Contacts of the helix formed by residues 113 - 143 (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 ASP 113 (chain 7).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17 MET 5.5 1.7 - - - +
27 LEU* 3.7 17.5 - - - +
37 SER 5.4 0.7 + - - -
67 MET* 3.8 12.8 - - + +
607 TYR* 4.5 0.2 + - - -
647 ARG* 4.6 6.4 + - - -
1087 ALA* 2.8 18.8 + - - +
1117 GLU* 2.9 10.3 + - + +
1127 LYS* 1.3 72.8 - - - +
1147 TYR* 1.3 62.1 + - - +
1157 SER* 3.6 10.0 + - - -
1167 THR* 2.7 38.4 + - - +
1177 ARG* 3.1 22.8 + - - +
102Z TYR* 5.3 0.9 + - - -
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Residues in contact with TYR 114 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127 LYS* 3.2 43.8 + - + +
1137 ASP* 1.3 74.4 + - - +
1157 SER* 1.3 56.7 + - - +
1177 ARG* 3.8 7.3 - - + +
1187 ALA* 3.0 30.8 + - - +
102Z TYR* 3.5 57.0 - + + -
105Z ALA* 3.9 12.3 - - + -
106Z ALA* 3.4 20.6 - - + +
109Z GLU* 3.1 36.2 + - - -
117Z ARG* 3.4 22.6 + - - -
124Z ILE* 3.5 11.6 - - + +
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Residues in contact with SER 115 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607 TYR* 3.2 16.1 + - - -
647 ARG* 3.5 25.7 + - - -
1137 ASP* 3.2 4.6 + - - -
1147 TYR* 1.3 78.6 - - - +
1167 THR* 1.3 57.2 + - - +
1187 ALA* 3.5 2.8 + - - +
1197 PHE* 3.0 24.8 + - - +
102Z TYR* 2.6 29.9 + - - -
124Z ILE* 3.8 11.8 + - - +
125Z ASN* 5.2 0.7 - - - +
128Z VAL* 3.8 17.8 - - - +
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Residues in contact with THR 116 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27 LEU* 3.6 8.5 - - - +
67 MET* 3.7 23.8 - - + -
107 LEU* 4.0 18.4 - - + -
607 TYR* 2.8 24.5 + - + -
1087 ALA* 4.3 3.8 - - + -
1137 ASP* 2.7 33.7 + - - -
1157 SER* 1.3 74.1 - - - +
1177 ARG* 1.3 62.0 + - - +
1197 PHE* 3.3 1.5 + - + +
1207 LEU* 2.9 43.4 + - + +
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Residues in contact with ARG 117 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1140 TYR* 3.6 24.2 + - - +
1170 ARG* 5.3 9.9 - - - +
1180 ALA* 5.8 0.6 - - - +
1057 ALA* 3.7 28.6 - - - +
1087 ALA* 3.8 12.2 - - + +
1097 GLU* 2.8 33.3 + - + +
1137 ASP 3.1 16.4 + - - +
1147 TYR* 3.8 10.1 - - + +
1167 THR* 1.3 78.0 - - - +
1187 ALA* 1.3 59.2 + - - +
1207 LEU* 3.5 4.5 + - - +
1217 GLU* 2.9 36.5 + - - +
1247 ILE* 3.4 19.8 - - - +
117Z ARG* 5.3 9.9 - - - +
121Z GLU* 4.9 1.7 + - - +
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Residues in contact with ALA 118 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147 TYR 3.0 18.4 + - - +
1157 SER 3.8 2.5 - - - +
1177 ARG* 1.3 73.2 - - - +
1197 PHE* 1.3 64.0 + - - +
1217 GLU* 3.4 16.2 - - - +
1227 TRP* 4.5 1.0 + - - +
121Z GLU* 3.5 29.5 - - - +
124Z ILE* 3.8 18.2 - - + -
125Z ASN* 3.6 26.0 + - - +
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Residues in contact with PHE 119 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107 LEU* 4.3 4.0 - - + -
