Contacts of the helix formed by residues 135 - 158 (chain 7) in PDB entry 3J7Y
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 PRO 135 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1297 THR 4.4 3.1 - - - +
1307 PHE* 3.3 28.7 - - - +
1327 ASP* 3.7 19.1 - - - +
1337 CYS 3.5 9.6 - - - +
1347 ASP* 1.4 86.7 - - - +
1367 GLY* 1.3 60.7 + - - +
1377 GLU* 3.4 3.1 - - - +
1387 VAL* 3.3 9.2 + - + +
1397 ASN* 3.0 29.7 + - - +
142O LEU* 3.6 39.5 - - + +
143O THR* 3.9 5.4 - - + +
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Residues in contact with GLY 136 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1347 ASP* 3.4 4.0 - - - +
1357 PRO* 1.3 76.9 - - - +
1377 GLU* 1.3 66.3 + - - +
1397 ASN* 3.2 12.6 + - - +
1407 LYS* 3.1 34.4 + - - +
1747 VAL* 5.7 0.2 - - - +
142O LEU* 5.3 2.0 - - - +
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Residues in contact with GLU 137 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057 LEU* 3.4 19.8 - - + +
1077 LEU* 4.3 20.9 - - + +
1127 PRO* 5.0 11.4 - - + -
1287 LEU* 4.3 19.0 - - + +
1347 ASP* 3.0 31.0 - - - +
1357 PRO 4.2 0.7 - - - -
1367 GLY* 1.3 76.5 + - - +
1387 VAL* 1.3 63.4 + - - +
1407 LYS* 3.4 15.0 + - - +
1417 ALA* 3.2 17.3 + - - +
1447 ARG* 4.6 2.6 + - - -
2677 PRO* 5.8 0.2 - - - +
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Residues in contact with VAL 138 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047 ILE* 3.9 19.3 - - + -
1057 LEU* 3.6 13.2 - - + +
1287 LEU* 3.4 35.9 - - + +
1297 THR 3.4 24.7 - - - +
1307 PHE* 3.7 31.9 - - + -
1327 ASP* 4.6 1.3 - - - +
1357 PRO* 3.3 12.0 + - + +
1367 GLY 3.2 0.6 - - - -
1377 GLU* 1.3 76.4 - - + +
1397 ASN* 1.3 58.2 + - - +
1417 ALA* 3.2 4.7 + - - +
1427 TYR* 2.9 26.3 + - - +
2697 ILE* 4.9 0.5 - - - +
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Residues in contact with ASN 139 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1307 PHE* 4.2 11.9 - - - +
1357 PRO* 3.0 27.4 + - - +
1367 GLY* 3.2 11.1 + - - +
1387 VAL* 1.3 77.6 - - - +
1407 LYS* 1.3 56.5 + - - +
1427 TYR* 3.2 6.4 + - - +
1437 TRP* 2.9 31.4 + - - +
1747 VAL* 3.9 18.9 - - + +
142O LEU 2.9 27.9 + - - -
143O THR 4.1 0.2 - - - -
144O LEU* 3.5 43.2 + - + +
147O GLN* 4.5 3.0 - - - +
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Residues in contact with LYS 140 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1367 GLY* 3.1 21.2 + - - +
1377 GLU* 3.6 11.7 - - - +
1397 ASN* 1.3 79.0 - - + +
1417 ALA* 1.3 57.5 + - - +
1437 TRP* 3.2 11.4 + - + +
1447 ARG* 2.9 64.9 + - - +
1727 VAL 6.0 2.7 - - - +
1737 PRO* 6.5 0.7 - - + -
1747 VAL* 5.6 4.9 - - + -
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Residues in contact with ALA 141 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057 LEU* 3.9 26.9 - - + -
1377 GLU 3.2 10.6 + - - +
1387 VAL 3.4 8.7 - - - +
1407 LYS* 1.3 79.9 - - - +
1427 TYR* 1.3 57.2 + - - +
1447 ARG* 3.2 10.4 + - - +
1457 SER* 2.9 28.2 + - - -
2677 PRO* 3.5 23.8 - - + +
2687 LEU* 3.9 8.7 - - - +
2697 ILE* 4.3 4.9 - - + -
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Residues in contact with TYR 142 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1307 PHE* 3.9 15.7 - + + -
1387 VAL 2.9 12.7 + - - +
1397 ASN 3.3 8.7 - - - +
1417 ALA* 1.3 75.5 - - - +
1437 TRP* 1.3 60.9 + + - +
1457 SER* 3.2 3.1 + - - -
1467 CYS* 2.9 52.9 + - - -
2697 ILE* 3.4 33.8 - - + +
2747 ILE* 4.9 0.7 - - + -
2757 CYS* 3.6 28.4 - - - +
3017 SER* 3.5 23.7 + - - -
3027 LEU 3.2 5.9 + - - -
3037 PRO* 3.0 49.8 - - + +
144O LEU* 4.1 17.0 - - + -
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Residues in contact with TRP 143 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1397 ASN 2.9 12.2 + - - +
