.3 0.4 - - - -
152 ASP* 1.3 80.6 - - + +
172 CYS* 1.3 64.5 + - - +
192 ARG* 3.3 27.4 + - - +
202 SER* 3.0 27.1 + - - -
1222 GLN 5.0 1.1 - - - +
1252 GLU* 3.8 19.7 - - + +
1262 LEU* 3.5 46.4 - - + +
1292 LEU* 4.1 12.8 - - + -
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Residues in contact with CYS 17 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132 ARG 3.1 19.1 + - - +
142 ARG 3.2 8.0 + - - +
162 LEU* 1.3 78.7 - - - +
182 SER* 1.3 56.1 + - - +
202 SER* 3.7 1.4 - - - -
212 ILE* 2.9 38.9 + - + +
1262 LEU* 4.1 14.6 - - - -
1762 LEU* 3.6 32.0 - - + +
1792 ILE* 3.9 17.3 - - - -
1802 SER* 3.7 29.6 - - - -
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Residues in contact with SER 18 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142 ARG* 2.8 18.8 + - - +
152 ASP* 3.5 13.4 + - - -
162 LEU 3.2 0.2 - - - -
172 CYS* 1.3 75.8 - - - +
192 ARG* 1.3 66.5 + - - +
212 ILE* 3.8 9.3 - - - +
222 TRP* 3.0 23.7 + - - +
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Residues in contact with ARG 19 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152 ASP 2.9 15.7 + - - +
162 LEU* 3.3 34.3 + - - +
182 SER* 1.3 76.1 - - - +
202 SER* 1.3 62.2 + - - +
222 TRP* 3.3 9.2 + - - +
232 LEU* 3.1 21.7 + - - +
1222 GLN* 3.7 40.1 + - - +
1252 GLU* 3.2 23.4 + - - -
1073 GLN* 3.3 23.5 - - - +
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Residues in contact with SER 20 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162 LEU 3.0 15.3 + - - -
172 CYS 3.8 1.3 - - - -
192 ARG* 1.3 77.3 - - - +
212 ILE* 1.3 59.5 + - - +
232 LEU* 3.4 1.1 + - - +
242 ALA* 3.0 24.4 + - - +
1192 PHE* 3.5 16.8 - - - -
1222 GLN* 2.6 39.4 + - - +
1232 ILE* 4.7 4.1 - - - +
1262 LEU* 5.5 2.3 - - - +
1762 LEU* 3.5 27.4 - - - +
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Residues in contact with ILE 21 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172 CYS* 2.9 30.0 + - + +
182 SER* 3.2 8.9 + - - +
202 SER* 1.3 74.3 - - - +
222 TRP* 1.3 66.6 + - - +
242 ALA* 3.3 5.6 + - - +
252 ARG* 3.1 54.1 + - - +
1732 ILE* 4.5 12.5 - - + +
1762 LEU* 3.7 32.1 - - + +
1772 ARG* 4.0 22.9 - - + -
1802 SER* 5.4 2.5 - - - +
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Residues in contact with TRP 22 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 SER 3.0 12.9 + - - +
192 ARG* 3.5 11.0 - - - +
212 ILE* 1.3 80.2 - - - +
232 LEU* 1.3 101.2 + - + +
252 ARG* 3.3 7.3 + - + +
262 LYS* 2.9 46.9 + - + +
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Residues in contact with LEU 23 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192 ARG 3.1 11.5 + - - +
202 SER 3.7 7.4 - - - +
222 TRP* 1.3 102.2 - - + +
242 ALA* 1.3 63.0 + - - +
262 LYS* 3.0 8.2 + - + +
272 ILE* 3.0 29.9 + - + +
1152 GLN* 3.7 31.4 - - + +
1182 ALA* 3.8 8.5 - - + -
1192 PHE* 3.5 42.0 - - + +
1222 GLN* 3.7 20.2 - - - +
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Residues in contact with ALA 24 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202 SER 3.0 17.6 + - - +
212 ILE* 3.6 5.4 - - - +
232 LEU* 1.3 76.7 - - - +
252 ARG* 1.3 61.4 + - - +
272 ILE* 3.3 10.5 + - - +
282 ARG 3.1 16.8 + - - -
802 TYR* 5.1 0.9 - - - +
1192 PHE* 4.1 17.6 - - + -
1692 THR* 3.5 23.0 - - + +
1722 SER* 4.5 6.5 - - - -
1732 ILE* 3.7 21.8 - - + -
