Contacts of the helix formed by residues 1349 - 1363 (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 ASP1349 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1347D ILE* 3.5 2.9 - - + +
1348D ASN* 1.3 76.6 - - - +
1350D ARG* 1.3 60.9 + - - +
1351D GLU* 3.4 10.1 + - - +
1352D GLN* 3.0 43.5 + - + +
1353D LYS* 2.8 31.0 + - - +
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Residues in contact with ARG1350 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1348D ASN 3.4 5.9 + - - +
1349D ASP* 1.3 75.1 + - - +
1351D GLU* 1.3 64.0 + - - +
1353D LYS* 3.3 21.8 + - - +
1354D LEU* 3.0 43.1 + - + +
1423D THR* 6.1 3.0 - - - +
1427D LEU* 3.5 27.7 - - - +
1430D GLN* 5.9 0.8 + - - -
1431D GLN* 5.3 4.9 + - - -
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Residues in contact with GLU1351 (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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1349D ASP* 3.4 7.8 + - - +
1350D ARG* 1.3 78.4 - - - +
1352D GLN* 1.3 69.6 + - - +
1354D LEU* 3.2 9.6 + - - +
1355D HIS* 3.1 53.8 + - + +
1434D PHE* 6.4 0.2 - - + -
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Residues in contact with GLN1352 (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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1347D ILE* 3.5 26.5 - - + +
1349D ASP* 3.0 29.7 + - + +
1351D GLU* 1.3 79.6 - - - +
1353D LYS* 1.3 65.1 + - - +
1355D HIS* 3.2 16.9 + - - +
1356D ALA* 2.9 22.5 + - - +
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Residues in contact with LYS1353 (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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1344D ALA 4.1 7.2 - - - +
1345D HIS* 2.9 58.6 + - - +
1347D ILE* 3.3 25.3 + - - +
1348D ASN* 4.9 9.2 + - - +
1349D ASP 2.8 17.6 + - - +
1350D ARG* 3.4 23.6 - - - +
1352D GLN* 1.3 76.9 - - - +
1354D LEU* 1.3 57.6 + - + +
1356D ALA* 3.3 5.0 + - - +
1357D LEU* 2.9 44.1 + - + +
1423D THR* 5.5 0.8 - - - +
1427D LEU* 4.3 14.3 - - + +
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Residues in contact with LEU1354 (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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1350D ARG* 3.0 38.5 + - + +
1351D GLU* 3.2 8.0 + - + +
1353D LYS* 1.3 74.8 - - + +
1355D HIS* 1.3 60.5 + - - +
1357D LEU* 3.3 13.6 + - + +
1358D LYS 2.9 24.1 + - - -
1427D LEU* 4.4 14.6 - - + -
1431D GLN* 4.0 28.0 - - + +
1434D PHE* 3.5 30.4 - - + -
1435D PHE* 3.5 30.3 - - + -
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Residues in contact with HIS1355 (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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1351D GLU* 3.1 56.9 + - + +
1352D GLN* 3.6 16.2 + - - +
1354D LEU* 1.3 73.4 - - - +
1356D ALA* 1.3 67.2 + - - +
1358D LYS* 3.0 7.4 + - + +
1359D GLU* 2.9 27.6 + - + +
1434D PHE* 3.8 26.4 - + - -
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Residues in contact with ALA1356 (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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1344D ALA* 3.4 24.4 - - + +
1347D ILE* 3.4 27.8 - - + -
1352D GLN 2.9 6.1 + - - +
1353D LYS 3.4 7.2 - - - +
1355D HIS* 1.3 76.8 - - - +
1357D LEU* 1.3 62.6 + - - +
1359D GLU* 3.1 20.4 + - - +
1360D VAL* 3.2 11.4 + - - +
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Residues in contact with LEU1357 (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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1341D LEU* 3.6 45.1 - - + +
1344D ALA* 4.2 9.9 - - + -
1345D HIS* 4.7 4.3 - - - +
1353D LYS* 2.9 33.1 + - + +
1354D LEU* 3.6 13.0 - - + +
1355D HIS 3.1 0.2 - - - -
1356D ALA* 1.3 73.6 - - - +
1358D LYS* 1.3 65.9 + - - +
1360D VAL* 3.1 8.0 + - - +
1361D LEU* 2.9 20.4 + - - +
1424D ILE* 4.4 15.7 - - + -
1427D LEU* 4.0 29.2 - - + -
1428D PHE* 4.4 5.9 - - + -
1435D PHE* 3.8 15.7 - - + -
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Residues in contact with LYS1358 (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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1354D LEU 2.9 17.3 + - - +
1355D HIS* 3.0 8.5 + - + +
1357D LEU* 1.3 76.9 - - - +
1359D GLU* 1.3 61.9 - - - +
1361D LEU* 3.1 11.7 + - + +
1362D LYS* 3.0 20.1 + - - +
1434D PHE* 2.8 47.5 + - + +
1435D PHE* 3.6 31.3 - - + +
1437D TYR 5.7 3.0 + - - -
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Residues in contact with GLU1359 (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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1355D HIS* 2.9 15.3 + - + +
1356D ALA* 3.2 14.6 - - - +
1357D LEU 3.0 0.2 - - - -
1358D LYS* 1.3 73.7 - - - +
1360D VAL* 1.3 67.1 + - + +
1362D LYS* 3.0 26.3 + - - +
1363D LYS* 3.5 9.8 + - - +
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Residues in contact with VAL1360 (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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1337D MET* 3.7 25.4 - - - +
1340D ASP* 3.4 39.7 - - + +
1341D LEU* 3.7 24.5 - - + +
1344D ALA* 4.7 4.7 - - + -
1356D ALA 3.2 11.0 + - - +
1357D LEU 3.1 7.2 + - - +
1359D GLU* 1.3 76.4 - - + +
1361D LEU* 1.3 55.2 + - - +
1363D LYS* 2.7 34.1 + - - +
1364D PHE* 3.5 14.2 - - + -
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Residues in contact with LEU1361 (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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1341D LEU* 5.1 0.2 - - - +
1357D LEU 2.9 13.4 + - - +
1358D LYS* 3.2 14.6 - - + +
1360D VAL* 1.3 76.8 - - - +
1362D LYS* 1.3 59.4 + - - +
1363D LYS 3.4 0.3 + - - -
1364D PHE* 3.5 34.6 + - + +
1369D HIS* 3.2 37.4 + - + +
1372D PHE* 4.2 18.4 - - + -
1428D PHE* 4.1 11.9 - - + -
1435D PHE* 3.6 34.5 - - + +
1436D PHE* 3.5 26.7 - - + -
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Residues in contact with LYS1362 (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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1358D LYS 3.0 9.3 + - - +
1359D GLU* 3.0 22.7 + - - +
1361D LEU* 1.3 78.1 - - - +
1363D LYS* 1.3 60.0 + - + +
1364D PHE 3.3 5.1 + - - +
1369D HIS* 5.4 1.8 - - - -
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Residues in contact with LYS1363 (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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1337D MET* 3.4 25.4 - - + +
1340D ASP* 4.9 10.8 - - - +
1359D GLU* 4.1 10.8 - - - +
1360D VAL* 2.7 19.9 + - - +
1362D LYS* 1.3 72.1 - - + +
1364D PHE* 1.3 64.5 + - - +
1365D PRO* 3.5 4.0 - - - +
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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
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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