Contacts of the helix formed by residues 1376 - 1394 (chain B) in PDB entry 1KI1
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 LEU1376 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LYS* 4.6 6.5 - - - +
56A PHE* 3.9 32.8 - - + -
70A LEU* 3.0 29.8 - - + +
71A SER* 4.0 23.3 - - - +
1336B GLN* 3.7 18.6 - - - +
1372B SER 4.0 10.1 - - - +
1373B SER 3.3 10.7 + - - +
1374B PHE 3.0 0.8 - - - -
1375B ILE* 1.3 80.6 - - + +
1377B LYS* 1.3 63.6 + - - +
1378B PRO 3.3 1.4 - - - -
1379B MET* 3.3 12.2 + - + +
1380B GLN* 3.2 33.9 + - + +
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Residues in contact with LYS1377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 4.1 27.2 + - - +
39A ASN* 4.2 19.6 + - - +
1252B TYR* 3.6 18.4 - - + -
1255B ASP* 3.3 39.4 + - + +
1256B LEU* 5.5 1.1 - - + -
1285B TRP* 5.4 2.9 - - + -
1373B SER 4.3 2.5 - - - +
1374B PHE* 3.0 49.4 + - + +
1376B LEU* 1.3 77.6 - - - +
1378B PRO* 1.3 59.0 - - + +
1380B GLN* 3.3 16.1 + - - +
1381B ARG* 2.8 31.5 + - - +
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Residues in contact with PRO1378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252B TYR* 3.4 16.4 - - + +
1256B LEU* 4.3 2.2 - - + -
1285B TRP* 3.9 13.9 - - + -
1288B LEU* 3.7 20.9 - - + -
1329B TYR* 3.4 24.4 - - + -
1332B PHE* 3.8 25.4 - - + -
1333B CYS* 4.5 0.2 - - - -
1374B PHE 3.8 4.9 - - - +
1375B ILE 3.4 15.3 - - - +
1376B LEU 3.6 0.2 - - - -
1377B LYS* 1.3 94.2 - - + +
1379B MET* 1.3 62.6 + - - +
1381B ARG* 3.2 1.6 + - - +
1382B VAL* 3.1 23.0 + - - +
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Residues in contact with MET1379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN* 3.5 44.9 - - - +
67A LEU* 3.9 41.3 - - + +
70A LEU* 4.3 13.9 - - + -
71A SER* 3.6 16.8 - - - +
1333B CYS* 3.8 17.3 - - - -
1336B GLN* 4.2 11.3 + - - +
1376B LEU* 3.3 12.0 + - + +
1378B PRO* 1.3 78.4 - - - +
1380B GLN* 1.3 72.1 + - + +
1382B VAL* 3.0 21.8 - - + +
1383B THR* 2.8 20.0 + - - +
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Residues in contact with GLN1380 (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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38A ASP* 5.2 1.4 - - - +
39A ASN* 3.1 38.2 + - - +
56A PHE* 4.4 2.8 - - - +
57A ASP 4.1 10.3 + - - -
61A GLN* 4.2 5.0 - - - +
71A SER* 5.0 2.0 + - - -
1376B LEU* 3.2 28.3 + - - +
1377B LYS* 3.6 20.8 + - - +
1379B MET* 1.3 92.1 - - + +
1381B ARG* 1.3 62.1 + - - +
1383B THR* 3.1 11.3 + - - -
1384B ARG* 3.0 62.9 + - - +
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Residues in contact with ARG1381 (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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36A VAL* 4.4 9.9 - - - +
1245B LEU* 3.5 10.9 + - - +
1248B THR* 3.1 45.0 + - - -
1249B GLU* 2.7 37.1 + - - +
1252B TYR* 3.6 40.0 - - + +
1329B TYR* 4.6 2.9 - - - +
1377B LYS 2.8 17.6 + - - +
1378B PRO 3.2 5.6 + - - +
1380B GLN* 1.3 78.0 - - - +
1382B VAL* 1.3 62.2 + - - +
1384B ARG* 3.0 18.4 + - - +
1385B TYR* 3.2 43.1 + - + +
1388B ILE* 4.1 12.5 - - - +
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Residues in contact with VAL1382 (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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67A LEU* 5.4 0.4 - - + -
1326B MET* 6.0 0.2 - - + -
1329B TYR* 3.3 43.1 - - + -
