Contacts of the helix formed by residues 120 - 143 (chain 4) 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 120 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104 LEU* 5.0 0.9 - - + -
574 PHE* 4.1 24.5 - - + -
1014 ILE* 4.4 14.8 - - + +
1044 LEU* 3.7 58.3 - - + +
1054 ALA* 3.9 7.9 - - + +
1084 ALA* 4.7 0.7 - - + -
1164 THR* 3.0 34.3 + - + +
1174 ARG* 4.0 7.4 - - - +
1184 ALA 3.4 0.4 - - - -
1194 PHE* 1.3 77.9 - - + +
1214 GLU* 1.3 63.0 + - - +
1224 TRP 3.2 2.7 - - - -
1234 PHE* 3.1 9.6 + - + +
1244 ILE* 3.0 34.1 + - + +
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Residues in contact with GLU 121 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1174 ARG* 3.0 38.4 + - - +
1184 ALA 3.4 16.4 - - - +
1194 PHE 3.2 0.8 - - - -
1204 LEU* 1.3 78.0 - - - +
1224 TRP* 1.3 61.0 + - - +
1244 ILE* 3.6 5.6 + - - +
1254 ASN* 2.9 40.6 + - - +
1218 GLU* 4.5 15.0 - - - +
1179 ARG* 4.9 1.7 + - - +
1189 ALA* 3.6 31.5 - - - +
1219 GLU* 4.3 20.5 - - + +
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Residues in contact with TRP 122 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534 HIS* 3.5 35.4 - + - -
564 ARG* 3.4 52.1 - - - +
1184 ALA 4.6 0.8 + - - -
1194 PHE* 3.5 12.6 + - + +
1204 LEU 3.2 0.4 - - - -
1214 GLU* 1.3 78.8 - - - +
1234 PHE* 1.3 83.0 + + + +
1254 ASN* 3.5 4.9 + - - +
1264 GLU* 2.9 41.8 + - + +
11734 AG 4.0 5.4 - - - -
170M MET* 3.6 26.0 - - + +
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Residues in contact with PHE 123 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174 GLU* 4.1 8.5 - - - -
534 HIS* 3.7 19.3 - - + -
564 ARG* 3.7 25.6 - - + -
574 PHE* 3.4 36.6 - + - -
1014 ILE* 4.2 20.4 - - + -
1194 PHE* 3.4 42.0 - + - -
1204 LEU* 3.1 12.3 + - + +
1224 TRP* 1.3 98.7 - + + +
1244 ILE* 1.3 58.6 + - - +
1264 GLU* 3.2 20.9 - - - +
1274 GLN* 2.9 34.5 + - - +
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Residues in contact with ILE 124 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014 ILE* 3.8 18.2 - - + -
1024 TYR* 4.7 6.7 - - + -
1054 ALA* 4.4 11.7 - - + -
1174 ARG* 3.5 37.5 - - - +
1204 LEU* 3.0 17.5 + - + +
1214 GLU* 3.9 9.2 - - - +
1224 TRP 3.4 0.2 - - - -
1234 PHE* 1.3 77.6 - - - +
1254 ASN* 1.3 60.6 + - - +
1264 GLU 3.6 0.2 + - - -
1274 GLN* 3.7 4.7 + - - +
1284 VAL* 3.3 21.7 + - - +
1149 TYR* 3.4 43.7 - - + +
1159 SER* 3.8 11.5 + - - +
1189 ALA* 3.9 8.1 - - + -
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Residues in contact with ASN 125 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1214 GLU* 2.9 32.4 + - - +
1224 TRP* 3.8 4.9 - - - +
1244 ILE* 1.3 77.3 - - - +
1264 GLU* 1.3 63.1 + - - +
1274 GLN 3.4 0.2 - - - -
1284 VAL* 3.6 18.8 + - - +
1294 GLU* 3.9 8.5 + - - +
1159 SER 5.1 1.2 - - - +
1189 ALA* 3.6 38.1 + - - +
1199 PHE* 4.1 4.2 + - - +
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Residues in contact with GLU 126 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534 HIS* 3.2 22.2 - - - +
1224 TRP* 2.9 32.5 + - + +
1234 PHE* 3.2 31.8 + - - +
1254 ASN* 1.3 75.2 - - - +
1274 GLN* 1.3 85.6 + - - +
1284 VAL 3.2 0.7 - - - -
1294 GLU* 3.2 8.2 + - - +
1304 GLU* 3.0 39.2 + - + +
11734 AG 3.8 17.9 - - - -
170M MET* 4.0 15.4 - - + +
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Residues in contact with GLN 127 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174 GLU* 4.6 8.5 + - - -
504 GLU* 5.1 3.4 + - - -
944 GLU* 2.9 32.6 + - - +
974 ILE* 3.6 26.6 - - + +
984 SER* 3.3 30.4 + - - +
1014 ILE* 4.7 7.4 - - + -
1234 PHE 2.9 21.5 + - - +
1244 ILE* 4.1 5.6 - - - +
