Contacts of the helix formed by residues 1288 - 1309 (chain B) in PDB entry 1XTB
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 GLY1288 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136B ARG* 3.2 27.3 - - - +
1284B ALA 2.7 25.6 + - - +
1286B HIS 3.6 0.2 - - - -
1287B VAL* 1.3 79.6 - - - +
1289B PHE* 1.3 65.6 + - - -
1290B ASP* 3.4 2.7 - - - -
1291B ASN 3.4 0.2 + - - -
1292B PHE* 3.2 18.4 + - - +
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Residues in contact with PHE1289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125B LEU* 3.2 46.9 - - + -
1128B MET* 3.6 12.1 - - + -
1129B LYS* 3.4 60.1 - - + -
1132B CYS* 4.3 9.5 - - + +
1133B GLN* 6.3 0.2 - - + -
1136B ARG* 5.5 0.2 - - - +
1284B ALA* 3.9 19.1 + - + -
1288B GLY* 1.3 69.7 - - - -
1290B ASP* 1.3 61.2 + - - +
1292B PHE* 3.1 18.8 + + - +
1293B GLU* 2.8 61.6 + - + +
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Residues in contact with ASP1290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1129B LYS* 4.5 16.5 + - - -
1288B GLY* 3.4 0.8 - - - -
1289B PHE* 1.3 75.6 - - - +
1291B ASN* 1.3 67.6 + - - +
1293B GLU* 3.3 14.9 + - - +
1294B GLN* 3.0 26.8 + - + +
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Residues in contact with ASN1291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1170B LEU* 5.6 0.6 - - - +
1173B TYR* 3.4 34.1 - - - +
1287B VAL* 2.9 38.8 - - + +
1288B GLY 3.4 1.4 + - - -
1289B PHE 3.2 0.2 - - - -
1290B ASP* 1.3 80.9 - - - +
1292B PHE* 1.3 60.6 + - - +
1294B GLN* 3.1 13.5 + - - +
1295B LEU* 2.9 24.4 + - - +
1483B PRO* 3.5 24.9 - - + +
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Residues in contact with PHE1292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125B LEU* 3.9 14.8 - - + -
1128B MET* 4.1 13.9 - - + -
1275B LEU 3.9 19.3 - - - -
1276B TRP 4.0 17.5 - - - -
1277B SER 4.1 8.1 - - - -
1280B GLY* 3.9 12.8 - - - -
1283B ILE* 4.0 22.4 - - + -
1284B ALA* 4.2 11.0 - - + -
1287B VAL* 4.5 3.1 - - - +
1288B GLY 3.2 13.1 + - - +
1289B PHE* 3.1 33.5 + + - +
1291B ASN* 1.3 76.6 - - - +
1293B GLU* 1.3 57.5 + - - +
1295B LEU* 3.0 23.4 + - + +
1296B LEU* 3.0 49.3 + - + +
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Residues in contact with GLU1293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1105B ARG* 3.1 34.6 + - - +
1129B LYS* 5.0 9.4 + - - +
1289B PHE* 2.8 48.8 + - + +
1290B ASP* 3.7 15.7 - - - +
1292B PHE* 1.3 73.9 - - - +
1294B GLN* 1.3 58.3 + - - +
1296B LEU* 3.7 11.5 - - + +
1297B SER* 2.7 38.5 + - - +
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Residues in contact with GLN1294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047B HIS* 5.1 11.9 + - - +
1290B ASP 3.0 18.0 + - - +
1291B ASN* 3.1 18.6 + - - +
1293B GLU* 1.3 75.5 - - - +
1295B LEU* 1.3 61.1 + - - +
1297B SER* 3.2 8.9 + - - -
1298B GLY 2.9 24.8 + - - -
1483B PRO* 3.7 14.8 - - + -
1484B PHE* 3.2 37.8 - - - +
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Residues in contact with LEU1295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1166B VAL* 4.2 18.2 - - + -
1170B LEU* 4.6 4.3 - - + -
1275B LEU* 4.0 23.3 - - + -
1276B TRP* 3.3 19.5 - - + -
1283B ILE* 4.4 4.0 - - + -
1291B ASN 2.9 12.0 + - - +
1292B PHE* 3.2 32.3 - - + +
