Contacts of the helix formed by residues 1315 - 1323 (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 ILE1315 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1242D ILE* 4.1 31.6 - - + -
1245D LEU* 4.1 19.3 - - + -
1246D ILE* 5.1 6.7 - - + -
1299D LEU* 3.7 25.6 - - + +
1302D ARG* 4.2 11.7 - - + +
1312D VAL* 4.5 11.7 - - + -
1314D MET* 1.3 79.0 - - - +
1316D GLY* 1.3 71.3 + - - +
1317D ASP* 3.3 4.5 - - - -
1318D ILE* 3.2 24.9 + - + +
1319D LEU* 3.4 13.4 + - + +
1392D ILE* 4.5 8.3 - - + -
1402D ASP* 3.0 13.2 + - - +
1406D LEU* 4.1 14.4 - - + -
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Residues in contact with GLY1316 (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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1315D ILE* 1.3 82.8 - - - +
1317D ASP* 1.3 56.0 + - - -
1319D LEU* 3.8 5.1 - - - +
1320D SER* 2.9 31.7 + - - -
1402D ASP* 2.9 15.2 + - - -
1405D HIS* 3.4 15.8 - - - +
1406D LEU* 3.7 20.4 - - - -
1409D ALA* 4.1 0.6 - - - +
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Residues in contact with ASP1317 (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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1302D ARG* 2.9 41.4 + - - -
1314D MET* 3.6 22.0 - - + +
1315D ILE 3.7 6.2 + - - -
1316D GLY* 1.3 72.7 - - - +
1318D ILE* 1.3 65.4 + - - +
1320D SER* 3.8 2.4 - - - -
1321D ALA* 3.1 24.6 + - - +
1402D ASP* 4.0 0.4 + - - -
1405D HIS* 3.4 35.1 - - + +
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Residues in contact with ILE1318 (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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1295D LEU* 4.1 10.3 - - + -
1298D ALA* 3.7 35.9 - - + +
1299D LEU* 3.9 18.2 - - + -
1302D ARG* 3.5 59.2 - - + +
1315D ILE* 3.2 16.7 + - + +
1317D ASP* 1.3 80.8 + - - +
1319D LEU* 1.3 62.7 + - - +
1321D ALA* 3.2 5.2 + - - +
1322D GLN* 2.9 27.2 + - - +
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Residues in contact with LEU1319 (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* 4.0 35.7 - - + -
1295D LEU* 4.4 23.8 - - + -
1299D LEU* 4.8 1.8 - - + -
1315D ILE* 3.4 16.0 + - + +
1316D GLY 3.8 2.5 - - - +
1317D ASP 3.4 0.2 - - - -
1318D ILE* 1.3 77.9 - - + +
1320D SER* 1.3 65.4 + - - +
1322D GLN* 3.1 3.7 + - + -
1323D LEU* 2.9 36.1 + - + +
1385D TYR* 5.2 6.1 - - + -
1389D ILE* 3.8 32.3 - - + -
1392D ILE* 5.1 2.2 - - + -
1406D LEU* 4.5 16.8 - - + -
1409D ALA* 3.8 14.4 - - + -
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Residues in contact with SER1320 (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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1316D GLY 2.9 19.2 + - - -
1317D ASP* 3.8 6.5 - - - -
1319D LEU* 1.3 78.3 - - - +
1321D ALA* 1.3 58.9 + - - +
1324D PRO* 3.3 13.0 - - - +
1405D HIS* 4.1 18.1 + - - -
1408D HIS* 3.8 15.2 + - - +
1409D ALA* 3.8 10.5 - - - +
1412D LYS* 3.1 38.5 + - - +
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Residues in contact with ALA1321 (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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1317D ASP 3.1 18.8 + - - +
1318D ILE* 3.8 4.5 - - - +
1320D SER* 1.3 77.0 - - - +
1322D GLN* 1.3 64.7 + - - +
1324D PRO* 3.7 8.5 - - - +
1325D HIS* 3.6 19.3 + - - -
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Residues in contact with GLN1322 (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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1291D CYS 4.7 3.4 + - - +
1294D LYS* 3.2 47.0 - - - +
1295D LEU* 3.5 43.8 - - + +
1298D ALA* 4.3 11.1 - - - +
1318D ILE* 2.9 19.9 + - - +
1319D LEU* 3.8 3.6 - - + +
1321D ALA* 1.3 79.1 - - - +
1323D LEU* 1.3 60.6 + - - +
1324D PRO 3.2 2.7 - - - -
1325D HIS* 2.8 49.7 + - + +
1326D MET* 3.7 9.6 - - + +
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Residues in contact with LEU1323 (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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1319D LEU* 2.9 27.9 + - + +
1322D GLN* 1.3 72.2 - - + +
1324D PRO* 1.4 62.3 - - + +
1326D MET* 2.9 48.7 + - + +
1327D GLN* 5.4 0.7 - - - +
1385D TYR* 4.2 16.8 - - + -
1389D ILE* 4.1 9.0 - - + -
1409D ALA* 3.3 32.1 - - + +
1412D LYS* 3.8 14.4 - - + +
1413D ALA* 3.4 24.2 - - + +
1416D LEU* 4.2 25.1 - - + +
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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