1254 ASN 3.4 0.2 - - - -
1264 GLU* 1.3 97.9 + - - +
1284 VAL* 1.3 60.0 + - - +
1304 GLU* 3.7 6.1 + - - +
1314 GLU* 2.9 35.5 + - - +
649 ARG* 5.3 0.9 - - - -
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Residues in contact with VAL 128 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1244 ILE 3.3 18.2 - - - +
1254 ASN* 3.7 12.6 - - - +
1264 GLU 3.2 0.2 - - - -
1274 GLN* 1.3 78.3 - - + +
1294 GLU* 1.3 62.4 + - + +
1314 GLU* 4.2 1.2 - - - +
1324 ALA* 3.3 23.2 + - - +
609 TYR* 4.1 17.0 - - + -
639 ASP* 4.1 20.1 - - + +
649 ARG* 4.0 27.6 - - - +
1159 SER* 3.8 30.5 - - - +
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Residues in contact with GLU 129 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254 ASN 3.9 6.4 + - - +
1264 GLU* 3.2 10.4 + - - +
1284 VAL* 1.3 78.5 - - + +
1304 GLU* 1.3 55.9 + - + +
1324 ALA* 3.4 5.1 + - - +
1334 SER* 2.8 37.1 + - - -
639 ASP* 5.7 6.1 - - - +
170M MET* 3.4 25.3 - - + +
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Residues in contact with GLU 130 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464 GLN* 2.8 37.5 + - - +
494 GLU* 4.5 1.9 - - - +
504 GLU* 3.4 6.9 - - - +
534 HIS* 3.7 12.6 - - - -
944 GLU* 3.2 33.7 - - - +
1264 GLU* 3.0 40.8 + - + +
1274 GLN* 3.7 8.3 - - - +
1284 VAL 3.4 0.4 - - - -
1294 GLU* 1.3 77.2 - - + +
1314 GLU* 1.3 60.7 + - - +
1334 SER* 3.5 6.5 + - - -
1344 VAL* 3.2 30.3 + - - +
11734 AG 4.0 4.5 - - - -
170M MET* 5.5 2.9 - - + +
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Residues in contact with GLU 131 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914 TYR* 4.0 19.1 + - + -
944 GLU* 3.9 25.5 - - + +
954 LYS* 4.0 22.2 - - - +
984 SER* 2.7 31.8 + - - +
1024 TYR* 5.0 0.9 + - - -
1274 GLN 2.9 20.2 + - - +
1284 VAL* 4.2 3.6 - - - +
1304 GLU* 1.3 73.4 - - - +
1324 ALA* 1.3 61.9 + - - +
1344 VAL* 3.2 2.9 + - - +
1354 LYS* 2.8 33.6 + - - +
19 MET 5.5 4.3 + - - -
639 ASP 5.4 2.7 - - - +
649 ARG* 3.9 22.5 + - - +
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Residues in contact with ALA 132 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1284 VAL 3.3 18.4 + - - +
1294 GLU* 3.8 4.5 - - - +
1314 GLU* 1.3 77.9 - - - +
1334 SER* 1.3 57.3 + - - +
1354 LYS* 4.1 6.3 - - - -
1364 LYS* 3.2 29.1 + - - +
629 TYR 5.3 0.9 - - - +
639 ASP* 3.6 40.5 + - - +
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Residues in contact with SER 133 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424 TRP* 3.6 20.6 - - - -
464 GLN* 5.1 3.9 + - - -
1294 GLU 2.8 18.5 + - - -
1304 GLU* 3.6 8.3 - - - -
1314 GLU 3.1 0.2 - - - -
1324 ALA* 1.3 78.8 - - - +
1344 VAL* 1.3 62.0 + - - +
1364 LYS* 3.8 8.9 - - - +
1374 ILE* 3.5 23.7 - - - +
1614 ARG* 5.2 0.7 + - - -
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Residues in contact with VAL 134 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244 TYR* 4.8 7.2 - - + +
424 TRP* 4.4 17.3 - - + -
434 MET* 6.6 0.2 - - + -
464 GLN* 5.5 3.1 - - - +
874 PHE* 3.8 27.8 - - + +
904 ALA* 4.2 7.0 - - + -
914 TYR* 3.8 35.2 - - + +
944 GLU* 4.1 19.3 - - + -
1304 GLU* 3.2 19.0 + - - +
1314 GLU 3.2 4.1 + - - +
1334 SER* 1.3 76.1 - - - +
1354 LYS* 1.3 59.5 + - - +
1374 ILE* 3.3 3.5 + - - -
1384 LEU* 3.0 24.3 + - - +
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Residues in contact with LYS 135 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914 TYR* 3.6 42.3 - - + +
1314 GLU 2.8 24.0 + - - +
1324 ALA* 4.3 5.4 - - - +
1344 VAL* 1.3 70.6 - - - +
1364 LYS* 1.3 60.1 + - - +
1384 LEU* 3.5 12.6 - - + +
1394 ASP* 2.8 72.6 + - - +
