Contacts of the helix formed by residues 1383 - 1404 (chain G) in PDB entry 5TJ4
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 ASP1383 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G SER* 6.6 0.4 - - - -
1369G ASN* 3.9 19.7 + - - +
1382G TYR* 1.3 94.8 - - - +
1384G PRO* 1.4 78.3 - - - +
1385G GLU* 3.0 20.4 + - - +
1386G ALA* 3.8 16.2 + - + +
1387G ARG* 3.7 13.5 + - - +
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Residues in contact with PRO1384 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1226G ILE* 4.1 31.6 - - + +
1229G ARG* 6.0 4.7 - - + -
1382G TYR* 4.0 18.3 - - + +
1383G ASP* 1.4 92.3 - - - +
1385G GLU* 1.3 64.3 + - + +
1386G ALA 3.3 0.2 - - - -
1387G ARG* 3.3 14.6 + - + +
1388G ILE* 3.2 26.6 + - + +
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Residues in contact with GLU1385 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G GLN* 4.8 8.7 - - - +
73G SER* 5.7 6.5 - - - +
1223G GLY 4.9 2.0 - - - +
1224G LEU* 4.7 25.6 - - + -
1226G ILE* 4.2 20.9 - - + -
1369G ASN* 5.3 3.6 - - - +
1383G ASP* 3.0 14.2 + - - +
1384G PRO* 1.3 80.8 - - + +
1386G ALA* 1.3 62.1 + - - +
1388G ILE* 3.5 4.6 + - - +
1389G LEU* 3.2 38.3 + - + +
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Residues in contact with ALA1386 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1369G ASN* 4.0 31.5 + - - +
1372G GLU* 4.8 12.6 - - - +
1383G ASP* 3.8 16.3 + - + +
1384G PRO 3.3 0.2 - - - -
1385G GLU* 1.3 75.5 - - - +
1387G ARG* 1.3 65.3 + - - +
1388G ILE 3.1 2.0 + - - -
1389G LEU* 3.3 6.4 + - - +
1390G CYS* 3.0 30.8 + - - -
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Residues in contact with ARG1387 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1338G GLU* 3.7 26.9 - - + +
1382G TYR* 4.1 18.2 - - + +
1383G ASP 3.7 10.4 + - - +
1384G PRO* 3.3 12.7 + - + +
1386G ALA* 1.3 77.7 - - - +
1388G ILE* 1.3 62.1 + - + +
1390G CYS* 3.6 6.8 - - - +
1391G ALA* 3.3 20.3 + - - +
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Residues in contact with ILE1388 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1223G GLY* 3.8 22.2 - - - +
1226G ILE* 4.3 10.3 - - + -
1229G ARG* 3.2 51.4 - - + +
1338G GLU* 4.8 13.5 - - - +
1339G LEU* 4.4 9.4 - - + -
1342G GLU* 3.8 19.1 - - - +
1384G PRO* 3.2 18.8 + - + +
1385G GLU 3.7 5.6 - - - +
1386G ALA 3.1 0.6 - - - -
1387G ARG* 1.3 75.2 - - + +
1389G LEU* 1.3 64.3 + - + +
1390G CYS 3.1 1.6 - - - -
1391G ALA* 3.1 8.7 + - - +
1392G LEU* 2.8 28.8 + - + +
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Residues in contact with LEU1389 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220G MET* 4.7 17.9 - - + +
1223G GLY* 4.6 21.1 - - - +
1224G LEU* 5.3 7.4 - - + -
1362G VAL* 3.8 8.2 - - + +
1365G VAL* 4.1 33.2 - - + +
1366G MET* 3.4 21.8 - - + +
1369G ASN* 5.1 8.3 - - - +
1385G GLU* 3.2 28.8 + - + +
1386G ALA* 3.3 5.1 + - - +
1388G ILE* 1.3 78.5 - - - +
1390G CYS* 1.3 57.7 + - - +
1392G LEU* 3.3 19.7 + - + +
1393G TYR* 2.8 25.6 + - - +
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Residues in contact with CYS1390 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1249G MET* 4.4 36.3 - - + -
1366G MET* 3.4 19.3 - - - +
1372G GLU* 4.1 20.0 - - - -
1386G ALA* 3.0 21.9 + - - +