1333B CYS* 4.9 3.6 - - - -
1378B PRO 3.1 8.8 + - - +
1379B MET* 3.0 26.9 - - + +
1381B ARG* 1.3 76.4 - - - +
1383B THR* 1.3 62.1 + - + +
1385B TYR* 3.5 13.3 + - + +
1386B PRO* 3.1 16.3 - - - +
1413B ALA 4.8 0.9 - - - +
1416B LEU* 4.0 22.1 - - + +
1417B CYS* 3.1 23.1 - - - -
1420B VAL* 4.9 16.2 - - + -
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Residues in contact with THR1383 (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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59A ALA 4.5 1.4 + - - -
60A GLY* 3.5 39.9 - - - +
61A GLN* 3.9 10.9 + - + +
64A TYR* 4.5 4.0 - - + -
67A LEU* 3.6 29.6 - - + -
1379B MET* 2.8 33.2 + - - +
1380B GLN* 3.1 13.2 + - - -
1382B VAL* 1.3 77.6 - - + +
1384B ARG* 1.3 60.0 + - - +
1386B PRO* 3.7 8.7 - - - +
1387B LEU* 3.9 3.6 - - - +
1417B CYS* 3.7 12.6 - - - -
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Residues in contact with ARG1384 (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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35A THR* 4.9 2.8 + - - +
36A VAL* 3.8 32.5 - - + +
37A PHE 3.0 33.3 + - - +
38A ASP* 3.6 19.2 + - - +
39A ASN* 5.1 0.4 + - - -
57A ASP* 3.7 24.3 + - - +
59A ALA* 4.3 16.7 + - + +
61A GLN* 4.9 2.6 - - - +
1380B GLN* 3.0 60.4 + - - +
1381B ARG* 3.0 13.2 + - - +
1383B THR* 1.3 80.5 + - - +
1385B TYR* 1.3 67.3 + - - +
1386B PRO* 3.3 2.5 - - - -
1387B LEU* 3.0 17.9 + - + +
1388B ILE* 3.0 26.7 + - + +
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Residues in contact with TYR1385 (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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1245B LEU* 4.4 14.1 - - + -
1249B GLU* 2.8 29.3 + - - -
1292B ASN* 3.1 18.8 + - - -
1295B LEU* 3.6 12.9 - - + +
1319B LEU* 5.2 6.3 - - + -
1323B LEU* 4.2 15.3 - - + -
1326B MET* 3.5 22.1 - - + +
1329B TYR* 5.5 1.6 - - - -
1381B ARG* 3.2 52.7 + - + +
1382B VAL* 4.0 15.7 - - + +
1384B ARG* 1.3 75.3 - - - +
1386B PRO* 1.3 69.7 - - + +
1388B ILE* 3.2 6.9 + - + -
1389B ILE* 2.8 38.7 + - + +
1413B ALA* 4.2 12.8 - - + -
1416B LEU* 5.6 0.9 - - + -
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Residues in contact with PRO1386 (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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64A TYR* 5.1 3.6 - - + +
1382B VAL 3.1 14.4 - - - +
1383B THR 3.7 7.9 - - - +
1384B ARG 3.3 3.8 - - - -
1385B TYR* 1.3 92.0 - - + +
1387B LEU* 1.3 58.5 + - + +
1389B ILE* 4.6 0.2 - - + -
1390B LYS* 2.8 34.3 + - - +
1410B LEU* 3.7 14.9 - - + +
1413B ALA* 3.9 19.3 - - + +
1414B GLU* 4.2 20.6 - - + +
1417B CYS* 3.8 21.1 - - - -
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Residues in contact with LEU1387 (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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35A THR* 3.6 31.0 - - + +
59A ALA* 3.8 19.3 - - + +
60A GLY* 3.8 33.0 - - - +
1383B THR 3.9 13.7 - - - +
1384B ARG* 3.0 13.8 + - + +
1386B PRO* 1.3 82.0 - - + +
1388B ILE* 1.3 62.8 + - - +
1390B LYS* 3.6 9.8 - - + +
1391B ASN* 3.0 30.0 + - - -
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Residues in contact with ILE1388 (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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35A THR* 3.9 19.1 - - - +
36A VAL* 4.0 23.3 - - + -
1241B TYR* 4.0 14.3 - - + +