567 ARG* 3.5 28.3 - - + -
577 PHE* 3.6 34.5 - + - -
607 TYR* 3.6 46.7 - + + -
1157 SER 3.0 18.2 + - - +
1167 THR 3.5 6.7 - - - +
1187 ALA* 1.3 76.5 - - - +
1207 LEU* 1.3 66.7 + - + +
1217 GLU 3.1 2.6 + - - -
1227 TRP* 3.5 18.6 + - + +
1237 PHE* 3.5 31.7 - + - -
125Z ASN* 4.3 4.4 + - - -
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Residues in contact with LEU 120 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107 LEU* 5.1 0.4 - - + -
577 PHE* 4.1 22.2 - - + -
1017 ILE* 4.4 14.1 - - + +
1047 LEU* 3.6 60.1 - - + +
1057 ALA* 3.7 9.9 - - + +
1087 ALA* 4.4 2.2 - - + -
1167 THR* 2.9 33.7 + - + +
1177 ARG* 3.5 6.5 + - - +
1187 ALA 3.4 0.2 - - - -
1197 PHE* 1.3 81.1 - - + +
1217 GLU* 1.3 63.3 + - - +
1227 TRP 3.2 0.7 - - - -
1237 PHE* 3.1 10.0 + - + +
1247 ILE* 3.0 32.9 + - + +
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Residues in contact with GLU 121 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1170 ARG 5.0 0.5 - - - +
1180 ALA* 3.7 27.5 - - - +
1210 GLU* 4.2 22.2 - - + +
1177 ARG* 2.9 37.9 + - - +
1187 ALA 3.4 16.6 - - - +
1197 PHE 3.1 0.6 - - - -
1207 LEU* 1.3 77.8 - - - +
1227 TRP* 1.3 61.0 + - - +
1247 ILE* 3.4 10.3 + - - +
1257 ASN* 3.2 39.2 + - - +
121Z GLU* 4.3 16.0 - - + +
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Residues in contact with TRP 122 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537 HIS* 3.6 34.1 - + - -
567 ARG* 3.4 51.8 - - - +
1187 ALA 4.5 1.0 + - - +
1197 PHE* 3.5 13.5 + - + +
1207 LEU 3.2 0.2 - - - -
1217 GLU* 1.3 79.4 - - - +
1237 PHE* 1.3 81.5 + + + +
1257 ASN* 3.6 6.1 + - - +
1267 GLU* 3.0 44.5 + - + +
11737 AG 4.1 4.9 - - - -
170P MET* 4.2 23.1 - - + -
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Residues in contact with PHE 123 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177 GLU* 4.3 7.4 - - - -
537 HIS* 3.5 36.1 - - + -
567 ARG* 3.7 15.7 - - + -
577 PHE* 3.5 32.3 - + - -
1017 ILE* 4.0 22.2 - - + -
1197 PHE* 3.5 43.1 - + - -
1207 LEU* 3.1 11.9 + - - +
1227 TRP* 1.3 95.6 - + + +
1247 ILE* 1.3 59.4 + - - +
1267 GLU* 3.3 20.9 - - - -
1277 GLN* 2.9 35.7 + - - +
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Residues in contact with ILE 124 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1140 TYR* 3.5 42.0 - - + +
1150 SER* 3.8 11.1 + - - +
1180 ALA* 3.8 10.3 - - + -
1017 ILE* 3.8 19.3 - - + -
1027 TYR* 4.5 7.6 - - + -
1057 ALA* 4.4 9.9 - - + -
1177 ARG* 3.4 37.9 - - - +
1207 LEU 3.0 14.6 + - - +
1217 GLU* 3.4 13.4 + - - +
1237 PHE* 1.3 78.0 - - - +
1257 ASN* 1.3 61.4 + - - +
1277 GLN* 3.5 4.3 + - - +
1287 VAL* 3.3 23.3 + - - +
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Residues in contact with ASN 125 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1150 SER 4.9 1.2 - - - +
