Contacts of the helix formed by residues 250 - 279 (chain 3) in PDB entry 4BOG
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 LYS 250 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2433 PRO* 5.6 2.7 - - + -
2463 ALA* 2.9 21.7 - - + +
2473 GLY 2.5 57.7 - - - +
2483 GLY 2.6 9.9 + - - -
2493 GLN* 1.3 107.3 - - - +
2513 CYS* 1.3 53.5 + - - +
2523 THR 3.1 2.7 - - - -
2533 LEU* 2.8 35.9 - - + +
2543 SER* 2.6 33.8 + - - -
243Z MET* 3.8 7.4 - - + -
244Z THR* 5.1 1.3 - - - +
300Z HIS* 4.5 9.3 - - - +
306Z HIS* 2.7 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 251 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2412 GLU 5.4 2.2 - - - -
2422 LYS* 4.9 4.5 - - + -
2452 LEU* 4.6 8.7 - - + -
2473 GLY 4.8 0.2 + - - -
2483 GLY 3.5 8.9 + - - +
2503 LYS* 1.3 77.6 - - - +
2523 THR* 1.3 95.5 + - - +
2543 SER* 3.2 17.8 - - - -
2553 ILE* 3.3 12.7 + - - +
3043 LEU* 4.7 3.6 - - + +
3073 SER* 4.7 15.6 + - - +
3143 HIS* 3.0 42.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 252 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2422 LYS* 5.8 0.2 - - - -
2442 THR* 5.8 5.7 - - + +
2452 LEU* 4.0 20.5 - - - +
2493 GLN* 4.2 17.3 - - + +
2513 CYS* 1.3 94.0 - - - +
2533 LEU* 1.3 68.5 - - - +
2543 SER 3.1 0.4 - - - -
2553 ILE* 3.0 12.3 + - - +
2563 SER* 2.8 23.2 + - - -
244Z THR* 5.5 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2423 LEU* 2.8 36.3 - - + -
2493 GLN 3.7 5.8 + - - +
2503 LYS* 2.8 49.8 + - + +
2523 THR* 1.3 81.0 + - - +
2543 SER* 1.3 65.7 + - - +
2563 SER* 2.8 26.3 + - - -
2573 VAL* 3.3 9.0 + - + +
244Z THR* 4.0 17.0 - - - +
247Z ILE* 3.1 37.0 - - + -
300Z HIS* 3.8 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 254 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2393 VAL* 2.5 42.5 + - - +
2423 LEU* 5.3 2.7 - - - -
2433 PRO* 5.9 2.2 - - - +
2503 LYS 2.6 13.9 + - - -
2513 CYS* 3.2 14.4 - - - -
2533 LEU* 1.3 80.8 - - - +
2553 ILE* 1.3 65.8 + - - +
2573 VAL* 3.0 21.2 + - - +
2583 LEU* 3.1 10.7 + - - +
3033 VAL* 4.1 6.9 - - - +
3073 SER* 5.0 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 255 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2452 LEU* 2.9 50.3 - - + -
2482 SER* 3.8 14.4 - - - +
2492 VAL* 3.8 10.5 - - + -
2513 CYS 3.4 8.5 - - - +
2523 THR* 3.0 8.2 + - - +
2543 SER* 1.3 75.4 - - - +
2563 SER* 1.3 69.8 + - - +
2573 VAL 2.9 1.8 - - - -
2583 LEU* 2.7 24.2 + - + +
2593 LEU* 2.9 15.4 + - + +
3033 VAL* 6.1 1.1 - - + -
3043 LEU* 3.2 44.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 256 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2482 SER* 5.7 1.6 - - - -
2523 THR* 2.8 13.2 + - - -
2533 LEU* 2.8 15.6 + - - -
2553 ILE* 1.3 77.4 - - - +
2573 VAL* 1.3 54.2 + - - +
2593 LEU* 3.5 10.2 + - - +
2603 ALA 3.0 15.4 + - - -
247Z ILE* 3.2 36.2 - - - +
248Z SER* 5.7 1.1 - - - -
251Z LEU* 2.7 27.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2353 LEU* 2.9 48.7 - - + -
2393 VAL* 4.4 14.4 - - + -
2423 LEU* 5.1 6.5 - - + -
2533 LEU* 3.4 20.6 - - + +
2543 SER* 3.1 13.5 - - - +
2553 ILE 2.8 1.6 + - - -
2563 SER* 1.3 80.6 + - - +
2583 LEU* 1.3 55.3 + - - +
2603 ALA 3.0 0.7 + - - -
2613 GLN* 2.3 43.1 + - + +
247Z ILE* 3.9 18.8 - - + -
251Z LEU* 4.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2282 LEU* 3.3 34.3 - - + -
2312 LEU* 5.9 1.8 - - + -
2492 VAL* 4.3 2.5 - - + -
2393 VAL* 5.6 1.0 - - + +
2543 SER 3.1 9.0 + - - +
2553 ILE* 2.7 26.8 + - + +
2573 VAL* 1.3 70.2 - - - +
2593 LEU* 1.3 76.9 + - + +
2613 GLN* 3.5 6.6 - - - +
2623 THR* 3.0 34.0 + - - +
2973 VAL* 5.4 4.0 - - + +
3003 CYS* 3.2 34.9 - - + +
