Contacts of the helix formed by residues 1350 - 1362 (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 ALA1350 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1346D LYS* 3.1 16.7 + - + +
1347D THR 3.3 11.7 - - - +
1348D ASP 3.4 2.3 - - - -
1349D GLU* 1.3 87.3 - - + +
1351D PRO* 1.3 69.3 - - + +
1352D ASP* 4.5 3.8 - - + +
1353D PHE* 4.1 14.1 - - + +
1354D LYS* 3.3 16.5 + - - +
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Residues in contact with PRO1351 (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 GLU 4.3 3.8 - - - +
1350D ALA* 1.3 81.9 - - + +
1352D ASP* 1.3 76.9 + - - +
1354D LYS* 3.5 16.3 + - - +
1355D GLU* 3.0 25.8 + - - +
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Residues in contact with ASP1352 (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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1272D LEU* 4.6 18.5 - - + +
1350D ALA* 3.3 3.9 - - + +
1351D PRO* 1.3 87.9 - - - +
1353D PHE* 1.3 56.6 + - - +
1355D GLU* 3.7 4.1 - - - +
1356D PHE* 2.8 32.6 + - - +
1359D ARG* 5.7 0.3 + - - -
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Residues in contact with PHE1353 (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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1267D LEU* 4.1 13.9 - - + -
1272D LEU* 4.0 22.6 - - + +
1273D LEU* 3.7 38.1 - - + -
1281D ILE* 4.9 9.6 - - + -
1342D LEU* 5.4 0.2 - - + -
1343D ILE* 3.7 34.8 - - + -
1346D LYS* 3.6 38.4 - - + +
1347D THR* 3.6 16.4 - - - -
1350D ALA* 3.5 10.2 + - + +
1351D PRO 3.4 0.2 - - - -
1352D ASP* 1.3 78.7 - - - +
1354D LYS* 1.3 64.6 + - - +
1356D PHE* 3.2 0.7 + - - +
1357D VAL* 3.0 48.0 + - + +
1371D LEU* 6.2 0.7 - - + -
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Residues in contact with LYS1354 (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 THR* 3.3 46.1 + - + +
1348D ASP* 5.4 4.0 + - - +
1350D ALA 3.3 6.3 + - - +
1351D PRO* 3.9 17.0 + - - +
1352D ASP 3.4 0.2 - - - -
1353D PHE* 1.3 84.5 - - - +
1355D GLU* 1.3 60.4 + - - +
1357D VAL* 3.6 4.4 + - - +
1358D LYS* 3.1 58.7 + - - +
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Residues in contact with GLU1355 (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 PRO 3.0 17.9 + - - +
1352D ASP* 3.7 5.2 - - - +
1354D LYS* 1.3 75.1 - - - +
1356D PHE* 1.3 66.2 + - - +
1358D LYS* 3.0 27.0 + - - +
1359D ARG* 2.9 45.7 + - - +
1362D MET* 6.2 0.2 - - - +
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Residues in contact with PHE1356 (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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1266D PRO* 3.9 18.2 - - + -
1267D LEU* 3.9 19.5 - - + -
1270D SER* 3.7 23.8 - - - -
1272D LEU* 3.9 18.8 - - + -
1352D ASP 2.8 20.0 + - - +
1353D PHE 3.7 3.1 - - - +
1355D GLU* 1.3 72.5 - - - +
1357D VAL* 1.3 58.8 + - + +
1359D ARG* 3.1 38.0 + - + +
1360D LEU* 2.9 61.6 + - + +
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Residues in contact with VAL1357 (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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1263D PHE* 4.2 5.5 - - + -
1267D LEU* 4.3 17.9 - - + -
1343D ILE* 5.7 5.4 - - + -
1347D THR* 5.7 2.2 - - - +
1353D PHE* 3.0 53.7 + - + +
1354D LYS* 4.0 5.2 - - - +
1356D PHE* 1.3 76.6 - - + +
1358D LYS* 1.3 60.0 - - + +
1360D LEU* 3.4 8.8 + - + +
1361D GLU* 3.2 22.0 + - + +
1370D PRO* 6.4 0.9 - - + -
1371D LEU* 4.5 28.0 - - + +
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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 LYS* 3.1 50.7 + - + +
1355D GLU* 3.0 29.3 + - - +
1357D VAL* 1.3 75.7 - - + +
1359D ARG* 1.3 64.0 + - - +
1361D GLU* 3.2 8.3 + - - +
1362D MET* 3.2 27.4 + - + +
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Residues in contact with ARG1359 (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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1352D ASP 5.7 0.4 + - - -
1355D GLU* 2.9 36.6 + - - +
1356D PHE* 3.4 40.4 - - + +
1358D LYS* 1.3 75.3 - - - +
1360D LEU* 1.3 67.0 + - + +
1362D MET* 3.2 41.6 + - + +
1363D ASP 4.3 1.2 + - - -
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Residues in contact with LEU1360 (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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1262D ILE* 3.4 35.3 - - + +
1263D PHE* 3.8 15.7 - - + +
1266D PRO* 3.5 24.2 - - + -
1267D LEU* 4.1 16.2 - - + -
1356D PHE* 2.9 52.7 + - + +
1357D VAL* 3.8 10.8 - - - +
1358D LYS 3.3 0.2 - - - -
1359D ARG* 1.3 76.5 - - + +
1361D GLU* 1.3 61.2 + - - +
1362D MET 3.3 1.0 + - - -
1363D ASP* 3.4 19.4 + - - +
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Residues in contact with GLU1361 (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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1263D PHE* 3.8 20.6 - - + -
1357D VAL* 3.2 14.4 + - + +
1358D LYS* 3.6 11.0 - - - +
1359D ARG 3.2 0.4 - - - -
1360D LEU* 1.3 73.5 - - - +
1362D MET* 1.3 60.1 + - - +
1363D ASP 3.0 15.6 + - - +
1366D CYS* 3.5 11.8 - - - +
1368D GLY* 5.2 5.0 + - - -
1369D MET 4.3 12.5 - - - +
1370D PRO* 4.6 8.5 - - + -
1371D LEU 5.1 0.7 - - - +
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Residues in contact with MET1362 (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* 3.3 15.3 - - + +
1359D ARG* 3.2 41.8 + - + +
1361D GLU* 1.3 74.1 - - - +
1363D ASP* 1.3 66.3 + - - +
1364D PRO* 2.9 10.4 - - - +
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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