Contacts of the helix formed by residues 1376 - 1394 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C LYS* 4.6 6.5 - - - +
56C PHE* 3.9 32.8 - - + -
70C LEU* 3.0 29.8 - - + +
71C SER* 4.0 23.1 - - - +
1336D GLN* 3.7 18.6 - - - +
1372D SER 4.0 10.1 - - - +
1373D SER 3.3 10.7 + - - +
1374D PHE 3.0 0.8 - - - -
1375D ILE* 1.3 80.6 - - + +
1377D LYS* 1.3 64.0 + - - +
1378D PRO 3.3 1.2 - - - -
1379D MET* 3.3 12.2 + - + +
1380D GLN* 3.2 33.9 + - + +
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Residues in contact with LYS1377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ASP* 4.1 27.2 + - - +
39C ASN* 4.2 19.8 + - - +
1252D TYR* 3.6 18.8 - - + -
1255D ASP* 3.3 39.8 + - + +
1256D LEU* 5.5 1.1 - - + -
1285D TRP* 5.3 2.9 - - + -
1373D SER 4.3 2.5 - - - +
1374D PHE* 3.0 49.2 + - + +
1376D LEU* 1.3 77.4 - - - +
1378D PRO* 1.3 59.6 - - + +
1380D GLN* 3.3 16.1 + - - +
1381D ARG* 2.8 31.5 + - - +
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Residues in contact with PRO1378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252D TYR* 3.4 17.0 - - + +
1256D LEU* 4.3 2.2 - - + -
1285D TRP* 3.9 13.9 - - + -
1288D LEU* 3.7 20.6 - - + -
1329D TYR* 3.4 23.8 - - + -
1332D PHE* 3.8 25.1 - - + -
1333D CYS* 4.5 0.2 - - - -
1374D PHE 3.8 4.9 - - - +
1375D ILE 3.4 15.0 - - - +
1376D LEU 3.6 0.2 - - - -
1377D LYS* 1.3 93.8 - - + +
1379D MET* 1.3 62.1 + - - +
1381D ARG* 3.2 1.6 + - - +
1382D VAL* 3.1 23.2 + - - +
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Residues in contact with MET1379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLN* 3.5 44.9 - - - +
67C LEU* 3.9 41.5 - - + +
70C LEU* 4.3 13.9 - - + -
71C SER* 3.6 16.4 - - - +
1333D CYS* 3.8 17.0 - - - -
1336D GLN* 4.2 11.3 + - - +
1376D LEU* 3.3 12.2 + - + +
1378D PRO* 1.3 78.8 - - - +
1380D GLN* 1.3 72.3 + - + +
1382D VAL* 3.0 22.0 - - - +
1383D THR* 2.8 20.3 + - - +
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Residues in contact with GLN1380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ASP* 5.2 1.6 - - - +
39C ASN* 3.1 38.2 + - - +
56C PHE* 4.4 2.8 - - - +
57C ASP 4.1 10.3 + - - -
61C GLN* 4.2 5.0 - - - +
71C SER* 5.0 2.0 + - - -
1376D LEU* 3.2 27.9 + - - +
1377D LYS* 3.6 20.6 + - - +
1379D MET* 1.3 91.7 - - + +
1381D ARG* 1.3 62.8 + - - +
1383D THR* 3.1 11.3 + - - -
1384D ARG* 3.0 62.6 + - - +
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Residues in contact with ARG1381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C VAL* 4.4 9.9 - - - +
1245D LEU* 3.5 11.1 + - - +
1248D THR* 3.1 44.8 + - - -
1249D GLU* 2.7 37.3 + - - +
1252D TYR* 3.6 40.0 - - + +
1329D TYR* 4.6 2.9 - - - +
1377D LYS 2.8 17.6 + - - +
1378D PRO 3.2 5.6 + - - +
1380D GLN* 1.3 78.0 - - - +
1382D VAL* 1.3 62.2 + - - +
1384D ARG* 3.0 18.6 + - - +
1385D TYR* 3.2 42.9 + - + +
1388D ILE* 4.1 12.5 - - - +
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Residues in contact with VAL1382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C LEU* 5.4 0.4 - - + -