3013 VAL* 3.9 23.3 - - + +
3043 LEU* 6.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2482 SER* 2.8 48.2 - - - +
2492 VAL* 3.2 22.2 - - + -
2522 SER* 2.8 35.2 - - - +
2562 PHE* 3.6 6.2 - - + -
2553 ILE* 2.9 15.8 + - + +
2563 SER* 3.7 9.4 - - - +
2583 LEU* 1.3 87.4 - - + +
2603 ALA* 1.3 58.7 + - - +
2633 ILE* 2.9 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2563 SER 3.0 5.3 + - - +
2573 VAL 3.0 1.3 + - - +
2593 LEU* 1.3 76.9 - - - +
2613 GLN* 1.3 57.0 + - - +
2633 ILE* 3.2 5.6 + - - -
2643 PHE* 2.5 47.1 + - + -
251Z LEU* 2.5 62.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 261 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2323 ILE* 3.4 27.6 - - + +
2353 LEU* 5.0 3.5 - - + +
2363 VAL* 2.9 32.4 - - + +
2573 VAL* 2.3 40.8 + - + +
2583 LEU* 3.5 8.5 - - - +
2603 ALA* 1.3 67.6 - - - +
2623 THR* 1.3 63.4 + - - +
2643 PHE* 3.5 7.4 - - - +
2653 LEU* 2.8 44.8 + - + +
2963 ILE* 2.7 37.8 - - - +
2973 VAL* 5.2 0.4 - - - +
3003 CYS* 4.1 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 262 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2242 LEU* 5.6 6.1 - - + -
2562 PHE* 3.2 27.6 - - + -
2583 LEU* 3.0 20.1 + - - +
2613 GLN* 1.3 79.0 - - - +
2633 ILE* 1.3 68.7 + - - +
2643 PHE 2.8 2.2 - - - -
2653 LEU* 2.3 42.3 - - + +
2663 PHE* 2.9 22.0 + - + +
2973 VAL* 4.0 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 263 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2552 VAL* 5.2 7.9 - - + -
2562 PHE* 3.1 24.5 - - + -
2593 LEU* 2.9 24.4 + - + +
2603 ALA* 3.2 4.2 + - - +
2623 THR* 1.3 77.4 - - - +
2643 PHE* 1.3 86.1 + - + +
2663 PHE* 5.1 0.5 - - - +
2673 LEU* 3.2 25.8 + - + +
255Z VAL* 4.2 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 264 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2313 LEU* 6.4 1.6 - - + -
2323 ILE* 5.3 12.1 - - + -
2353 LEU* 5.6 6.1 - - + -
2603 ALA* 2.5 41.1 - - + +
2613 GLN* 3.5 9.2 - - - +
2633 ILE* 1.3 90.7 - - + +
2653 LEU* 1.3 49.5 + - - +
2673 LEU* 3.3 9.4 - - - +
2683 ILE* 2.8 37.5 + - + +
251Z LEU* 3.2 23.6 - - + -
254Z THR* 3.7 18.6 - - + -
255Z VAL* 2.7 39.9 - - + -
258Z LEU* 3.2 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2242 LEU* 5.7 0.2 - - + -
2323 ILE* 5.8 1.6 - - + -
2613 GLN* 2.8 40.3 + - - +
2623 THR* 2.3 43.9 + - + +
2643 PHE* 1.3 73.0 - - - +
2663 PHE* 1.3 65.3 + - - +
2673 LEU 3.0 0.7 - - - -
2683 ILE* 2.6 39.1 + - + +
2693 ALA* 2.7 7.7 + - - +
2933 SER* 4.6 11.2 - - - +
2963 ILE* 3.0 20.6 - - + -
2973 VAL* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 266 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2172 ASN* 6.1 3.1 - - - -
2562 PHE* 5.2 16.6 - + + -
2592 VAL* 4.5 13.2 - - + -
2602 ILE* 5.5 4.3 - - + -
2632 LEU* 2.9 42.2 - - + -
2623 THR* 2.9 18.2 + - + +
2633 ILE 5.1 0.4 - - - +
2653 LEU* 1.3 79.9 - - - +
2673 LEU* 1.3 54.0 + - - +
2693 ALA* 2.6 21.7 + - + -
2703 GLN* 2.6 67.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2633 ILE* 3.2 25.1 + - + +
2643 PHE* 3.3 8.1 - - - +
2653 LEU 3.0 0.8 - - - -
2663 PHE* 1.3 77.3 - - - +
2683 ILE* 1.3 61.2 + - - +
2703 GLN* 2.7 59.1 - - - +
2713 LYS* 2.9 16.7 + - - +
255Z VAL* 4.9 13.2 - - + -
258Z LEU* 5.0 10.5 - - + -
259Z VAL* 4.6 17.3 - - + -
262Z GLU* 4.0 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 268 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2253 ILE* 4.8 16.6 - - + -
2643 PHE* 2.8 22.4 + - + +
2653 LEU* 2.6 37.1 + - + +
2673 LEU* 1.3 71.1 - - - +
2693 ALA* 1.3 69.0 + - + +
2713 LYS* 3.0 21.8 + - + +
2723 VAL* 3.2 30.8 + - + +
2733 PRO* 3.5 1.0 - - - +
2893 VAL* 4.8 16.8 - - + -