1294B GLN* 1.3 77.4 - - - +
1296B LEU* 1.3 62.2 + - - +
1298B GLY 3.3 8.7 + - - -
1299B ALA 3.3 9.0 + - - -
1483B PRO* 3.3 23.9 + - + +
1486B LEU* 4.3 19.7 - - + -
1487B GLY* 3.5 22.5 - - - +
1490B ILE* 4.7 3.4 - - + -
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Residues in contact with LEU1296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102B LEU 4.2 8.1 - - - +
1103B ARG* 3.5 24.0 - - + +
1105B ARG* 3.9 28.0 - - - +
1125B LEU* 3.9 14.4 - - + -
1276B TRP* 3.6 50.3 - - + +
1292B PHE* 3.0 41.9 + - + +
1293B GLU* 3.7 9.2 - - + +
1295B LEU* 1.3 75.8 - - - +
1297B SER* 1.3 58.5 + - - +
1299B ALA* 3.2 1.9 + - - +
1300B HIS* 2.9 25.1 + - - +
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Residues in contact with SER1297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105B ARG* 3.9 24.4 + - - +
1293B GLU* 2.7 26.1 + - - +
1294B GLN* 3.2 13.8 + - - -
1296B LEU* 1.3 78.1 - - - +
1298B GLY* 1.3 56.1 + - - +
1300B HIS* 3.2 3.3 + - - +
1301B TRP* 2.9 25.6 + - - +
1484B PHE* 3.5 19.3 - - - -
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Residues in contact with GLY1298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1294B GLN 2.9 10.9 + - - -
1295B LEU 3.3 2.0 + - - -
1296B LEU 3.2 0.2 - - - -
1297B SER* 1.3 78.1 - - - +
1299B ALA* 1.3 61.1 + - - +
1301B TRP* 3.3 5.0 + - - +
1302B MET 3.2 16.5 + - - -
1484B PHE* 3.1 40.8 - - - -
1488B ALA* 3.3 17.6 - - - +
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Residues in contact with ALA1299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103B ARG* 3.6 19.5 - - - +
1276B TRP* 3.4 37.5 - - + -
1295B LEU 3.3 3.8 + - - -
1296B LEU 3.2 5.9 + - - +
1298B GLY* 1.3 72.5 - - - +
1300B HIS* 1.3 61.3 + - - +
1302B MET* 3.1 4.2 + - - +
1303B ASP* 2.8 33.7 + - - +
1487B GLY 3.5 11.5 - - - +
1491B ALA* 3.7 7.8 - - + +
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Residues in contact with HIS1300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100B VAL 5.2 0.6 + - - -
1103B ARG* 3.1 26.2 + - - +
1104B ASN* 3.3 28.8 - - - -
1105B ARG* 3.8 21.8 - - + -
1106B SER* 2.8 25.6 + - - -
1296B LEU 2.9 9.3 + - - +
1297B SER* 3.5 8.1 - - - +
1299B ALA* 1.3 77.2 - - - +
1301B TRP* 1.3 64.0 + - - +
1303B ASP* 3.1 16.4 + - + +
1304B GLN* 2.9 51.1 + - + +
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Residues in contact with TRP1301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043B LEU* 3.9 29.6 - - + -
1044B ASN 3.7 19.4 + - - -
1045B THR* 3.8 34.7 + - + +
1046B ASN* 5.8 0.8 + - - -
1047B HIS* 5.9 0.2 - + - -
1050B ILE* 5.7 0.2 - - + -
1297B SER 2.9 13.1 + - - +
1298B GLY 3.4 10.1 - - - +
1299B ALA 3.2 0.2 - - - -
1300B HIS* 1.3 78.2 - - - +
1302B MET* 1.3 83.3 + - + +
1304B GLN* 3.1 17.4 + - + +
1305B HIS* 2.9 49.8 + + + -
1484B PHE* 3.6 21.5 - + + -
1488B ALA* 4.9 2.5 - - + -
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Residues in contact with MET1302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043B LEU* 4.2 12.8 - - + -
1050B ILE* 4.8 6.3 - - + -
1298B GLY 3.2 8.0 + - - +
1299B ALA 3.1 8.3 + - - +
1301B TRP* 1.3 97.7 - - + +
1303B ASP* 1.3 61.0 + - - +
1305B HIS* 3.1 22.3 + - - +
1306B PHE* 2.8 28.6 + - - +
1315B ALA* 5.3 0.2 - - + -
