Contacts of the helix formed by residues 1340 - 1359 (chain D) in PDB entry 4OIR
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 GLY1340 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1335D LEU 3.3 1.8 + - - -
1336D LEU* 3.2 19.8 + - - -
1337D GLU 5.1 0.2 + - - -
1339D LYS* 1.3 77.7 - - - +
1341D PRO* 1.3 75.5 - - - +
1342D GLU* 3.4 4.3 - - - -
1343D ALA* 3.1 16.5 + - - +
1344D VAL* 3.3 14.5 + - - +
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Residues in contact with PRO1341 (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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1336D LEU* 3.9 13.7 - - + -
1340D GLY* 1.3 79.1 - - - -
1342D GLU* 1.3 78.0 + - - +
1344D VAL* 3.1 5.8 + - + +
1345D GLU* 2.9 34.7 + - - +
1376D MET* 4.2 15.4 - - + +
1397D LYS* 5.7 6.1 - - - +
1419D PRO* 3.8 31.4 - - + -
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Residues in contact with GLU1342 (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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1339D LYS 5.6 0.2 - - - +
1340D GLY* 3.3 1.9 + - - -
1341D PRO* 1.3 89.1 - - - +
1343D ALA* 1.3 57.6 + - - +
1345D GLU* 3.3 19.6 + - - +
1346D ARG* 2.9 43.8 + - - +
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Residues in contact with ALA1343 (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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1335D LEU* 3.9 9.4 - - + +
1339D LYS* 3.6 40.8 - - + +
1340D GLY 3.1 11.8 + - - +
1342D GLU* 1.3 77.2 - - - +
1344D VAL* 1.3 60.1 + - - +
1346D ARG* 3.3 21.7 + - - +
1347D TYR* 2.9 30.5 + - - +
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Residues in contact with VAL1344 (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 PRO* 4.0 9.2 - - + +
1335D LEU* 4.0 11.4 - - + +
1336D LEU* 3.5 43.1 - - + +
1340D GLY 3.5 13.9 - - - +
1341D PRO* 3.1 6.5 + - + +
1343D ALA* 1.3 77.3 - - - +
1345D GLU* 1.3 63.1 + - - +
1347D TYR* 3.2 2.2 + - + +
1348D LEU* 2.9 36.5 + - + +
1376D MET* 4.4 10.5 - - - -
1421D LEU* 3.7 29.6 - - + -
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Residues in contact with GLU1345 (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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1118D ILE* 5.1 3.6 - - - +
1192D LEU* 3.4 55.7 - - + +
1193D THR* 5.8 1.4 - - - +
1341D PRO* 2.9 27.2 + - - +
1342D GLU* 3.3 19.8 + - - +
1344D VAL* 1.3 76.4 - - - +
1346D ARG* 1.3 62.7 + - - +
1348D LEU* 3.9 0.9 - - - +
1349D VAL* 2.9 31.0 + - - +
1372D VAL* 4.1 17.7 - - + -
1376D MET* 4.6 16.0 - - + +
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Residues in contact with ARG1346 (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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1119D SER 5.9 1.0 + - - -
1121D PRO* 5.9 9.3 - - + +
1339D LYS* 4.8 12.3 - - - +
1342D GLU* 2.9 29.6 + - - +
1343D ALA* 3.4 35.4 + - - +
1344D VAL 3.3 0.2 - - - -
1345D GLU* 1.3 76.0 - - - +
1347D TYR* 1.3 63.7 + - - +
1349D VAL* 3.9 3.2 - - - +
1350D GLU* 2.9 30.7 + - + +
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Residues in contact with TYR1347 (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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1258D ARG* 3.4 19.6 + - - -
1262D LEU* 4.4 9.0 - - + -
1328D GLY 4.8 0.5 + - - -
1329D ALA* 3.7 4.3 - - - -
1330D ILE* 3.0 65.1 + - + +
1332D PRO* 5.3 7.2 - - + -
1335D LEU* 3.7 19.3 - - + -
1343D ALA 2.9 17.1 + - - +
1344D VAL* 3.7 3.6 - - + +
1346D ARG* 1.3 76.2 - - - +
1348D LEU* 1.3 71.9 + - + +
1350D GLU* 4.8 2.7 - - + -
1351D GLU* 2.9 62.3 + - + +
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Residues in contact with LEU1348 (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 LEU* 3.7 39.3 - - + +
1265D ALA* 5.6 0.7 - - + -
1332D PRO* 4.5 19.3 - - + -
1344D VAL* 2.9 37.0 + - + +
1345D GLU 3.9 2.7 - - - +
1347D TYR* 1.3 79.7 - - + +
1349D VAL* 1.3 65.1 + - - +
1351D GLU* 3.9 0.5 - - - +
1352D ILE* 2.9 34.0 + - + +
1372D VAL* 3.9 32.1 - - + -
1375D MET* 4.3 11.0 - - + -
1421D LEU* 4.2 17.5 - - + -
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Residues in contact with VAL1349 (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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1192D LEU* 5.2 3.1 - - + -
1345D GLU 2.9 21.2 + - - +
1346D ARG* 4.0 3.1 - - - +
1348D LEU* 1.3 76.8 - - - +
1350D GLU* 1.3 61.1 + - - +
1352D ILE* 3.8 1.4 - - - +
1353D GLN* 2.9 34.8 + - + +
1365D ASP* 3.9 32.3 - - + +
1368D ILE* 4.0 24.6 - - + +
1369D GLU* 3.8 29.4 - - + +
1372D VAL* 4.2 10.8 - - + -
