Contacts of the helix formed by residues 1365 - 1385 (chain D) in PDB entry 3FK2
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 PRO1365 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1334D PRO* 4.1 24.7 - - + -
1336D ASN* 5.4 4.9 - - - +
1337D MET* 4.3 6.5 - - + -
1363D LYS 3.5 5.8 - - - +
1364D PHE* 1.3 85.0 - - + +
1366D LYS* 1.3 61.0 + - - +
1367D GLU* 3.3 8.5 - - - +
1368D ASN* 3.2 24.0 + - - +
1369D HIS* 2.9 24.1 + - - +
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Residues in contact with LYS1366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1364D PHE 3.3 5.3 + - - +
1365D PRO* 1.3 68.9 - - - +
1367D GLU* 1.3 77.1 + - - +
1369D HIS* 3.7 7.3 - - + +
1370D GLU* 3.1 44.3 + - + +
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Residues in contact with GLU1367 (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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1251D LEU* 4.3 7.9 - - + -
1252D THR* 3.6 31.9 - - + +
1255D VAL* 4.5 19.7 - - + +
1256D THR 6.5 0.4 - - - -
1257D PRO* 5.7 5.2 - - + +
1260D PRO* 4.8 3.8 - - - +
1365D PRO* 4.1 9.5 - - - +
1366D LYS* 1.3 89.7 + - - +
1368D ASN* 1.3 66.8 - - - +
1370D GLU* 3.5 5.1 + - - +
1371D VAL* 3.4 24.9 + - - +
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Residues in contact with ASN1368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251D LEU* 4.1 21.5 - - - +
1331D PRO 4.2 4.2 + - - -
1332D LEU* 2.8 34.4 + - - +
1334D PRO* 3.7 18.3 - - + +
1364D PHE* 4.6 6.5 - - + -
1365D PRO* 3.2 28.0 + - + +
1367D GLU* 1.3 80.1 - - - +
1369D HIS* 1.3 55.2 + - - +
1371D VAL* 3.1 1.9 + - - +
1372D PHE* 2.7 38.4 + - - +
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Residues in contact with HIS1369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1361D LEU* 3.2 54.6 + - + +
1362D LYS* 5.5 0.9 - - - -
1364D PHE* 3.8 18.1 - - + +
1365D PRO 2.9 16.1 + - - +
1366D LYS* 3.3 11.2 + - + +
1368D ASN* 1.3 76.3 - - - +
1370D GLU* 1.3 74.9 + - - +
1372D PHE* 3.7 2.5 - - - +
1373D LYS* 2.8 35.0 + - + +
1435D PHE 5.3 1.1 - - - -
1436D PHE* 4.1 15.0 - + - -
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Residues in contact with GLU1370 (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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1260D PRO* 3.9 33.8 - - + +
1261D ILE* 3.7 8.1 - - + +
1366D LYS* 3.1 39.8 + - + +
1367D GLU* 3.7 5.8 - - - +
1368D ASN 3.1 0.2 - - - -
1369D HIS* 1.3 95.7 - - - +
1371D VAL* 1.3 59.7 + - - +
1373D LYS* 3.2 20.6 + - - +
1374D TYR* 2.9 28.2 + - - +
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Residues in contact with VAL1371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251D LEU* 4.2 15.0 - - + -
1255D VAL* 4.8 0.4 - - + -
1260D PRO 3.6 20.4 - - - +
1261D ILE* 4.1 7.6 - - + -
1262D PRO* 3.9 21.1 - - + -
1265D ILE* 5.3 2.9 - - + -
1325D PHE* 3.5 38.6 - - + -
1332D LEU* 3.8 13.0 - - + -
1367D GLU 3.4 15.0 - - - +
1368D ASN 3.1 2.5 + - - +
1370D GLU* 1.3 71.9 - - - +
1372D PHE* 1.3 67.8 + - - +
1374D TYR* 3.1 2.1 + - + +
1375D VAL* 2.9 31.1 + - + +
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Residues in contact with PHE1372 (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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1332D LEU* 3.9 19.0 - - + +
1333D VAL* 3.6 27.8 - - + -
1361D LEU* 4.2 7.4 - - + -
1364D PHE* 4.0 20.4 - + + -
1368D ASN 2.7 22.3 + - - +