1180 ALA* 3.4 33.4 + - - +
1190 PHE* 4.1 4.2 + - - +
1217 GLU* 3.2 31.6 + - - +
1227 TRP* 3.9 6.0 - - - +
1247 ILE* 1.3 74.2 - - - +
1267 GLU* 1.3 64.2 + - - +
1287 VAL* 3.4 21.8 + - - +
1297 GLU* 3.6 10.8 + - - +
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Residues in contact with GLU 126 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537 HIS* 3.1 30.1 - - - +
1227 TRP* 3.0 35.6 + - + +
1237 PHE* 3.3 31.3 - - - +
1247 ILE 3.4 0.2 - - - -
1257 ASN* 1.3 76.0 - - - +
1277 GLN* 1.3 85.9 + - - +
1297 GLU* 3.3 10.1 + - - +
1307 GLU* 3.0 42.5 + - + +
11737 AG 3.8 6.3 - - - -
170P MET* 4.2 13.9 - - + +
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Residues in contact with GLN 127 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640 ARG* 5.2 1.1 - - - -
177 GLU* 4.9 4.4 + - - -
507 GLU* 5.0 4.6 + - - -
537 HIS* 4.9 2.4 - - - -
947 GLU* 2.9 31.6 + - - +
977 ILE* 3.7 26.2 - - + +
987 SER* 3.3 25.7 + - - +
1017 ILE* 4.5 12.3 - - + -
1027 TYR* 6.0 1.1 - - + +
1237 PHE* 2.9 21.7 + - + +
1247 ILE* 4.0 5.4 - - - +
1257 ASN 3.3 0.2 - - - -
1267 GLU* 1.3 99.2 + - - +
1287 VAL* 1.3 59.8 + - - +
1307 GLU* 3.8 5.3 + - - +
1317 GLU* 3.1 34.1 + - - +
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Residues in contact with VAL 128 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600 TYR* 4.1 17.0 - - + -
630 ASP* 4.1 18.9 - - + +
640 ARG* 3.9 29.8 + - - +
1150 SER* 3.8 31.9 - - - +
1247 ILE 3.3 17.5 - - - +
1257 ASN* 3.5 12.8 - - - +
1267 GLU 3.2 0.8 - - - -
1277 GLN* 1.3 77.8 - - - +
1297 GLU* 1.3 63.0 + - + +
1317 GLU* 4.1 1.9 - - - +
1327 ALA* 3.2 22.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU 129 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630 ASP* 5.7 5.6 - - - +
1257 ASN 3.6 9.3 + - - +
1267 GLU* 3.3 10.6 + - - +
1287 VAL* 1.3 78.9 - - + +
1307 GLU* 1.3 58.5 + - + +
1327 ALA* 3.3 5.7 + - - +
1337 SER* 2.8 31.8 + - - -
170P MET* 3.7 25.5 - - + +
----------------------------------------------------------
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Residues in contact with GLU 130 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467 GLN* 2.7 32.5 + - - +
497 GLU* 4.6 1.9 - - - +
507 GLU* 3.1 18.3 - - - +
537 HIS* 3.6 12.3 - - - -
947 GLU* 3.1 28.5 - - - +
1267 GLU* 3.0 40.9 + - + +
1277 GLN* 3.9 7.1 + - - +
1297 GLU* 1.3 77.6 - - + +
1317 GLU* 1.3 60.0 + - - +
1337 SER* 3.4 6.3 + - - -
1347 VAL* 3.1 31.2 + - - +
1617 ARG* 5.6 0.2 + - - -
11737 AG 4.1 4.5 - - - -
170P MET* 5.4 1.6 - - - +
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Residues in contact with GLU 131 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10 MET 5.5 3.5 + - - -
630 ASP 5.3 2.7 - - - +
640 ARG* 3.9 23.3 + - - +
917 TYR* 3.7 21.8 + - + -
947 GLU* 3.5 25.7 - - + +
957 LYS* 3.8 21.3 - - - +
987 SER* 2.7 33.0 + - - +
1027 TYR* 5.0 1.0 + - - -
