Contacts of the helix formed by residues 1411 - 1431 (chain B) in PDB entry 6V65
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 PRO1411 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309B ILE* 4.0 23.3 - - + -
1313B ASP* 6.1 4.3 - - + -
1409B LYS 4.5 0.7 - - - +
1410B PRO* 1.3 93.0 - - + +
1412B PRO* 1.3 76.3 - - + +
1413B ARG* 3.2 5.4 - - + +
1414B ILE* 3.1 29.8 + - + +
1415B GLU* 3.1 8.7 + - - +
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Residues in contact with PRO1412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1410B PRO 3.7 1.1 - - - +
1411B PRO* 1.3 87.4 - - + +
1413B ARG* 1.3 60.6 + - - +
1415B GLU* 3.3 17.8 + - - +
1416B ARG* 3.2 21.8 + - - +
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Residues in contact with ARG1413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1315B GLN 5.5 1.4 + - - -
1316B HIS* 3.1 42.3 + - - +
1317B VAL* 3.4 29.1 + - + +
1318B SER* 4.1 17.5 - - - +
1319B PHE* 3.7 11.4 + - - +
1330B GLU* 4.6 4.2 + - - -
1411B PRO* 3.2 4.3 - - + +
1412B PRO* 1.3 79.6 - - - +
1414B ILE* 1.3 66.5 + - + +
1416B ARG* 3.6 7.1 + - + +
1417B GLY 3.4 14.0 + - - -
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Residues in contact with ILE1414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1305B LEU* 5.8 1.6 - - + -
1308B VAL* 3.7 43.7 - - + +
1309B ILE* 4.7 4.9 - - + -
1317B VAL* 4.4 16.2 - - + -
1319B PHE* 4.0 21.0 - - + -
1342B MET* 5.5 0.8 - - - +
1410B PRO* 4.0 13.2 - - + -
1411B PRO* 3.1 30.8 + - + +
1413B ARG* 1.3 77.2 - - + +
1415B GLU* 1.3 60.7 + - - +
1417B GLY* 3.1 2.1 + - - -
1418B LEU* 2.9 48.9 + - + +
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Residues in contact with GLU1415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1398B VAL* 5.3 10.2 - - - +
1400B PRO* 6.0 0.7 - - - +
1409B LYS* 3.7 28.4 - - - +
1410B PRO* 3.6 29.1 - - + +
1411B PRO 3.1 10.7 + - - +
1412B PRO* 3.3 20.0 + - - +
1414B ILE* 1.3 77.9 - - - +
1416B ARG* 1.3 59.3 + - - +
1418B LEU* 4.0 7.1 - - - +
1419B LYS* 3.1 26.3 + - - +
70C GLN* 4.3 12.7 - - - +
504C FMT 4.5 25.9 - - - +
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Residues in contact with ARG1416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1319B PHE 5.2 0.7 - - - +
1320B GLU* 2.6 43.3 + - + +
1322B ASP* 4.1 19.4 + - - +
1325B ARG* 5.1 6.3 - - - +
1412B PRO 3.2 12.1 + - - +
1413B ARG* 3.9 10.3 - - + +
1414B ILE 3.2 0.6 - - - -
1415B GLU* 1.3 77.0 - - - +
1417B GLY* 1.3 59.8 + - - +
1419B LYS* 3.6 37.9 + - - +
1420B LEU* 3.2 52.9 + - + +
1439B HIS* 4.9 3.2 + - - -
37C GLU* 4.9 1.0 + - - -
39C SER* 5.6 6.9 - - - -
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Residues in contact with GLY1417 (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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1319B PHE* 3.5 34.9 - - - +
1339B LEU* 3.8 2.9 - - - +
1342B MET* 3.6 9.7 - - - +
1413B ARG 3.4 5.7 + - - -
1414B ILE 3.1 6.2 + - - -
1416B ARG* 1.3 78.3 - - - +
1418B LEU* 1.3 58.8 + - - +
1420B LEU* 3.3 2.8 + - - +
1421B MET* 2.8 30.5 + - - +
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Residues in contact with LEU1418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1305B LEU* 4.1 27.8 - - + -
1308B VAL* 5.4 1.3 - - + -
1342B MET* 4.1 16.6 - - - -
1346B PHE* 4.7 2.5 - - + -
1397B ILE* 3.6 31.4 - - + +
1398B VAL* 4.6 6.0 - - - +
1400B PRO* 4.5 5.6 - - + -
1410B PRO* 4.3 16.6 - - + -
1414B ILE* 2.9 36.8 + - + +