1407 LYS* 3.2 11.4 + - - +
1427 TYR* 1.3 82.2 - + - +
1447 ARG* 1.3 56.6 + - + +
1467 CYS* 3.2 10.0 + - - +
1477 ALA* 2.9 29.2 + - - +
1727 VAL* 3.9 13.7 - - + +
1737 PRO 3.3 24.5 + - - -
1747 VAL* 3.4 28.4 - - + +
1787 ALA 4.0 17.2 + - - -
1797 PHE* 3.4 43.7 - + + +
3007 VAL* 4.7 3.8 - - + -
3017 SER* 3.6 28.5 - - - -
144O LEU* 3.9 27.1 - - + -
148O LEU* 4.0 23.1 - - + -
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Residues in contact with ARG 144 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1377 GLU 4.6 2.4 + - - -
1407 LYS* 2.9 51.6 + - - +
1417 ALA 3.3 9.2 - - - +
1437 TRP* 1.3 77.7 - - + +
1457 SER* 1.3 56.7 + - - +
1477 ALA* 3.2 9.4 + - - +
1487 MET* 2.9 30.0 + - - +
1717 GLU* 5.3 12.5 + - - +
2647 SER* 5.3 8.7 - - - -
2657 GLU* 4.0 18.8 + - - +
2667 GLY* 3.5 26.9 - - - +
2677 PRO* 3.6 33.4 - - - +
2687 LEU* 3.4 14.8 - - + +
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Residues in contact with SER 145 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1417 ALA 2.9 12.8 + - - -
1427 TYR* 3.3 12.8 - - - -
1447 ARG* 1.3 75.3 - - - +
1467 CYS* 1.3 59.2 + - - +
1487 MET* 3.2 5.1 + - - +
1497 MET* 2.9 33.8 + - - +
2167 PHE* 2.9 36.1 - - - -
2687 LEU* 3.4 8.9 - - - +
2697 ILE* 4.1 24.4 - - - +
2717 ARG 5.3 0.3 + - - -
2727 THR* 5.8 0.2 - - - -
2757 CYS* 5.0 5.9 - - - -
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Residues in contact with CYS 146 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1427 TYR* 2.9 49.3 + - - -
1437 TRP* 3.4 13.7 - - + +
1457 SER* 1.3 75.9 - - - +
1477 ALA* 1.3 57.0 + - - +
1497 MET* 3.2 3.9 + - - +
1507 MET 2.9 13.0 + - - -
1797 PHE* 3.3 25.4 - - + -
2757 CYS* 4.3 3.4 - - - -
2787 TYR* 2.6 34.4 + - + -
3017 SER* 2.9 25.1 - - - +
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Residues in contact with ALA 147 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437 TRP 2.9 13.0 + - - +
1447 ARG* 3.3 12.1 - - - +
1467 CYS* 1.3 76.6 - - - +
1487 MET* 1.3 56.9 + - - +
1507 MET* 3.2 5.7 + - - +
1517 GLY 2.9 24.4 + - - -
1697 ALA* 4.2 11.7 - - + -
1707 PRO 5.9 1.6 - - - +
1797 PHE* 3.4 13.0 - - + -
1807 CYS 3.8 19.7 - - - +
1817 TYR* 3.5 19.3 - - + -
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Residues in contact with MET 148 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1447 ARG 2.9 11.2 + - - +
1457 SER* 3.2 11.2 + - - +
1477 ALA* 1.3 76.8 - - - +
1497 MET* 1.3 57.4 + - - +
1517 GLY* 3.2 2.4 + - - -
1527 CYS* 2.9 28.6 + - - +
1817 TYR* 4.9 6.3 - - - -
2167 PHE* 4.3 1.3 - - - -
2557 HIS* 3.9 18.6 - - + +
2567 ARG* 5.5 0.2 - - - -
2577 ILE* 3.7 27.8 - - + -
2607 PHE* 3.7 17.7 - - + -
2627 ASP* 3.9 22.9 - - + +
2637 VAL 4.8 0.9 - - - +
2647 SER* 3.7 22.9 - - - +
2687 LEU* 3.5 34.5 - - + -
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Residues in contact with MET 149 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1457 SER* 2.9 19.0 + - - +
1467 CYS* 3.4 6.7 - - - +
1487 MET* 1.3 77.0 - - - +
1507 MET* 1.3 57.0 + - - +
1527 CYS* 3.2 8.8 + - - +
1537 VAL* 2.9 34.2 + - + +
2067 ALA* 5.0 4.5 - - + +
2097 LEU* 4.2 10.3 - - + +
2107 ILE* 3.7 20.0 - - + -
2167 PHE* 4.3 13.7 - - + -
2577 ILE* 4.7 5.2 - - + -
2727 THR* 3.6 33.0 - - + -
2757 CYS* 3.4 24.5 - - - -
2787 TYR* 3.3 37.0 - - + +
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Residues in contact with MET 150 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467 CYS 2.9 7.2 + - - +
1477 ALA* 3.3 10.1 - - - +
1497 MET* 1.3 77.5 - - - +
1517 GLY* 1.3 56.3 + - - +
1537 VAL* 3.2 9.7 + - - +
1547 ILE* 2.9 51.2 + - + +
