Contacts of the helix formed by residues 36 - 64 (chain 7) in PDB entry 2X17
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 LEU 36 (chain 7).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317 PHE* 3.0 35.6 + - + +
327 GLU* 4.9 0.7 - - - -
347 LEU* 4.3 19.3 - - + +
357 GLY* 1.3 75.7 - - - +
377 GLU* 1.3 58.9 + - - +
397 PHE* 4.1 13.5 - - + -
407 ALA* 3.1 26.0 + - - +
837 PRO* 4.1 20.0 - - + -
1517 LEU* 4.3 27.4 - - + +
1527 PHE* 5.6 2.2 - - + -
1557 ASP* 3.3 31.9 - - + +
143O PHE* 5.3 9.0 - - + -
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Residues in contact with GLU 37 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327 GLU* 3.5 19.4 - - - +
357 GLY* 3.2 14.5 + - - +
367 LEU* 1.3 72.3 - - - +
387 GLY* 1.3 60.4 + - - +
407 ALA* 3.6 6.3 - - - +
417 ASN* 3.0 41.1 + - - +
1557 ASP* 3.6 4.3 + - - +
1597 SER* 5.3 0.7 - - - -
136O LYS* 2.9 48.6 + - + +
140O LYS* 6.4 0.7 - - - +
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Residues in contact with GLY 38 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377 GLU* 1.3 77.2 - - - +
397 PHE* 1.3 58.7 + - - +
417 ASN* 3.5 1.2 + - - +
427 TRP* 3.1 27.9 + - - +
1557 ASP* 2.9 32.2 + - - -
1587 LEU* 3.4 12.3 - - - +
1597 SER* 3.7 19.6 - - - -
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Residues in contact with PHE 39 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317 PHE* 3.5 34.8 - + + -
367 LEU* 3.8 11.0 - - + +
377 GLU 3.4 0.2 - - - -
387 GLY* 1.3 74.2 - - - +
407 ALA* 1.3 62.1 + - - +
427 TRP* 3.4 8.1 + - - +
437 MET* 3.1 27.4 + - - +
877 PHE* 3.6 32.4 - + - -
1377 ILE* 4.3 1.6 - - + -
1417 LEU* 3.9 30.3 - - + -
1517 LEU* 4.1 16.6 - - + -
1547 LEU* 4.1 12.1 - - + -
1557 ASP* 3.1 51.1 + - + -
1587 LEU* 3.6 22.2 - - + -
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Residues in contact with ALA 40 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287 ALA* 3.5 29.5 - - - +
317 PHE* 3.9 2.2 - - - +
327 GLU* 3.4 33.0 - - - +
367 LEU 3.1 18.6 + - - +
377 GLU 3.6 5.4 - - - +
387 GLY 3.3 0.2 - - - -
397 PHE* 1.3 76.3 - - - +
417 ASN* 1.3 58.1 + - - +
437 MET 3.3 1.7 + - - -
447 LYS* 3.0 32.5 + - - +
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Residues in contact with ASN 41 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327 GLU* 4.7 1.2 - - - +
377 GLU* 3.0 27.5 + - - +
387 GLY* 4.1 5.1 - - - +
397 PHE 3.4 0.2 - - - -
407 ALA* 1.3 73.7 - - - +
427 TRP* 1.3 60.1 + - - +
447 LYS* 3.3 26.0 + - - +
457 ALA* 3.1 28.2 + - - +
1597 SER* 5.2 8.5 + - - +
1617 ARG 3.6 14.7 - - - +
1627 ALA* 4.6 6.6 - - + +
1637 PRO* 3.5 21.9 - - + +
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Residues in contact with TRP 42 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247 TYR* 5.7 1.3 - + - -
387 GLY 3.1 18.8 + - - +
397 PHE* 3.5 7.6 - - - +
407 ALA 3.3 0.2 - - - -
417 ASN* 1.3 76.8 - - - +
437 MET* 1.3 89.1 + - + +
457 ALA* 3.4 3.6 + - - +
467 GLN* 3.0 41.7 + - + +
877 PHE* 4.4 9.9 - + - -
1337 SER* 3.6 21.7 + - - -
1347 VAL* 4.2 23.1 - - + -
1377 ILE* 3.6 26.0 - - + +
1587 LEU* 3.7 34.4 - - + +
1617 ARG* 3.3 45.8 + - + +
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Residues in contact with MET 43 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247 TYR* 3.3 50.1 - - + +
277 MET* 3.8 30.7 - - + -
287 ALA* 3.8 7.9 - - + +
317 PHE* 4.0 10.5 - - + -