1387G ARG* 3.6 7.0 - - - +
1389G LEU* 1.3 72.1 - - - +
1391G ALA* 1.3 61.6 + - - +
1393G TYR* 3.1 4.6 + - - +
1394G VAL* 2.8 34.8 + - - +
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Residues in contact with ALA1391 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1335G ALA* 3.4 36.3 - - + +
1338G GLU* 3.6 23.8 - - + -
1339G LEU* 3.7 5.8 - - + -
1387G ARG 3.3 5.3 + - - +
1388G ILE 3.1 8.4 + - - +
1390G CYS* 1.3 78.7 - - - +
1392G LEU* 1.3 58.8 + - - +
1394G VAL* 3.2 3.5 + - - +
1395G VAL* 2.8 34.9 + - - +
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Residues in contact with LEU1392 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370G ALA* 4.5 18.2 - - + +
1220G MET* 4.5 13.7 - - + -
1223G GLY* 5.2 4.7 - - - -
1339G LEU* 3.5 20.3 - - + +
1342G GLU* 4.5 10.3 - - + -
1346G VAL* 3.6 31.4 - - + -
1358G LEU* 5.1 4.5 - - + -
1362G VAL* 4.0 26.9 - - + -
1388G ILE* 2.8 16.9 + - + +
1389G LEU* 3.6 17.9 - - + +
1391G ALA* 1.3 73.1 - - - +
1393G TYR* 1.3 65.2 + - - +
1395G VAL* 3.7 0.7 - - - +
1396G VAL* 2.9 33.3 + - + +
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Residues in contact with TYR1393 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1249G MET* 6.5 0.7 - - + -
1253G LEU* 3.7 27.4 - - + +
1359G LYS* 3.8 31.2 - - + +
1362G VAL* 3.8 21.3 - - + +
1363G LYS* 4.2 19.1 - - + +
1366G MET* 3.5 24.9 - - + -
1389G LEU 2.8 21.4 + - - +
1390G CYS* 3.1 4.7 + - - +
1392G LEU* 1.3 73.3 - - - +
1394G VAL* 1.3 56.5 + - + +
1396G VAL* 3.9 3.5 - - - +
1397G SER* 2.5 45.1 + - - -
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Residues in contact with VAL1394 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1249G MET* 4.4 24.0 - - + -
1253G LEU* 4.1 23.6 - - + -
1256G MET* 4.2 19.1 - - + -
1331G ASP 5.1 0.4 - - - +
1332G PHE* 4.9 2.5 - - - -
1335G ALA* 4.0 18.4 - - + -
1390G CYS 2.8 23.2 + - - +
1391G ALA* 3.5 8.1 - - - +
1393G TYR* 1.3 73.9 - - + +
1395G VAL* 1.3 67.6 + - - +
1397G SER* 3.1 2.3 + - - -
1398G ILE* 2.9 38.7 + - + +
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Residues in contact with VAL1395 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1279G LEU* 4.6 0.7 - - + -
1332G PHE* 3.7 22.6 - - + +
1335G ALA* 4.1 5.4 - - + -
1336G LEU* 3.7 37.0 - - + +
1339G LEU* 3.7 27.6 - - + -
1346G VAL* 4.2 10.5 - - + -
1391G ALA 2.8 22.6 + - - +
1392G LEU 3.7 3.1 - - - +
1394G VAL* 1.3 73.0 - - - +
1396G VAL* 1.3 64.5 + - - +
1399G LEU* 3.1 42.0 + - + +
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Residues in contact with VAL1396 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1346G VAL* 4.3 7.0 - - + -
1355G LEU* 3.9 27.0 - - + +
1358G LEU* 3.8 25.6 - - + -
1359G LYS* 3.7 33.4 - - + +
1362G VAL* 5.0 2.0 - - + -
1392G LEU* 2.9 35.4 + - + +
1393G TYR* 3.9 4.7 - - - +
1395G VAL* 1.3 75.1 - - - +
1397G SER* 1.3 55.3 + - - +
1399G LEU* 3.2 6.9 + - - +
1400G LEU* 2.8 33.2 + - + +
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Residues in contact with SER1397 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253G LEU* 3.9 19.5 - - - -
1257G GLU* 3.9 14.0 - - - +
1359G LYS* 3.9 18.3 - - - +
1393G TYR* 2.5 51.4 + - - -
1394G VAL 3.7 3.1 - - - -
1396G VAL* 1.3 72.3 - - - +