1369D HIS* 3.7 5.6 - - - +
1371D VAL* 1.3 73.0 - - - +
1373D LYS* 1.3 63.0 + - - +
1375D VAL* 3.9 1.5 - - + +
1376D ILE* 2.8 60.5 + - + +
1404D LEU* 4.1 13.2 - - + -
1405D MET* 5.5 0.7 - - + -
1425D ILE* 3.9 17.7 - - + -
1428D PHE* 4.0 33.4 - + - -
1436D PHE* 3.9 13.7 - + - -
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Residues in contact with LYS1373 (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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1369D HIS* 2.8 26.3 + - + +
1370D GLU* 3.2 25.6 + - - +
1372D PHE* 1.3 76.8 - - - +
1374D TYR* 1.3 57.9 - - - +
1376D ILE* 3.8 1.0 - - - +
1377D SER* 2.4 39.3 + - - +
1436D PHE* 2.9 69.8 + - + +
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Residues in contact with TYR1374 (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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1261D ILE* 3.6 46.4 - - + -
1265D ILE* 3.8 16.8 - - + -
1266D GLU* 3.3 32.4 - - + +
1269D ILE* 3.4 39.8 - - + +
1270D GLU* 3.8 15.4 + - - +
1370D GLU 2.9 5.4 + - - +
1371D VAL* 3.1 7.8 + - - +
1373D LYS* 1.3 79.5 - - - +
1375D VAL* 1.3 63.4 + - + +
1377D SER* 3.4 4.5 + - - -
1378D HIS* 3.0 24.1 + - + +
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Residues in contact with VAL1375 (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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1265D ILE* 4.8 2.9 - - + -
1269D ILE* 4.4 5.6 - - + -
1321D MET* 3.9 19.7 - - + -
1325D PHE* 3.5 35.0 - - + -
1332D LEU* 4.5 4.5 - - + -
1371D VAL* 2.9 27.0 + - + +
1372D PHE* 3.9 4.5 - - - +
1374D TYR* 1.3 70.5 - - + +
1376D ILE* 1.3 64.6 + - + +
1378D HIS* 3.2 9.3 + - + +
1379D LEU* 2.9 38.5 + - + +
1400D PHE* 4.5 12.1 - - + -
1404D LEU* 4.6 13.7 - - + -
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Residues in contact with ILE1376 (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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1372D PHE* 2.8 65.3 + - + +
1373D LYS 3.9 2.0 - - - +
1375D VAL* 1.3 73.1 - - + +
1377D SER* 1.3 58.5 + - - +
1379D LEU* 3.0 14.2 + - + +
1380D ASN* 2.8 25.8 + - - +
1404D LEU* 4.5 8.5 - - + -
1425D ILE* 4.6 5.2 - - + -
1428D PHE* 3.1 35.4 - - + +
1429D ILE* 3.8 21.5 - - + -
1432D CYS* 4.3 4.0 - - - -
1436D PHE* 3.9 14.6 - - + -
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Residues in contact with SER1377 (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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1373D LYS* 2.4 39.5 + - - +
1374D TYR* 3.5 5.3 + - - -
1376D ILE* 1.3 76.0 - - - +
1378D HIS* 1.3 63.2 + - - +
1380D ASN* 3.0 5.1 + - - +
1381D LYS* 2.9 23.0 + - - +
1432D CYS* 3.5 24.8 - - - -
1436D PHE* 5.5 0.8 - - - +
1437D TYR* 5.7 4.3 - - - -
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Residues in contact with HIS1378 (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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1269D ILE* 3.3 41.1 - - + +
1272D ILE* 4.1 8.3 - - + +
1273D GLU* 2.8 45.8 + - + +
1277D LEU* 4.9 0.2 - - + -
1283D TYR* 2.6 37.2 + + - -
1321D MET* 5.1 2.9 - - + -
1374D TYR* 3.0 13.6 + - + +
1375D VAL 3.3 8.1 - - - +
1377D SER* 1.3 76.4 - - - +
1379D LEU* 1.3 67.1 + - + +
1381D LYS* 3.0 7.5 + - - +
1382D VAL* 2.9 39.4 + - + +
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Residues in contact with LEU1379 (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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1283D TYR* 4.0 16.8 - - + -