397 PHE 3.1 17.0 + - - +
407 ALA 3.6 7.9 - - - +
427 TRP* 1.3 90.9 - - + +
447 LYS* 1.3 58.6 + - - +
467 GLN* 3.3 3.0 + - - +
477 ALA* 2.9 28.9 + - - +
877 PHE* 3.7 40.6 - - + -
907 ALA* 4.8 4.9 - - + -
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Residues in contact with LYS 44 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257 PHE* 4.8 11.4 - - + -
287 ALA* 3.9 9.9 - - + -
327 GLU* 3.1 28.7 + - - -
407 ALA 3.0 17.9 + - - +
417 ASN* 3.3 28.7 + - - +
437 MET* 1.3 76.8 - - - +
457 ALA* 1.3 59.9 - - - +
477 ALA* 3.2 8.3 + - - +
487 GLU* 3.2 26.9 + - - +
1637 PRO* 4.0 21.5 - - + -
55P LEU* 4.9 13.9 - - + +
58P TYR* 3.6 28.2 - - - -
59P ASN* 4.4 7.3 + - - -
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Residues in contact with ALA 45 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417 ASN 3.1 18.6 + - - +
427 TRP 3.6 2.2 - - - +
447 LYS* 1.3 75.6 - - - +
467 GLN* 1.3 61.0 + - - +
487 GLU* 3.6 7.6 + - - +
497 GLU* 3.4 24.8 + - - +
1617 ARG* 3.6 27.7 + - + +
1627 ALA 3.7 23.8 - - - +
1637 PRO* 4.1 8.9 - - - +
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Residues in contact with GLN 46 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247 TYR* 3.7 23.8 - - + -
427 TRP* 3.0 40.7 + - + +
437 MET* 3.5 6.7 - - - +
457 ALA* 1.3 76.5 - - - +
477 ALA* 1.3 63.7 + - - +
497 GLU* 3.2 7.7 + - - +
507 GLU* 2.9 35.1 + - - +
1307 GLU* 2.7 35.5 + - - +
1337 SER* 5.2 2.8 + - - -
1347 VAL* 5.8 2.9 - - + +
1617 ARG* 3.0 32.8 + - - +
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Residues in contact with ALA 47 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217 ALA* 3.3 42.8 - - + +
247 TYR* 4.2 6.2 - - + +
257 PHE* 4.3 10.1 - - + +
437 MET 2.9 16.6 + - - +
447 LYS* 3.4 10.1 - - - +
467 GLN* 1.3 78.2 - - - +
487 GLU* 1.3 61.0 + - + +
507 GLU* 3.2 2.0 + - - -
517 ILE* 3.1 24.1 + - + +
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Residues in contact with GLU 48 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447 LYS 3.2 11.0 + - - +
457 ALA* 3.7 8.9 - - - +
467 GLN 3.3 0.2 - - - -
477 ALA* 1.3 73.2 - - + +
497 GLU* 1.3 60.7 + - - +
517 ILE* 3.4 14.9 + - + +
527 GLY* 3.0 21.0 + - - -
1637 PRO* 3.4 19.2 - - + +
1647 LYS* 2.8 31.4 + - - +
1657 LEU* 3.1 36.4 + - + +
1667 PRO* 3.5 2.6 - - - +
55P LEU* 5.6 1.7 - - - +
165P LEU* 4.2 13.7 - - + +
169P LEU* 3.8 21.6 - - + +
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Residues in contact with GLU 49 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457 ALA 3.4 15.0 + - - +
467 GLN* 3.2 19.6 + - - +
487 GLU* 1.3 76.9 - - + +
507 GLU* 1.3 57.4 + - - +
527 GLY* 3.2 2.6 + - - -
537 HIS* 2.9 34.8 + - + -
1307 GLU* 4.6 1.1 - - - +
1617 ARG* 3.5 18.5 + - - +
1647 LYS* 5.4 4.2 + - - -
11737 AG 3.0 22.6 - - - -
169P LEU* 3.4 27.8 - - + +
170P MET* 3.3 23.3 + - - +
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Residues in contact with GLU 50 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177 GLU* 2.9 48.1 - - - +
207 SER* 3.6 21.0 + - - -
217 ALA* 3.6 7.4 - - - +
247 TYR* 3.8 18.7 - - + -
467 GLN* 2.9 34.8 + - - +
477 ALA 3.2 6.3 + - - +
497 GLU* 1.3 74.3 - - - +
517 ILE* 1.3 59.7 + - - +
537 HIS* 3.1 14.9 + - - +
547 ALA* 2.9 23.6 + - - +
947 GLU* 3.9 3.4 - - - +
977 ILE* 5.6 1.2 - - - +
1277 GLN* 5.0 4.3 + - - -
1307 GLU* 3.1 15.8 - - - +