1415B GLU* 4.0 5.2 - - - +
1417B GLY* 1.3 74.9 - - - +
1419B LYS* 1.3 62.6 + - - +
1421B MET* 3.3 26.4 + - + +
1422B SER* 3.0 24.6 + - - -
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Residues in contact with LYS1419 (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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1398B VAL* 4.5 18.5 - - + +
1415B GLU 3.1 17.9 + - - +
1416B ARG* 3.8 34.9 - - - +
1417B GLY 3.3 0.4 - - - -
1418B LEU* 1.3 78.0 - - - +
1420B LEU* 1.3 61.7 + - + +
1422B SER* 2.9 21.1 + - - -
1423B LYS* 3.2 18.8 - - + +
36C ILE* 4.9 7.9 - - + -
37C GLU* 2.6 48.7 + - + +
67C MET* 4.9 6.3 - - - -
70C GLN* 3.8 19.7 - - - +
504C FMT 4.3 15.0 - - - -
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Residues in contact with LEU1420 (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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1319B PHE 3.2 27.1 - - - +
1321B VAL* 4.1 17.9 - - + +
1339B LEU* 3.7 15.0 - - + -
1416B ARG* 3.2 56.8 + - + +
1417B GLY* 3.8 2.5 - - - +
1418B LEU 3.3 0.2 - - - -
1419B LYS* 1.3 75.1 - - + +
1421B MET* 1.3 65.5 + - - +
1423B LYS* 3.3 17.9 + - + +
1424B ILE* 3.2 26.5 + - - +
1439B HIS* 5.0 4.5 - - - +
1440B MET* 4.1 24.8 - - + +
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Residues in contact with MET1421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1339B LEU* 4.3 2.8 - - + +
1342B MET* 3.8 17.0 - - + +
1343B THR* 3.3 46.9 - - + +
1346B PHE* 3.6 41.3 - - + -
1397B ILE* 3.7 25.8 - - + -
1417B GLY 2.8 16.5 + - - +
1418B LEU* 3.3 20.4 + - + +
1420B LEU* 1.3 77.0 - - - +
1422B SER* 1.3 56.1 + - - +
1424B ILE* 3.1 5.8 + - - +
1425B LEU* 2.8 33.1 + - + +
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Residues in contact with SER1422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1394B ASN* 3.3 36.8 - - - +
1397B ILE* 4.5 6.2 - - - +
1398B VAL* 3.4 25.6 - - - +
1418B LEU 3.0 11.9 + - - -
1419B LYS 2.9 17.2 + - - -
1421B MET* 1.3 76.3 - - - +
1423B LYS* 1.3 57.0 + - - +
1425B LEU* 4.3 3.1 - - - -
1426B GLN* 3.0 26.2 + - - +
36C ILE* 3.5 12.5 - - - +
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Residues in contact with LYS1423 (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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1419B LYS* 3.2 23.6 - - + +
1420B LEU* 3.3 24.4 + - + +
1421B MET 3.2 0.6 - - - -
1422B SER* 1.3 78.3 + - - +
1424B ILE* 1.3 61.5 + - - +
1426B GLN* 3.6 3.1 + - - +
1427B SER* 3.2 15.9 + - - -
1434B PHE* 3.3 17.7 - - + -
1437B GLU* 2.9 21.7 + - - -
1440B MET* 4.1 20.4 - - + -
36C ILE* 4.0 23.3 - - + +
37C GLU 2.7 20.4 + - - +
38C ASP* 2.5 31.1 + - - -
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Residues in contact with ILE1424 (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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1339B LEU* 4.2 19.1 - - + -
1340B LEU* 4.6 4.3 - - + -
1343B THR* 4.0 32.3 - - + +
1420B LEU 3.5 13.9 - - - +
1421B MET 3.1 5.9 + - - +
1423B LYS* 1.3 75.7 - - - +
1425B LEU* 1.3 66.9 + - - +
1427B SER* 3.0 13.5 + - - -
1428B ILE* 3.1 14.8 + - + +
1434B PHE* 3.6 11.0 - - + -
1440B MET* 3.8 15.0 - - + -
1443B PHE* 4.2 25.1 - - + -
1446B PHE* 4.2 10.8 - - + -
1447B VAL* 3.6 22.2 - - + -
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Residues in contact with LEU1425 (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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1343B THR* 4.1 12.1 - - + +