1244B GLU* 5.1 4.9 - - + +
1245B LEU* 3.9 37.9 - - + +
1248B THR* 4.0 16.2 - - - +
1381B ARG* 4.1 16.4 - - - +
1384B ARG 3.0 21.8 + - - +
1385B TYR* 3.7 9.9 - - + +
1387B LEU* 1.3 75.2 - - - +
1389B ILE* 1.3 60.2 + - + +
1391B ASN* 3.3 5.5 + - - +
1392B ILE* 3.0 30.7 + - + +
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Residues in contact with ILE1389 (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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1245B LEU* 6.0 0.9 - - + -
1319B LEU* 3.8 28.7 - - + -
1323B LEU* 4.1 9.4 - - + -
1385B TYR* 2.8 32.8 + - + +
1386B PRO 3.9 2.2 - - - +
1388B ILE* 1.3 71.6 - - + +
1390B LYS* 1.3 56.6 + - - +
1392B ILE* 3.1 9.1 + - - +
1393B LEU* 2.8 33.5 + - + +
1406B LEU* 3.7 35.9 - - + +
1409B ALA* 4.1 13.2 - - + +
1410B LEU* 3.8 13.9 - - + +
1413B ALA* 3.8 24.9 - - + -
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Residues in contact with LYS1390 (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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1386B PRO 2.8 20.0 + - - +
1387B LEU* 3.6 9.9 - - + +
1389B ILE* 1.3 77.3 - - - +
1391B ASN* 1.3 59.0 + - - +
1393B LEU* 3.2 6.4 + - + +
1394B GLU* 2.7 59.9 + - + +
1410B LEU* 4.3 23.7 - - + +
1414B GLU* 5.9 2.0 - - - +
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Residues in contact with ASN1391 (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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33A VAL 4.9 1.0 + - - -
35A THR* 2.7 43.9 + - - +
1241B TYR* 3.5 41.6 + - + -
1387B LEU 3.0 14.3 + - - +
1388B ILE 3.3 2.9 + - - +
1390B LYS* 1.3 76.1 - - - +
1392B ILE* 1.3 61.4 + - - +
1394B GLU* 3.7 12.5 + - - +
1395B ASN* 2.8 30.4 + - - +
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Residues in contact with ILE1392 (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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1238B ARG* 4.4 6.0 - - + +
1241B TYR* 3.5 35.9 - - + +
1242B ILE* 4.0 30.5 - - + -
1245B LEU* 4.5 9.4 - - + -
1315B ILE* 4.5 11.4 - - + -
1319B LEU* 5.1 2.5 - - + -
1388B ILE* 3.0 30.5 + - + +
1389B ILE* 3.5 9.2 - - - +
1391B ASN* 1.3 78.1 - - - +
1393B LEU* 1.3 58.5 + - - +
1395B ASN* 3.2 12.0 + - - +
1396B THR* 2.7 26.1 + - - +
1406B LEU* 3.6 27.8 - - + -
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Residues in contact with LEU1393 (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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1389B ILE 2.8 20.2 + - - +
1390B LYS* 3.6 5.8 - - + +
1392B ILE* 1.3 73.5 - - - +
1394B GLU* 1.3 59.8 + - + +
1396B THR* 2.8 33.0 + - - +
1403B HIS* 3.6 41.3 - - + +
1406B LEU* 3.9 27.3 - - + +
1407B LYS* 4.1 25.1 - - + +
1410B LEU* 4.1 26.0 - - + -
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Residues in contact with GLU1394 (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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1234B THR* 5.1 1.9 - - - +
1390B LYS* 2.7 54.6 + - + +
1391B ASN* 4.1 14.3 - - - +
1392B ILE 3.3 0.2 - - - -
1393B LEU* 1.3 76.6 - - + +
1395B ASN* 1.3 66.7 + - - +
1396B THR 3.4 1.9 - - - +
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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
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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