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Residues in contact with ILE 51 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187 LEU* 4.9 15.7 - - + -
217 ALA* 3.7 15.5 - - + -
477 ALA* 3.1 19.7 + - + +
487 GLU* 3.6 17.9 - - + +
497 GLU 3.4 0.2 - - - -
507 GLU* 1.3 75.2 - - - +
527 GLY* 1.3 57.2 + - - +
547 ALA* 3.3 8.4 + - - +
557 LEU* 3.1 38.6 + - + +
1657 LEU* 6.3 0.9 - - + -
51P ILE* 4.7 27.6 - - + -
165P LEU* 4.3 19.1 - - + -
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Residues in contact with GLY 52 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487 GLU 3.0 13.4 + - - -
497 GLU 3.2 5.6 + - - -
507 GLU 3.2 0.4 - - - -
517 ILE* 1.3 74.9 - - - +
537 HIS* 1.3 64.2 + - - +
557 LEU* 3.4 12.1 + - - +
567 ARG* 3.3 28.9 + - - +
165P LEU* 5.4 0.6 - - - +
169P LEU* 4.1 21.5 - - - -
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Residues in contact with HIS 53 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177 GLU* 3.3 24.5 + - - +
497 GLU 2.9 21.9 + - - -
507 GLU* 3.1 24.5 + - - +
527 GLY* 1.3 76.5 - - - +
547 ALA* 1.3 61.8 + - - +
567 ARG* 3.4 8.3 + - - +
577 PHE* 3.4 19.8 + - - -
1227 TRP* 3.6 25.4 - + - -
1237 PHE* 3.5 13.7 - + + -
1267 GLU* 3.1 30.2 + - - +
1277 GLN* 5.1 0.4 + - - -
1307 GLU* 3.6 14.4 - - - -
11737 AG 2.2 31.5 - - - -
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Residues in contact with ALA 54 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147 LEU* 3.6 22.1 - - + +
177 GLU* 3.8 15.0 - - + +
187 LEU* 3.8 34.3 - - + +
507 GLU 2.9 12.7 + - - +
517 ILE* 3.3 8.3 + - + +
537 HIS* 1.3 77.4 - - - +
557 LEU* 1.3 57.5 + - + +
577 PHE* 3.3 3.4 + - - +
587 TYR* 3.0 22.7 + - - +
25P PHE* 5.4 2.5 - - + -
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Residues in contact with LEU 55 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517 ILE* 3.1 34.5 + - + +
527 GLY* 3.8 10.1 - - - +
537 HIS 3.3 0.2 - - - -
547 ALA* 1.3 73.8 - - + +
567 ARG* 1.3 60.2 + - - +
577 PHE 3.3 0.2 - - - -
587 TYR* 3.4 12.9 - - + +
597 ASN* 2.9 41.7 + - - +
25P PHE* 3.7 31.4 - - + -
44P LYS* 4.9 16.6 - - + +
48P GLU* 5.6 1.8 - - - +
163P PRO* 6.2 0.7 - - + -
165P LEU* 5.5 5.4 - - + -
166P PRO* 4.3 29.2 - - + -
169P LEU* 6.2 0.2 - - + -
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Residues in contact with ARG 56 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527 GLY 3.3 17.3 + - - +
537 HIS* 3.5 10.1 - - - +
547 ALA 3.2 0.8 - - - -
557 LEU* 1.3 74.4 - - - +
577 PHE* 1.3 59.5 + - - +
597 ASN* 4.0 8.5 - - - +
607 TYR* 3.2 27.4 + - - +
1197 PHE* 3.5 10.2 - - + -
1227 TRP* 3.4 62.1 - - - +
1237 PHE* 3.7 11.7 - - + -
169P LEU 5.0 1.0 + - - -
170P MET* 3.3 25.3 + - - +
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Residues in contact with PHE 57 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107 LEU* 3.7 36.1 - - + +
137 GLN* 3.4 33.0 - - + -
147 LEU* 4.0 20.4 - - + -
177 GLU* 4.1 14.4 - - + -
537 HIS 3.4 19.6 + - - -
547 ALA* 3.3 8.8 + - - +
567 ARG* 1.3 74.3 - - - +
587 TYR* 1.3 65.3 + - - +
607 TYR* 3.4 1.4 + - - +
617 ILE* 3.1 30.0 + - - +
1017 ILE* 4.1 5.4 - - + -
1047 LEU* 4.3 0.9 - - + -
1197 PHE* 3.6 23.1 - + - -
1207 LEU* 4.1 19.1 - - + -
1237 PHE* 3.5 31.2 - + - -
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Residues in contact with TYR 58 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147 LEU* 3.6 11.8 - - + +