1346B PHE* 4.9 4.9 - - + -
1347B PHE* 3.7 43.7 - - + -
1350B ILE* 4.7 5.6 - - + -
1389B PHE* 4.2 19.5 - - + -
1394B ASN* 4.0 12.1 - - - +
1397B ILE* 3.8 28.9 - - + -
1421B MET* 2.8 38.3 + - + +
1422B SER 4.0 3.8 - - - +
1424B ILE* 1.3 76.0 - - - +
1426B GLN* 1.3 62.3 + - - +
1428B ILE* 3.4 10.1 + - + +
1429B ALA* 3.0 22.5 + - - +
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Residues in contact with GLN1426 (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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1276B ARG* 5.8 0.5 + - - -
1386B SER* 3.5 8.3 - - - +
1389B PHE* 3.6 6.5 - - - +
1390B LEU* 3.4 52.5 - - + +
1394B ASN* 2.5 29.1 + - - +
1422B SER 3.0 18.4 + - - +
1423B LYS* 3.9 4.9 - - - +
1424B ILE 3.1 0.2 - - - -
1425B LEU* 1.3 75.4 - - - +
1427B SER* 1.3 60.4 + - - +
1429B ALA* 3.1 1.5 + - - +
1430B ASN* 2.8 66.1 + - - +
34C PRO* 5.2 5.2 - - - +
36C ILE* 4.3 11.6 - - + +
64C TYR* 4.5 0.4 + - - -
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Residues in contact with SER1427 (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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1423B LYS 3.2 7.4 + - - -
1424B ILE 3.0 10.1 + - - -
1426B GLN* 1.3 78.2 - - - +
1428B ILE* 1.3 62.7 + - - +
1430B ASN* 3.8 6.2 - - - +
1431B HIS* 3.1 18.4 + - - -
1432B VAL* 3.3 29.2 + - - +
1433B LEU 4.5 1.0 + - - -
1434B PHE* 3.3 39.4 + - - -
1447B VAL* 4.6 6.3 - - - -
1451B PHE* 3.8 3.0 - - - -
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Residues in contact with ILE1428 (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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1347B PHE* 3.7 27.8 - - + -
1389B PHE* 6.5 0.4 - - + -
1424B ILE* 3.1 17.0 + - + +
1425B LEU* 3.6 13.5 - - + +
1426B GLN 3.2 0.2 - - - -
1427B SER* 1.3 76.0 - - - +
1429B ALA* 1.3 62.7 + - - +
1431B HIS* 3.2 13.2 + - - +
1446B PHE* 4.2 15.9 - - + -
1447B VAL* 3.7 23.6 - - + +
1450B ASN* 3.2 53.2 - - + +
1451B PHE* 3.9 15.6 - - - +
1454B ALA* 4.0 7.4 - - + +
1458B PHE* 5.3 0.5 - - - -
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Residues in contact with ALA1429 (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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1382B GLY* 4.6 6.9 - - - +
1385B GLY 4.0 8.5 - - - +
1386B SER* 4.4 8.2 + - - -
1389B PHE* 3.6 38.6 - - + -
1425B LEU 3.0 16.6 + - - +
1426B GLN* 3.1 4.9 + - - +
1428B ILE* 1.3 80.2 - - - +
1430B ASN* 1.3 65.0 + - - +
1431B HIS* 3.4 2.9 + - - +
1454B ALA* 5.1 0.7 - - - -
1458B PHE* 4.1 20.5 - - + -
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Residues in contact with ASN1430 (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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1276B ARG* 5.1 9.0 + - - +
1386B SER* 3.4 20.2 - - - -
1426B GLN* 2.8 57.2 + - - +
1427B SER* 4.2 5.2 - - - +
1429B ALA* 1.3 71.0 - - - +
1431B HIS* 1.3 69.5 + - - +
1432B VAL* 3.3 21.4 - - + +
33C ASP* 3.6 22.8 + - - +
34C PRO* 5.4 4.6 + - - +
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Residues in contact with HIS1431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1427B SER 3.1 4.8 + - - -
1428B ILE 3.2 4.4 + - - +
1429B ALA 3.2 6.1 - - - +
1430B ASN* 1.3 80.5 - - - +
1432B VAL* 1.3 60.9 + - - +
1451B PHE* 3.3 67.5 - + + +
1452B ASP* 3.7 12.9 + - - -
1455B ARG* 5.4 15.0 - - + -
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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