1326D MET* 6.0 0.2 - - + -
1329D TYR* 3.3 43.1 - - + -
1333D CYS* 4.9 3.6 - - - -
1378D PRO 3.1 8.8 + - - +
1379D MET* 3.0 26.7 - - + +
1381D ARG* 1.3 77.0 - - - +
1383D THR* 1.3 62.0 + - + +
1385D TYR* 3.5 13.8 + - + +
1386D PRO* 3.1 16.1 - - - +
1413D ALA 4.8 0.9 - - - +
1416D LEU* 4.0 22.1 - - + +
1417D CYS* 3.1 23.1 - - - -
1420D VAL* 4.9 16.2 - - + -
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Residues in contact with THR1383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ALA 4.5 1.4 + - - -
60C GLY* 3.5 39.9 - - - +
61C GLN* 3.9 10.7 + - + +
64C TYR* 4.5 4.0 - - + -
67C LEU* 3.6 29.4 - - + -
1379D MET* 2.8 33.4 + - - +
1380D GLN* 3.1 13.2 + - - -
1382D VAL* 1.3 77.8 - - + +
1384D ARG* 1.3 60.2 + - - +
1386D PRO* 3.7 8.7 - - - +
1387D LEU* 3.9 3.6 - - - +
1417D CYS* 3.7 12.6 - - - -
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Residues in contact with ARG1384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C THR* 4.9 2.8 + - - +
36C VAL* 3.7 32.7 - - + +
37C PHE 3.0 33.3 + - - +
38C ASP* 3.6 19.2 + - - +
39C ASN* 5.1 0.4 + - - -
57C ASP* 3.7 24.3 + - - +
59C ALA* 4.3 16.7 + - + +
61C GLN* 4.9 2.8 - - - +
1380D GLN* 3.0 59.7 + - - +
1381D ARG* 3.0 13.2 + - - +
1383D THR* 1.3 80.0 + - - +
1385D TYR* 1.3 67.3 + - - +
1386D PRO* 3.3 2.5 - - - -
1387D LEU* 3.0 18.1 + - + +
1388D ILE* 3.0 26.9 + - + +
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Residues in contact with TYR1385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1245D LEU* 4.4 14.4 - - + -
1249D GLU* 2.8 29.3 + - - -
1292D ASN* 3.1 18.8 + - - -
1295D LEU* 3.6 12.9 - - + +
1319D LEU* 5.2 6.3 - - + -
1323D LEU* 4.2 15.3 - - + -
1326D MET* 3.5 22.1 - - + +
1329D TYR* 5.5 1.6 - - - -
1381D ARG* 3.2 52.4 + - + +
1382D VAL* 4.0 15.7 - - + +
1384D ARG* 1.3 75.1 - - - +
1386D PRO* 1.3 69.5 - - + +
1388D ILE* 3.2 6.9 + - + -
1389D ILE* 2.8 38.9 + - + +
1413D ALA* 4.2 12.8 - - + -
1416D LEU* 5.6 0.9 - - + -
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Residues in contact with PRO1386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C TYR* 5.1 3.6 - - + +
1382D VAL 3.1 14.4 - - - +
1383D THR 3.7 7.9 - - - +
1384D ARG 3.3 3.8 - - - -
1385D TYR* 1.3 92.2 - - + +
1387D LEU* 1.3 58.3 + - + +
1389D ILE* 4.6 0.2 - - + -
1390D LYS* 2.8 34.4 + - - +
1410D LEU* 3.7 14.9 - - + +
1413D ALA* 3.9 19.3 - - + +
1414D GLU* 4.2 20.6 - - + +
1417D CYS* 3.8 20.9 - - - -
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Residues in contact with LEU1387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C THR* 3.6 31.2 - - + +
59C ALA* 3.8 19.1 - - + +
60C GLY* 3.8 32.5 - - - +
1383D THR 3.9 13.9 - - - +
1384D ARG* 3.0 14.0 + - + +
1386D PRO* 1.3 82.2 - - + +
1388D ILE* 1.3 63.0 + - - +
1390D LYS* 3.6 9.8 - - + +
1391D ASN* 3.0 30.2 + - - -
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Residues in contact with ILE1388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C THR* 3.9 19.1 - - - +