1424 LYS* 5.5 4.4 - - - +
659 ASN* 3.5 39.8 + - + +
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Residues in contact with LYS 136 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1324 ALA 3.2 21.7 + - - +
1334 SER* 3.8 8.3 - - - +
1344 VAL 3.3 0.4 - - - -
1354 LYS* 1.3 77.5 - - - +
1374 ILE* 1.3 63.1 + - + +
1394 ASP* 3.7 7.1 + - - +
1404 LYS* 3.4 51.7 + - - +
35R GLY 6.1 0.9 - - - +
37R GLU* 3.1 41.6 + - - +
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Residues in contact with ILE 137 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394 PHE* 4.3 8.3 - - + -
424 TRP* 3.5 37.9 - - + +
874 PHE* 3.7 35.0 - - + -
1334 SER 3.5 13.9 + - - +
1344 VAL 3.3 1.9 + - - +
1354 LYS 3.3 0.2 - - - -
1364 LYS* 1.3 77.8 - - + +
1384 LEU* 1.3 61.5 + - - +
1404 LYS* 3.1 10.4 + - + +
1414 LEU* 2.9 31.4 + - + +
1544 LEU* 4.8 10.5 - - + -
1584 LEU* 3.9 31.2 - - + -
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Residues in contact with LEU 138 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844 LEU* 3.8 3.9 - - + +
874 PHE* 3.4 37.1 - - + +
884 GLU* 3.7 25.4 - - + -
914 TYR* 3.6 27.8 - - + -
1344 VAL 3.0 12.6 + - - +
1354 LYS* 3.2 15.2 + - + +
1374 ILE* 1.3 77.1 - - - +
1394 ASP* 1.3 63.8 + - - +
1414 LEU* 3.1 9.8 + - - +
1424 LYS* 3.0 52.8 + - + +
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Residues in contact with ASP 139 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1354 LYS* 2.8 58.1 + - - +
1364 LYS* 4.0 6.5 - - - +
1384 LEU* 1.3 82.7 - - - +
1404 LYS* 1.3 58.9 + - + +
1424 LYS* 3.5 16.1 + - - +
1434 PHE* 3.1 24.6 + - - +
659 ASN* 4.5 3.6 - - - +
34R LEU 6.0 1.8 - - - +
35R GLY* 6.1 5.2 - - - -
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Residues in contact with LYS 140 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1364 LYS* 3.4 42.8 + - - +
1374 ILE* 3.1 14.6 + - + +
1394 ASP* 1.3 76.5 - - + +
1414 LEU* 1.3 58.0 + - - +
1424 LYS 3.4 0.2 - - - -
1434 PHE* 3.3 24.0 - - + +
1444 ALA* 3.3 14.2 + - - +
1504 ILE* 4.9 1.3 - - + +
1544 LEU* 3.8 35.5 - - + +
1574 GLU* 3.9 18.0 + - - -
35R GLY* 4.7 15.7 - - - +
152R PHE* 4.6 18.0 - - + -
155R ASP* 5.7 5.2 + - - -
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Residues in contact with LEU 141 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394 PHE* 4.1 13.2 - - + -
834 PRO* 3.4 33.9 - - + +
844 LEU* 3.8 26.7 - - + +
874 PHE* 3.6 31.0 - - + -
1374 ILE* 2.9 21.2 + - + +
1384 LEU* 3.1 8.2 + - - +
1404 LYS* 1.3 76.3 - - - +
1424 LYS* 1.3 61.9 + - - +
1434 PHE 3.2 0.4 - - - -
1444 ALA* 3.2 24.9 - - + +
1454 LYS* 3.9 1.2 + - - -
1514 LEU* 3.9 28.9 - - + -
1544 LEU* 4.2 8.7 - - + -
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Residues in contact with LYS 142 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844 LEU* 3.7 17.9 - - + -
884 GLU* 4.4 11.7 - - - -
1354 LYS* 5.5 3.6 - - - +
1384 LEU* 3.0 31.7 + - + +
1394 ASP* 3.6 18.7 + - - +
1414 LEU* 1.3 74.7 - - - +
1434 PHE* 1.3 62.1 + - - +
1444 ALA 3.1 2.6 + - - -
1454 LYS* 3.4 33.4 - - - +
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Residues in contact with PHE 143 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1394 ASP 3.1 14.7 + - - +
1404 LYS* 3.3 18.8 - - + +
1424 LYS* 1.3 75.1 - - - +
1444 ALA* 1.3 56.6 + - - +
1454 LYS 3.9 1.0 + - - -
1504 ILE* 4.1 18.0 - - + +
34R LEU 5.4 9.2 - - - -
36R LEU* 5.1 11.4 - - + -
148R PRO* 3.4 42.4 - - + +
151R LEU* 3.7 31.4 - - + -
152R PHE* 4.3 17.5 - + + -
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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