2933 SER* 6.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 269 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2653 LEU 2.7 6.2 + - - +
2663 PHE* 2.6 41.9 + - + +
2683 ILE* 1.3 81.8 - - + +
2703 GLN* 1.3 47.3 + - - -
2723 VAL* 5.5 0.7 - - - -
2733 PRO* 2.6 32.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 270 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2592 VAL* 4.6 11.7 - - - +
2632 LEU* 4.3 12.1 - - + +
2663 PHE* 2.6 54.2 + - + +
2673 LEU* 2.7 54.2 - - - +
2693 ALA* 1.3 71.8 - - - +
2713 LYS* 1.3 57.0 + - - +
2733 PRO* 2.5 26.3 - - - +
2743 GLU* 3.5 10.0 + - - +
262Z GLU* 4.1 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2243 ASN* 5.6 6.3 - - - +
2673 LEU* 2.9 18.6 + - - +
2683 ILE* 3.0 10.6 + - + +
2703 GLN* 1.3 71.8 + - - +
2723 VAL* 1.3 68.6 + - + +
2733 PRO* 2.9 4.3 - - - -
2743 GLU* 3.1 27.2 - - - +
2753 THR* 3.4 6.4 + - - +
258Z LEU 5.3 1.1 - - - -
261Z VAL* 5.0 11.4 - - + -
262Z GLU* 2.7 50.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 272 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2213 TYR* 6.0 8.1 - - + -
2253 ILE* 5.7 9.6 - - + -
2683 ILE* 3.2 26.9 + - + +
2693 ALA* 5.5 0.7 - - - -
2713 LYS* 1.3 80.0 - - + +
2733 PRO* 1.3 73.2 - - + +
2743 GLU 3.1 1.1 - - - -
2753 THR* 2.9 35.6 - - + +
2763 SER* 3.2 8.4 + - - +
2893 VAL* 6.1 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 273 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2683 ILE 3.5 1.1 - - - +
2693 ALA 2.6 29.8 - - - +
2703 GLN* 2.5 35.9 - - - +
2713 LYS 3.1 0.2 - - - +
2723 VAL* 1.3 88.5 - - + +
2743 GLU* 1.3 64.4 - - - +
2763 SER* 3.1 11.9 + - - -
2773 LEU* 2.9 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 274 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2703 GLN 3.7 8.6 - - - +
2713 LYS* 3.1 15.2 - - - +
2733 PRO* 1.3 82.5 - - + +
2753 THR* 1.3 63.1 + - - +
2773 LEU* 3.0 25.3 + - + +
2783 ASN* 2.9 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 275 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2213 TYR* 5.6 16.8 - - + -
2713 LYS* 3.4 5.4 + - - +
2723 VAL* 2.9 42.5 - - + +
2743 GLU* 1.3 80.2 - - - +
2763 SER* 1.3 57.8 + - - +
2783 ASN* 3.3 4.0 + - - +
2793 VAL* 2.6 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 276 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453 LYS* 4.6 0.5 - - - +
1343 PHE* 5.3 9.0 - - - -
2723 VAL* 3.2 6.3 + - - +
2733 PRO* 3.1 9.7 + - - -
2753 THR* 1.3 83.2 - - - +
2773 LEU* 1.3 56.6 + - - +
2793 VAL* 2.1 31.8 - - - +
2803 PRO 2.4 16.3 + - - +
2813 LEU* 3.3 34.9 - - - +
2863 LEU* 5.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453 LYS* 2.4 43.3 + - - +
2733 PRO* 2.9 25.4 - - + +
2743 GLU* 3.0 16.1 + - + +
2763 SER* 1.3 81.0 - - - +
2783 ASN* 1.3 52.1 + - - +
2813 LEU* 4.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 278 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433 ASN* 3.5 13.9 - - - +
453 LYS* 3.3 20.2 - - - +
2743 GLU* 2.9 43.8 + - - +
2753 THR* 4.1 5.5 - - - +
2773 LEU* 1.3 76.5 - - - +
2793 VAL* 1.3 62.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 279 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423 LEU 4.9 8.3 - - - +
433 ASN* 5.1 2.0 - - - +
443 GLU 5.6 0.2 - - - +
453 LYS* 3.1 18.0 - - - +
1343 PHE* 5.2 7.2 - - + -
2163 ARG* 4.8 14.4 - - - +
2753 THR* 2.6 40.6 + - + +
2763 SER* 2.1 26.7 - - - +
2773 LEU 3.2 0.2 - - - -
2783 ASN* 1.3 80.2 - - + +
2803 PRO* 1.4 76.5 - - + +
----------------------------------------------------------
Back to top of page
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