1375D VAL* 2.9 24.4 + - + +
1376D ILE* 3.0 14.1 + - + +
1378D HIS* 1.3 78.8 - - + +
1380D ASN* 1.3 67.5 + - - +
1382D VAL* 3.3 3.7 + - + +
1383D SER* 2.9 20.1 + - - -
1396D LEU* 3.3 21.9 - - + +
1400D PHE* 3.4 55.4 - - + -
1404D LEU* 5.2 0.9 - - + -
1429D ILE* 3.6 35.0 - - + -
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Residues in contact with ASN1380 (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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1376D ILE 2.8 12.9 + - - +
1377D SER* 3.2 10.6 - - - +
1379D LEU* 1.3 76.8 - - - +
1381D LYS* 1.3 60.8 + - - +
1383D SER* 2.7 27.0 + - - -
1384D HIS* 3.0 39.5 + - - -
1429D ILE* 2.8 32.0 + - - +
1430D GLN* 4.2 9.9 + - - +
1432D CYS* 3.8 19.1 - - + +
1433D PRO* 4.6 6.1 - - - +
1437D TYR* 4.7 9.9 + - - -
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Residues in contact with LYS1381 (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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1413B ASP* 3.1 31.7 + - - +
1414B ALA* 4.3 3.2 - - + +
1415B LEU* 4.4 15.3 - - + +
1273D GLU* 3.2 40.0 + - + +
1277D LEU* 4.3 14.4 - - + +
1377D SER 2.9 11.9 + - - +
1378D HIS* 3.0 10.5 + - - +
1380D ASN* 1.3 75.0 + - - +
1382D VAL* 1.3 68.6 + - + +
1383D SER 2.9 1.1 - - - -
1384D HIS* 2.8 32.2 + - + +
1385D ASN* 3.8 3.3 + - - +
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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
----------------------------------------------------------
1272D ILE* 5.3 1.6 - - + -
1277D LEU* 3.8 21.5 - - + -
1282D ILE* 3.8 23.1 - - + -
1283D TYR* 4.2 11.0 - - + -
1378D HIS* 2.9 45.5 + - + +
1379D LEU* 3.7 6.7 - - - +
1381D LYS* 1.3 74.7 - - - +
1383D SER* 1.3 62.2 + - - +
1385D ASN* 3.2 5.9 + - - +
1389D ASN* 2.9 41.7 + - - +
1391D MET* 4.5 1.8 - - + -
1396D LEU* 4.0 18.6 - - + -
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Residues in contact with SER1383 (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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1379D LEU 2.9 12.7 + - - -
1380D ASN* 2.7 22.8 + - - -
1381D LYS 2.9 1.2 + - - -
1382D VAL* 1.3 78.1 - - - +
1384D HIS* 1.3 60.7 + - - +
1385D ASN 3.1 1.6 + - - -
1386D ASN* 2.7 34.6 + - - +
1391D MET 3.4 14.1 - - - -
1393D SER* 4.0 24.5 + - - -
1396D LEU* 3.8 11.0 - - - -
1429D ILE* 4.7 0.4 - - - -
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Residues in contact with HIS1384 (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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1415B LEU* 5.8 6.3 - - + -
1380D ASN* 3.0 44.5 + - - -
1381D LYS* 2.8 22.3 + - + +
1383D SER* 1.3 84.1 + - - +
1385D ASN* 1.3 57.3 + - - +
1386D ASN* 3.5 4.3 + - - +
1387D LYS* 5.9 2.1 - - - +
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Residues in contact with ASN1385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1415B LEU* 5.8 6.3 - - + -
1418B THR* 5.2 3.1 - - - +
1419B ARG* 6.0 2.3 - - - +
1422B GLN* 4.9 2.6 + - - +
1277D LEU* 2.8 32.6 + - + +
1278D SER* 3.4 17.0 + - - -
1381D LYS 3.8 2.2 + - - +
1382D VAL 3.2 4.0 + - - +
1383D SER 3.1 1.0 - - - -
1384D HIS* 1.3 79.6 - - - +
1386D ASN* 1.3 57.4 + - - +
1387D LYS* 3.3 4.6 - - - +
1388D VAL* 3.0 27.6 + - - +
1389D ASN* 2.8 38.0 + - - +
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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