1797 PHE* 3.5 19.5 - - + +
1807 CYS 6.3 0.2 - - - -
1817 TYR* 4.6 9.0 - - + -
2027 PHE* 4.9 4.7 - - + -
2787 TYR* 3.1 18.8 + - + +
2807 VAL* 3.5 42.4 - - + -
2977 PHE* 3.4 37.0 - - + +
2987 GLN 4.5 7.2 - - - +
2997 GLY* 5.1 0.2 - - - -
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Residues in contact with GLY 151 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1477 ALA 2.9 13.8 + - - -
1487 MET 3.2 4.0 + - - -
1507 MET* 1.3 75.3 - - - +
1527 CYS* 1.3 57.2 + - - +
1547 ILE* 3.2 8.9 + - - +
1557 GLU* 2.9 29.3 + - - +
1667 LEU* 4.0 3.9 - - - +
1817 TYR* 3.8 30.7 - - - -
2607 PHE* 4.3 7.6 - - - -
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Residues in contact with CYS 152 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1487 MET 2.9 13.1 + - - +
1497 MET* 3.3 11.7 - - - +
1517 GLY* 1.3 76.3 - - - +
1537 VAL* 1.3 61.0 - - - +
1557 GLU* 3.2 11.3 + - - +
1567 ARG* 3.3 30.1 + - - +
2097 LEU* 3.9 26.7 - - + -
2577 ILE* 5.3 11.7 - - + -
2607 PHE* 3.6 43.4 - - + -
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Residues in contact with VAL 153 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497 MET 2.9 19.0 + - - +
1507 MET* 3.4 14.6 - - - +
1527 CYS* 1.3 77.7 - - - +
1547 ILE* 1.3 63.1 + - - +
1567 ARG* 3.5 3.0 + - - +
1577 ALA* 3.0 27.3 + - + +
2027 PHE* 3.4 41.7 - - + +
2057 ASP* 3.8 15.3 - - + +
2067 ALA* 3.6 26.0 - - + +
2097 LEU* 3.5 22.2 - - + -
2787 TYR* 5.5 0.2 - - + -
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Residues in contact with ILE 154 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1507 MET* 2.9 27.1 + - + +
1517 GLY 3.2 7.6 + - - +
1537 VAL* 1.3 79.0 - - - +
1557 GLU* 1.3 66.0 + - - +
1567 ARG 3.4 0.3 + - - -
1577 ALA* 3.6 3.5 + - - +
1587 PHE* 3.6 26.9 - - + -
1667 LEU* 3.6 25.4 - - + -
1817 TYR* 4.8 4.7 - - + -
1837 VAL* 3.5 21.8 - - + -
1857 LEU* 5.7 0.2 - - + -
2027 PHE* 3.6 26.5 - - + -
2977 PHE* 3.4 41.7 - - + -
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Residues in contact with GLU 155 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417 THR* 4.5 13.1 - - - +
447 ARG* 5.2 7.4 + - - -
1517 GLY 2.9 12.6 + - - +
1527 CYS* 3.2 9.3 + - - +
1547 ILE* 1.3 81.9 - - - +
1567 ARG* 1.3 91.4 + - - +
1587 PHE* 4.7 3.6 + - - +
1667 LEU* 4.8 10.6 - - + +
2367 LYS* 5.3 2.3 + - - -
2607 PHE* 3.1 30.9 - - + -
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Residues in contact with ARG 156 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417 THR* 4.4 14.4 - - - +
1527 CYS* 3.3 35.8 + - - +
1537 VAL* 4.2 3.1 - - - +
1547 ILE 3.3 0.2 - - - -
1557 GLU* 1.3 113.7 + - - +
1577 ALA* 1.3 66.6 + - - +
1587 PHE 2.8 13.9 + - - +
2057 ASP* 5.7 1.6 - - - +
2097 LEU* 5.8 5.8 - - - -
2597 ASP* 3.2 36.4 + - - +
2607 PHE* 4.0 6.1 - - - +
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Residues in contact with ALA 157 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1537 VAL 3.0 20.0 + - - +
1547 ILE 3.6 3.8 + - - +
1567 ARG* 1.3 74.0 - - - +
1587 PHE* 1.3 62.9 + - - +
2017 SER* 5.9 0.2 - - - +
2027 PHE* 3.7 35.4 - - + -
2057 ASP* 4.1 19.5 + - - +
----------------------------------------------------------
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Residues in contact with PHE 158 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1547 ILE* 3.6 22.4 + - + +
1557 GLU 5.3 2.5 - - - +
1567 ARG 2.8 17.8 + - - +
1577 ALA* 1.3 81.1 - - + +
1857 LEU* 3.9 38.6 - - + -
1947 PRO* 6.6 0.2 - - + -
1987 ASN* 6.2 2.0 - - - -
2027 PHE* 3.9 25.1 - + - -
2977 PHE* 4.6 9.9 - + - -
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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