1277 GLN 3.1 19.0 + - - +
1287 VAL 4.1 3.4 - - - +
1307 GLU* 1.3 75.8 - - - +
1327 ALA* 1.3 58.4 + - - +
1347 VAL* 3.3 1.3 + - - -
1357 LYS* 2.8 32.9 + - - +
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Residues in contact with ALA 132 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620 TYR 5.3 0.9 - - - +
630 ASP* 3.6 41.4 + - - +
1287 VAL 3.2 17.4 + - - +
1297 GLU* 3.8 5.2 - - - +
1317 GLU* 1.3 79.0 - - - +
1337 SER* 1.3 60.1 + - - +
1357 LYS* 4.2 5.7 - - - +
1367 LYS* 3.2 25.3 + - - +
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Residues in contact with SER 133 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427 TRP* 3.6 20.8 - - - -
467 GLN* 5.2 2.6 + - - -
1297 GLU 2.8 18.8 + - - -
1307 GLU* 3.5 9.0 - - - -
1327 ALA* 1.3 78.3 - - - +
1347 VAL* 1.3 63.2 + - - +
1367 LYS* 3.6 10.5 - - - +
1377 ILE* 3.6 22.0 - - - +
1617 ARG* 5.2 1.2 + - - -
----------------------------------------------------------
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Residues in contact with VAL 134 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247 TYR* 4.8 7.2 - - + +
427 TRP* 4.2 20.4 - - + -
467 GLN* 5.8 2.5 - - - +
877 PHE* 3.9 22.3 - - + +
907 ALA* 4.0 10.8 - - + -
917 TYR* 3.7 36.1 - - + +
947 GLU* 4.0 19.5 - - + -
1307 GLU* 3.1 18.4 + - - +
1317 GLU 4.0 2.9 - - - +
1337 SER* 1.3 74.3 - - - +
1357 LYS* 1.3 60.1 + - - +
1377 ILE* 3.3 3.1 + - - -
1387 LEU* 3.0 25.1 + - - +
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Residues in contact with LYS 135 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10 MET* 5.0 4.0 - - - -
650 ASN* 3.9 36.8 + - + +
917 TYR* 3.5 44.1 - - + +
1317 GLU 2.8 19.5 + - - +
1327 ALA* 4.2 5.8 - - - +
1347 VAL* 1.3 76.2 - - - +
1367 LYS* 1.3 57.4 + - - +
1387 LEU* 3.2 15.9 + - + +
1397 ASP* 2.7 74.3 + - - +
1427 LYS* 5.3 4.6 - - - +
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Residues in contact with LYS 136 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1327 ALA 3.2 20.5 + - - +
1337 SER* 3.6 9.4 - - - +
1347 VAL 3.3 0.2 - - - -
1357 LYS* 1.3 77.2 - - - +
1377 ILE* 1.3 64.9 + - + +
1397 ASP* 3.6 7.9 + - - +
1407 LYS* 3.4 52.2 + - + +
35I GLY* 6.1 1.3 - - - +
37I GLU* 3.0 42.5 + - + +
----------------------------------------------------------
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Residues in contact with ILE 137 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397 PHE* 4.3 6.5 - - + -
427 TRP* 3.6 38.8 - - + +
877 PHE* 3.7 31.6 - - + -
1337 SER* 3.6 13.2 - - - +
1347 VAL 3.3 2.7 + - - +
1357 LYS 3.3 0.2 - - - -
1367 LYS* 1.3 80.2 - - + +
1387 LEU* 1.3 65.7 + - - +
1407 LYS* 3.3 10.3 + - + +
1417 LEU* 3.1 24.7 + - + +
1547 LEU* 4.2 14.1 - - + -
1587 LEU* 3.8 32.3 - - + -
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Residues in contact with LEU 138 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847 LEU* 3.8 2.7 - - + +