1762 LEU* 5.2 0.4 - - + -
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Residues in contact with ARG 25 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212 ILE* 3.1 36.7 + - - +
222 TRP* 3.8 6.3 - - + +
242 ALA* 1.3 75.6 - - - +
262 LYS* 1.3 57.1 + - - +
282 ARG* 3.0 15.0 + - + +
292 SER* 2.9 31.0 + - - -
1732 ILE* 3.4 41.4 - - + +
1772 ARG* 5.2 7.9 - - - +
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Residues in contact with LYS 26 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222 TRP* 2.9 47.3 + - + +
232 LEU* 3.0 15.5 + - + +
252 ARG* 1.3 73.5 - - - +
272 ILE* 1.3 63.9 + - - +
292 SER* 3.5 8.6 + - - -
302 ASP* 2.9 50.2 + - - +
1152 GLN* 3.6 20.2 - - - +
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Residues in contact with ILE 27 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232 LEU* 3.0 24.2 + - + +
242 ALA* 3.5 9.2 - - - +
252 ARG 3.2 0.2 - - - -
262 LYS* 1.3 74.0 - - - +
282 ARG* 1.3 66.9 + - - +
302 ASP* 3.3 2.5 + - - +
312 LEU* 2.9 39.7 + - + +
802 TYR* 4.5 15.5 - - + -
1122 LEU* 4.2 9.6 - - + -
1152 GLN* 3.8 42.6 - - + +
1162 VAL* 4.0 21.3 - - + +
1192 PHE* 4.8 2.7 - - + -
1652 LEU* 4.2 7.0 - - + -
1692 THR* 3.7 16.8 - - + -
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Residues in contact with ARG 28 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242 ALA 3.1 9.4 + - - +
252 ARG* 3.0 17.5 + - - +
272 ILE* 1.3 78.8 - - - +
292 SER* 1.3 63.5 + - - +
312 LEU* 3.3 7.5 + - - +
322 THR* 3.2 27.0 + - - +
1662 SER* 4.9 9.0 + - - +
1692 THR* 3.6 25.1 - - - +
1702 VAL* 3.9 28.5 - - - +
1732 ILE* 5.0 13.5 - - - +
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Residues in contact with SER 29 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252 ARG 2.9 13.3 + - - -
262 LYS* 3.6 16.5 - - - -
282 ARG* 1.3 74.9 - - - +
302 ASP* 1.3 68.5 + - - +
322 THR* 3.2 20.4 + - - -
332 ALA* 3.6 6.2 + - - +
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Residues in contact with ASP 30 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262 LYS* 2.9 41.9 + - - +
272 ILE* 3.5 10.5 - - - +
292 SER* 1.3 80.6 - - - +
312 LEU* 1.3 59.5 + - - +
332 ALA* 3.1 9.1 + - - +
342 LEU* 2.9 30.2 + - + +
1112 THR* 4.7 7.4 - - - +
1122 LEU* 4.8 6.9 - - + +
1152 GLN* 3.0 29.5 + - - +
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Residues in contact with LEU 31 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272 ILE* 2.9 29.8 + - + +
282 ARG* 3.3 4.7 + - - +
302 ASP* 1.3 72.8 - - - +
322 THR* 1.3 58.7 + - - +
342 LEU* 4.1 8.7 - - + -
352 THR* 2.6 40.2 + - - +
1122 LEU* 3.7 32.5 - - + -
1622 LEU* 3.8 22.7 - - + +
1652 LEU* 3.6 34.3 - - + -
1662 SER* 3.6 31.6 - - - +
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Residues in contact with THR 32 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282 ARG* 3.2 16.6 + - - +
292 SER* 3.2 11.1 + - - -
312 LEU* 1.3 76.6 - - - +
332 ALA* 1.3 63.3 + - - +
352 THR* 4.0 2.3 - - - -
362 GLU* 3.0 41.3 + - - +
1662 SER* 5.4 0.2 + - - -
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Residues in contact with ALA 33 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292 SER 3.6 5.9 + - - +
302 ASP* 3.1 8.8 + - - +
322 THR* 1.3 78.0 - - - +
342 LEU* 1.3 65.3 + - - +