1398G ILE* 1.3 57.2 + - - +
1400G LEU* 3.4 3.3 + - - +
1401G GLU* 2.8 30.1 + - - +
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Residues in contact with ILE1398 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253G LEU* 3.9 12.6 - - + -
1256G MET* 3.8 46.2 - - + -
1257G GLU* 4.1 13.5 - - + +
1260G LEU* 3.7 26.7 - - + -
1275G LEU* 4.6 2.7 - - + -
1332G PHE* 3.6 29.2 - - + -
1394G VAL* 2.9 23.3 + - + +
1397G SER* 1.3 73.2 - - - +
1399G LEU* 1.3 59.8 + - - +
1401G GLU* 3.2 5.9 + - + +
1402G LEU* 2.9 37.4 + - + +
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Residues in contact with LEU1399 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272G LEU* 3.5 26.9 - - + +
1275G LEU* 4.6 11.9 - - + -
1276G ALA 5.0 2.5 - - - +
1279G LEU* 4.4 13.0 - - + -
1332G PHE* 4.1 18.4 - - + -
1346G VAL* 3.5 32.1 - - + -
1350G LEU* 4.3 13.2 - - + -
1355G LEU* 4.0 14.7 - - + +
1395G VAL* 3.1 30.6 + - + +
1396G VAL* 3.7 3.4 - - - +
1398G ILE* 1.3 78.6 - - - +
1400G LEU* 1.3 53.2 + - - +
1402G LEU* 3.7 5.0 - - - +
1403G ALA* 2.7 35.2 + - - +
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Residues in contact with LEU1400 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1355G LEU* 3.6 32.0 - - + +
1356G PRO* 3.6 32.8 - - + -
1359G LYS* 3.7 28.7 - - + -
1396G VAL* 2.8 21.0 + - + +
1397G SER* 3.5 5.6 - - - +
1399G LEU* 1.3 69.9 - - - +
1401G GLU* 1.3 67.7 + - - +
1403G ALA* 3.2 15.2 + - + +
1404G GLU 3.5 1.0 + - - -
1405G GLY* 3.4 17.8 + - - +
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Residues in contact with GLU1401 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1257G GLU* 4.3 23.3 - - + +
1260G LEU* 5.7 7.4 - - + -
1268G ARG* 4.5 9.0 + - - -
1397G SER 2.8 20.6 + - - +
1398G ILE* 3.5 9.0 - - + +
1400G LEU* 1.3 72.5 - - - +
1402G LEU* 1.3 58.9 + - + +
1404G GLU 3.1 27.5 - - - +
1405G GLY* 3.5 9.8 - - - -
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Residues in contact with LEU1402 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1260G LEU* 4.0 28.3 - - + -
1263G LEU* 5.5 1.1 - - + -
1268G ARG* 3.9 47.2 - - + +
1269G LYS* 5.9 0.2 - - - -
1271G VAL* 3.7 28.7 - - + -
1272G LEU* 3.8 31.1 - - + +
1275G LEU* 3.9 17.9 - - + -
1398G ILE* 2.9 23.5 + - + +
1399G LEU* 3.7 4.7 - - - +
1401G GLU* 1.3 72.9 - - - +
1403G ALA* 1.3 54.1 + - - +
1404G GLU* 2.6 19.0 + - - -
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Residues in contact with ALA1403 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272G LEU* 3.5 16.1 - - + +
1350G LEU* 4.6 5.2 - - + +
1355G LEU* 4.5 10.8 - - + -
1399G LEU 2.7 22.1 + - - +
1400G LEU* 3.2 14.7 + - + +
1402G LEU* 1.3 72.1 - - - +
1404G GLU* 1.3 65.7 + - + +
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Residues in contact with GLU1404 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1268G ARG* 4.3 16.8 + - - +
1401G GLU 3.1 9.1 - - - +
1402G LEU 2.6 6.9 + - - -
1403G ALA* 1.3 84.5 - - + +
1405G GLY* 1.3 69.9 + - - +
1406G PRO* 3.1 22.7 - - + +
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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) + - + + + + + -
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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