36C VAL* 4.0 23.6 - - + -
1241D TYR* 4.0 14.3 - - + +
1244D GLU* 5.1 4.9 - - + +
1245D LEU* 3.9 38.1 - - + +
1248D THR* 4.0 16.2 - - - +
1381D ARG* 4.1 16.4 - - - +
1384D ARG 3.0 21.4 + - - +
1385D TYR* 3.7 9.9 - - + +
1387D LEU* 1.3 75.0 - - - +
1389D ILE* 1.3 60.2 + - + +
1391D ASN* 3.3 5.5 + - - +
1392D ILE* 3.0 30.8 + - + +
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Residues in contact with ILE1389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1245D LEU* 6.0 0.9 - - + -
1319D LEU* 3.8 28.9 - - + -
1323D LEU* 4.1 9.4 - - + -
1385D TYR* 2.8 32.4 + - + +
1386D PRO 3.9 2.2 - - - +
1388D ILE* 1.3 71.6 - - + +
1390D LYS* 1.3 56.8 + - - +
1392D ILE* 3.1 9.3 + - - +
1393D LEU* 2.7 33.7 + - + +
1406D LEU* 3.7 35.9 - - + +
1409D ALA* 4.1 13.2 - - + +
1410D LEU* 3.8 14.1 - - + +
1413D ALA* 3.8 24.7 - - + -
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Residues in contact with LYS1390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1386D PRO 2.8 20.0 + - - +
1387D LEU* 3.6 9.9 - - + +
1389D ILE* 1.3 77.7 - - - +
1391D ASN* 1.3 59.2 + - - +
1393D LEU* 3.2 6.4 + - + +
1394D GLU* 2.7 60.1 + - + +
1410D LEU* 4.3 23.7 - - + +
1414D GLU* 5.9 2.0 - - - +
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Residues in contact with ASN1391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL 4.9 1.0 + - - -
35C THR* 2.7 43.8 + - - +
1241D TYR* 3.5 41.6 + - + -
1387D LEU 3.0 14.3 + - - +
1388D ILE 3.3 2.9 + - - +
1390D LYS* 1.3 75.9 - - - +
1392D ILE* 1.3 61.5 + - - +
1394D GLU* 3.7 12.5 + - - +
1395D ASN* 2.8 30.4 + - - +
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Residues in contact with ILE1392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238D ARG* 4.4 6.0 - - + +
1241D TYR* 3.5 35.9 - - + +
1242D ILE* 4.0 30.7 - - + -
1245D LEU* 4.5 9.4 - - + -
1315D ILE* 4.5 11.4 - - + -
1319D LEU* 5.1 2.5 - - + -
1388D ILE* 3.0 30.1 + - + +
1389D ILE* 3.5 9.0 - - - +
1391D ASN* 1.3 78.1 - - - +
1393D LEU* 1.3 58.2 + - - +
1395D ASN* 3.2 12.0 + - - +
1396D THR* 2.7 26.2 + - - +
1406D LEU* 3.6 27.8 - - + -
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Residues in contact with LEU1393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1389D ILE 2.7 20.2 + - - +
1390D LYS* 3.6 5.6 - - + +
1392D ILE* 1.3 74.0 - - - +
1394D GLU* 1.3 59.7 + - + +
1396D THR* 2.8 33.2 + - - +
1403D HIS* 3.6 41.5 - - + +
1406D LEU* 3.9 27.3 - - + +
1407D LYS* 4.1 25.1 - - + +
1410D LEU* 4.1 25.8 - - + -
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Residues in contact with GLU1394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1234D THR* 5.1 1.9 - - - +
1390D LYS* 2.7 54.5 + - + +
1391D ASN* 4.1 14.1 - - - +
1392D ILE 3.3 0.2 - - - -
1393D LEU* 1.3 76.8 - - + +
1395D ASN* 1.3 66.8 + - - +
1396D 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
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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