362 GLU* 3.3 8.0 + - - +
372 SER* 3.1 26.4 + - - -
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Residues in contact with LEU 34 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302 ASP* 2.9 18.4 + - + +
312 LEU* 4.0 12.6 - - + +
332 ALA* 1.3 76.7 - - - +
352 THR* 1.3 57.6 + - - +
372 SER* 3.2 10.9 + - - -
382 TYR* 2.8 29.0 + - + +
1052 PHE* 4.2 21.3 - - + -
1082 ALA* 3.7 33.0 - - + +
1092 ILE* 4.1 12.1 - - + -
1122 LEU* 4.1 29.4 - - + -
1622 LEU* 4.3 11.7 - - + -
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Residues in contact with THR 35 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312 LEU* 2.6 33.9 + - - +
322 THR* 4.0 3.4 - - - -
342 LEU* 1.3 68.9 - - - +
362 GLU* 1.3 70.8 + - - +
382 TYR* 3.1 6.7 + - + +
392 VAL* 2.9 33.7 + - + +
1592 LEU* 3.7 28.7 - - + -
1622 LEU* 4.0 22.6 - - + +
1632 GLN* 5.0 7.7 - - + +
1662 SER* 5.0 2.4 + - - -
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Residues in contact with GLU 36 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322 THR* 3.0 35.6 + - - +
332 ALA* 3.4 11.7 - - - +
352 THR* 1.3 78.4 - - - +
372 SER* 1.3 59.7 + - - +
392 VAL* 3.4 5.2 + - - +
402 LYS* 2.9 31.0 + - - +
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Residues in contact with SER 37 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332 ALA 3.1 11.7 + - - -
342 LEU* 3.3 14.3 - - - -
362 GLU* 1.3 76.1 - - - +
382 TYR* 1.3 55.3 + - - +
402 LYS* 3.1 7.1 + - - +
412 HIS* 2.7 58.5 + - - -
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Residues in contact with TYR 38 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342 LEU* 2.8 17.4 + - - +
352 THR* 3.5 11.7 - - - +
372 SER* 1.3 71.0 - - - +
392 VAL* 1.3 59.7 + - - +
412 HIS* 3.2 7.0 + - - +
422 GLN* 2.9 54.9 + - + +
442 LEU* 3.9 10.5 - - + -
902 LEU* 4.9 1.2 - - - +
1052 PHE* 3.3 48.2 - + + -
1542 LYS 3.2 15.1 + - - -
1552 LYS* 2.7 33.4 + - - -
1582 GLY* 3.2 9.0 - - - -
1592 LEU* 3.4 34.1 - - + -
1622 LEU* 4.4 9.0 - - + -
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Residues in contact with VAL 39 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352 THR* 2.9 25.0 + - + +
362 GLU* 3.7 5.2 - - - +
382 TYR* 1.3 76.2 - - + +
402 LYS* 1.3 63.4 + - - +
432 GLY* 3.1 20.1 + - - -
442 LEU* 3.2 38.6 + - + -
1592 LEU* 3.7 34.3 - - + -
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Residues in contact with LYS 40 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362 GLU 2.9 18.8 + - - +
372 SER* 3.6 5.6 - - - +
392 VAL* 1.3 77.6 - - - +
412 HIS* 1.3 87.8 + - - +
432 GLY* 3.9 6.4 + - - -
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Residues in contact with HIS 41 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372 SER* 2.7 38.2 + - - +
382 TYR* 3.7 3.1 - - - +
402 LYS* 1.3 105.7 + - - +
422 GLN* 1.3 77.9 + - - +
432 GLY 3.5 0.2 - - - -
1052 PHE* 6.5 1.3 - - + -
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Residues in contact with GLN 42 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382 TYR* 2.9 52.1 + - + +
412 HIS* 1.3 95.7 + - - +
432 GLY* 1.3 63.1 + - - +
442 LEU* 3.5 21.3 - - + -
1052 PHE* 6.3 0.6 - - - -
1552 LYS* 2.8 52.5 + - + +
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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