1316B PRO* 4.4 7.4 - - - -
1488B ALA* 3.7 28.3 - - + +
1491B ALA* 3.8 7.4 - - + +
1492B MET* 3.5 48.2 - - + +
1495B HIS* 4.5 4.5 - - + -
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Residues in contact with ASP1303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084B PHE* 3.9 18.2 - - + -
1100B VAL* 4.0 15.8 - - - +
1103B ARG* 2.6 43.9 + - - +
1299B ALA 2.8 19.0 + - - +
1300B HIS* 3.1 16.2 + - + +
1302B MET* 1.3 71.9 - - - +
1304B GLN* 1.3 58.3 + - + +
1306B PHE* 3.3 2.9 + - - +
1307B ARG* 3.0 29.6 + - - +
1491B ALA* 4.3 0.3 - - - +
1495B HIS* 2.6 35.8 + - - -
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Residues in contact with GLN1304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106B SER* 4.5 8.5 + - - -
1300B HIS* 2.9 45.4 + - + +
1301B TRP* 3.4 17.1 - - + +
1303B ASP* 1.3 75.2 - - + +
1305B HIS* 1.3 63.1 - - - +
1307B ARG* 4.6 4.3 - - - -
1308B THR* 2.8 39.9 + - + +
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Residues in contact with HIS1305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043B LEU* 3.4 32.1 - - + +
1301B TRP* 2.9 37.3 + + + +
1302B MET* 3.5 17.4 - - - +
1304B GLN* 1.3 76.2 - - - +
1306B PHE* 1.3 65.1 + - - +
1308B THR* 4.2 1.8 - - - -
1309B THR* 2.7 49.1 + - + +
1313B LYS 3.6 11.3 + - - -
1314B ASN* 3.8 7.4 - - - -
1315B ALA* 3.0 42.4 - - + -
1316B PRO* 4.0 3.0 - - + +
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Residues in contact with PHE1306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076B VAL* 5.0 4.9 - - + -
1080B ARG* 2.9 45.4 + - + -
1083B MET* 4.5 0.2 - - + -
1084B PHE* 4.0 11.0 - + - -
1302B MET 2.8 16.2 + - - +
1303B ASP 3.5 3.4 - - - +
1305B HIS* 1.3 79.5 + - - +
1307B ARG* 1.3 56.8 + - - +
1314B ASN* 2.8 39.0 + - - +
1316B PRO* 3.5 12.6 - - + -
1317B VAL* 3.9 12.1 - - + -
1495B HIS* 3.4 42.8 - + + -
1498B PHE* 3.8 27.4 - + - -
1499B VAL* 3.8 21.8 - - + -
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Residues in contact with ARG1307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080B ARG* 3.4 29.2 + - - +
1081B GLU* 3.0 37.9 + - - +
1084B PHE* 3.5 46.9 + - + +
1085B ASN* 3.4 25.3 + - - -
1108B THR* 5.8 1.8 + - - -
1303B ASP 3.0 16.6 + - - +
1304B GLN* 4.0 5.4 - - - +
1306B PHE* 1.3 79.4 - - - +
1308B THR* 1.3 64.7 + - + +
1309B THR 3.7 0.2 - - - -
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Residues in contact with THR1308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1304B GLN* 2.8 29.4 + - + +
1305B HIS* 4.2 1.2 - - - -
1307B ARG* 1.3 87.1 - - + +
1309B THR* 1.3 67.1 + - - +
1310B PRO* 3.9 5.7 - - - +
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Residues in contact with THR1309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077B GLU* 5.7 0.9 - - - +
1080B ARG* 4.4 6.2 + - - -
1305B HIS* 2.7 42.8 + - - +
1306B PHE 4.4 1.0 - - - +
1307B ARG 3.7 0.4 - - - -
1308B THR* 1.3 80.5 + - - +
1310B PRO* 1.3 82.3 - - + +
1311B LEU* 3.3 2.1 + - - +
1313B LYS* 3.3 36.3 - - + +
1314B ASN* 3.2 17.9 + - - -
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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) + - + + + + + -
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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