547 ALA 3.0 14.1 + - - +
557 LEU* 3.4 17.5 - - + +
577 PHE* 1.3 78.1 - - - +
597 ASN* 1.3 75.7 + - - +
617 ILE* 3.5 1.7 + - - +
627 TYR* 3.3 50.1 + + + -
687 VAL* 4.0 17.7 - - + -
25P PHE* 3.6 29.6 - + + -
28P ALA* 3.1 27.9 + - + -
29P ALA* 3.5 17.4 - - + -
32P GLU* 3.1 20.9 + - - +
44P LYS* 3.4 30.8 - - - -
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Residues in contact with ASN 59 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557 LEU* 2.9 30.4 + - - +
567 ARG* 4.0 7.9 - - - +
587 TYR* 1.3 91.8 - - - +
607 TYR* 1.3 62.7 + - - +
627 TYR* 3.5 4.3 + - - +
637 ASP* 3.1 33.2 + - - +
32P GLU* 5.2 0.9 - - - +
44P LYS* 4.1 9.4 + - - -
166P PRO* 6.3 0.8 - - - +
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Residues in contact with TYR 60 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27 LEU* 4.3 0.9 - - + -
107 LEU* 3.9 23.1 - - + -
567 ARG 3.2 19.0 + - - +
577 PHE 3.9 1.8 - - - +
587 TYR 3.4 0.2 - - - -
597 ASN* 1.3 74.7 - - - +
617 ILE* 1.3 68.2 + - + +
637 ASP* 3.0 17.9 + - + +
647 ARG* 3.1 43.8 + - + +
1157 SER* 3.2 12.8 - - - -
1167 THR* 2.8 46.2 + - + -
1197 PHE* 3.6 53.2 - + + -
128Z VAL* 4.2 17.3 - - + -
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Residues in contact with ILE 61 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27 LEU* 4.4 4.9 - - + +
77 LEU* 3.8 13.0 - - + +
107 LEU* 3.8 44.6 - - + +
117 ASN* 4.2 9.2 - - - +
147 LEU* 3.9 13.2 - - + -
577 PHE 3.1 22.6 + - - +
587 TYR 3.8 4.5 - - - +
597 ASN 3.4 0.2 - - - -
607 TYR* 1.3 78.1 - - + +
627 TYR* 1.3 58.0 + - + +
647 ARG* 3.2 11.8 + - - +
667 GLY* 2.8 24.9 + - - -
677 ARG* 3.5 26.7 - - - +
687 VAL* 3.7 26.9 - - + +
----------------------------------------------------------
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Residues in contact with TYR 62 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587 TYR* 3.3 45.7 + + + +
597 ASN* 4.1 4.5 - - - +
607 TYR 3.3 0.4 - - - -
617 ILE* 1.3 73.8 - - - +
637 ASP* 1.3 65.5 + - - +
647 ARG 3.2 0.9 - - - -
657 ASN* 3.5 11.0 + - - +
667 GLY 3.5 22.0 - - - +
677 ARG* 3.4 6.1 + - - -
687 VAL* 3.4 35.4 + - + -
29P ALA* 2.5 34.7 + - - +
32P GLU* 3.6 31.0 - - + -
33P ASP* 3.7 24.7 - - + -
132Z ALA* 5.3 0.9 - - - +
----------------------------------------------------------
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Residues in contact with ASP 63 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597 ASN* 3.1 27.4 + - - +
607 TYR* 3.0 13.6 + - - +
627 TYR* 1.3 78.6 - - - +
647 ARG* 1.3 63.7 + - - +
657 ASN* 3.3 2.7 + - - +
128Z VAL* 4.1 24.4 - - + +
129Z GLU* 6.0 3.1 - - - +
131Z GLU* 5.2 2.6 - - - +
132Z ALA* 3.6 35.7 + - + +
----------------------------------------------------------
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Residues in contact with ARG 64 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17 MET* 3.8 39.5 + - - +
27 LEU* 3.8 25.7 + - + +
607 TYR* 3.1 55.7 + - + +
617 ILE 3.2 4.9 + - - +
637 ASP* 1.3 77.4 + - - +
657 ASN* 1.3 69.7 + - - +
667 GLY* 3.2 1.4 + - - -
1137 ASP* 4.6 6.1 + - - -
1157 SER* 3.5 28.2 + - - -
102Z TYR* 3.5 11.3 + - - -
127Z GLN 5.3 0.4 - - - -
128Z VAL* 3.9 26.2 - - - +
131Z GLU* 4.1 27.4 + - - +
----------------------------------------------------------
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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