877 PHE* 3.4 39.6 - - + +
887 GLU* 3.7 24.2 - - + -
917 TYR* 3.6 28.5 - - + -
1347 VAL 3.0 13.5 + - - +
1357 LYS* 3.2 17.0 + - + +
1377 ILE* 1.3 76.7 - - - +
1397 ASP* 1.3 63.6 + - - +
1417 LEU* 3.2 6.1 + - - +
1427 LYS* 3.0 55.3 + - + +
----------------------------------------------------------
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Residues in contact with ASP 139 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650 ASN* 4.7 3.8 - - - +
1357 LYS* 2.7 53.2 + - - +
1367 LYS* 3.9 7.3 - - - +
1377 ILE 3.3 0.2 - - - -
1387 LEU* 1.3 76.5 - - - +
1407 LYS* 1.3 59.1 + - + +
1427 LYS* 3.4 20.0 + - - +
1437 PHE* 3.0 24.8 + - - +
34I LEU 6.0 1.1 - - - +
35I GLY* 6.0 6.3 - - - -
----------------------------------------------------------
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Residues in contact with LYS 140 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1367 LYS* 3.4 45.2 + - + +
1377 ILE* 3.3 13.9 + - + +
1387 LEU 3.2 0.6 - - - -
1397 ASP* 1.3 77.9 - - + +
1417 LEU* 1.3 59.3 + - - +
1437 PHE* 3.3 23.8 + - + +
1447 ALA* 3.5 10.0 + - - +
1507 ILE* 5.0 2.2 - - + +
1547 LEU* 3.8 34.6 - - + +
1577 GLU* 4.1 16.0 + - - -
35I GLY 4.7 14.6 - - - +
37I GLU* 6.5 0.2 - - - -
152I PHE* 4.6 21.4 - - + -
155I ASP* 5.9 3.3 + - - -
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Residues in contact with LEU 141 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397 PHE* 3.9 18.8 - - + -
837 PRO* 3.4 31.0 - - + +
847 LEU* 3.8 20.9 - - + +
877 PHE* 3.6 30.1 - - + -
1377 ILE* 3.1 18.9 + - + +
1387 LEU* 3.2 6.9 + - - +
1407 LYS* 1.3 72.8 - - - +
1427 LYS* 1.3 63.7 + - - +
1437 PHE 3.2 1.5 + - - -
1447 ALA* 3.6 21.1 + - - +
1457 LYS* 3.9 5.5 + - - +
1517 LEU* 3.8 29.4 - - + -
1547 LEU* 4.1 9.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 142 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847 LEU* 3.6 20.0 - - + -
887 GLU* 4.2 13.7 - - - -
1357 LYS* 5.3 4.0 - - - +
1387 LEU* 3.0 31.0 + - + +
1397 ASP* 3.5 20.7 + - - +
1417 LEU* 1.3 75.4 - - - +
1437 PHE* 1.3 63.0 + - - +
1447 ALA 3.3 0.2 - - - -
1457 LYS* 3.3 36.2 - - - +
----------------------------------------------------------
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Residues in contact with PHE 143 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1397 ASP 3.0 13.7 + - - +
1407 LYS* 3.3 19.3 - - + +
1417 LEU 3.2 0.4 - - - -
1427 LYS* 1.3 78.8 - - - +
1447 ALA* 1.3 54.9 + - - +
1457 LYS 3.8 0.6 + - - -
1507 ILE* 4.5 16.8 - - + +
34I LEU 5.5 7.9 - - - -
36I LEU* 5.3 9.4 - - + -
148I PRO* 3.7 42.5 - - + +
151I LEU* 3.8 29.6 - - + -
152I PHE* 4.6 15.7 - + + -
----------------------------------------------------------
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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