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Residues in contact with GLU1350 (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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1124D GLN* 5.0 7.1 - - - +
1135D ARG* 3.8 18.8 + - - -
1346D ARG* 2.9 22.5 + - + +
1347D TYR* 4.0 3.6 - - + +
1349D VAL* 1.3 78.6 - - - +
1351D GLU* 1.3 60.2 + - + +
1353D GLN* 3.2 5.2 + - - +
1354D LYS* 2.9 51.1 + - - +
1357D ARG* 2.6 33.7 + - - -
1365D ASP* 5.4 1.6 - - - +
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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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1258D ARG* 3.1 20.0 + - - +
1262D LEU* 3.6 24.5 - - + +
1347D TYR* 2.9 57.5 + - + +
1350D GLU* 1.3 77.6 - - + +
1352D ILE* 1.3 64.5 + - - +
1354D LYS* 2.6 54.3 + - - +
1355D VAL* 3.7 8.7 + - - +
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Residues in contact with ILE1352 (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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1259D VAL* 4.8 5.6 - - + +
1262D LEU* 3.6 28.5 - - + -
1263D PHE* 3.4 46.4 - - + +
1348D LEU* 2.9 25.9 + - + +
1349D VAL 3.8 2.9 - - - +
1351D GLU* 1.3 75.6 - - - +
1353D GLN* 1.3 64.0 + - - +
1355D VAL* 3.1 16.7 + - - +
1356D TYR* 3.4 34.1 + - + -
1368D ILE* 3.7 28.3 - - + -
1375D MET* 5.2 2.7 - - + -
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Residues in contact with GLN1353 (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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1142D ALA* 5.2 1.4 - - - +
1349D VAL* 2.9 27.5 + - + +
1350D GLU* 3.5 6.1 - - - +
1352D ILE* 1.3 76.6 - - - +
1354D LYS* 1.3 62.9 + - - +
1356D TYR* 3.2 6.5 + - - +
1357D ARG* 2.9 60.4 + - - +
1361D VAL 5.1 0.7 - - - +
1363D LEU* 2.7 39.2 + - - +
1365D ASP* 2.8 31.2 + - - +
1368D ILE* 3.5 23.2 - - + +
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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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1350D GLU* 2.9 38.8 + - - +
1351D GLU* 2.6 46.4 + - - +
1352D ILE 3.1 0.4 - - - -
1353D GLN* 1.3 76.6 - - - +
1355D VAL* 1.3 65.1 + - + +
1357D ARG* 3.3 11.5 + - - +
1358D ALA* 2.9 24.3 + - - +
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Residues in contact with VAL1355 (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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1236D LEU* 3.8 17.0 - - + -
1254D GLN* 5.3 3.1 - - + +
1255D GLY* 3.8 26.7 - - - +
1258D ARG* 3.8 26.2 - - + -
1259D VAL* 3.6 30.3 - - + -
1351D GLU 3.9 10.5 - - - +
1352D ILE* 3.1 7.9 + - - +
1354D LYS* 1.3 75.8 - - + +
1356D TYR* 1.3 62.7 + - - +
1358D ALA* 3.2 21.9 + - + +
1359D GLN* 3.4 10.8 + - + +
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Residues in contact with TYR1356 (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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1094D LEU* 4.6 4.9 - - - +
1229D ILE* 3.0 31.4 + - + +
1232D PRO* 3.6 36.6 - - + -
1233D GLY* 4.5 3.8 - - - -
1236D LEU* 3.7 30.9 - - + +
1256D LEU* 5.5 0.3 - - - +
1259D VAL* 3.8 22.6 - - + +
1352D ILE* 3.4 41.3 - - + -
1353D GLN* 3.2 14.1 + - - +
1355D VAL* 1.3 77.2 - - - +
1357D ARG* 1.3 59.0 + - - +
1359D GLN* 3.4 2.3 + - - +
1360D GLY 3.2 3.6 + - - -
1361D VAL* 2.8 48.4 + - + +
1363D LEU* 4.1 20.2 - - + -
1368D ILE* 5.2 0.2 - - + -
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Residues in contact with ARG1357 (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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1124D GLN* 5.8 0.6 + - - -
1135D ARG* 3.3 24.5 - - - +
1139D ASP* 3.3 48.0 + - - +
1142D ALA* 5.3 2.4 - - - +
1350D GLU* 2.6 33.9 + - - -
1353D GLN* 2.9 55.7 + - - +
1354D LYS* 3.6 12.5 - - - +
1356D TYR* 1.3 72.6 - - - +
1358D ALA* 1.3 59.3 + - - +
1360D GLY* 2.8 24.0 + - - +
1361D VAL 4.3 7.6 - - - +
1365D ASP* 4.5 6.5 + - - -
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Residues in contact with ALA1358 (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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1254D GLN 6.4 0.2 - - - +
1354D LYS 2.9 13.6 + - - +
1355D VAL* 3.2 14.8 + - + +
1357D ARG* 1.3 77.4 - - - +
1359D GLN* 1.3 69.4 + - + +
1360D GLY 3.5 0.3 + - - -
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Residues in contact with GLN1359 (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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1235D GLN* 3.6 24.4 - - + +
1236D LEU* 3.5 37.0 - - + +
1237D THR* 4.8 16.1 - - - +
1255D GLY* 5.6 4.8 - - - -
1355D VAL* 3.4 10.0 + - + +
1356D TYR 3.4 4.2 + - - +
1357D ARG 3.2 0.4 - - - -
1358D ALA* 1.3 85.0 + - - +
1360D GLY* 1.3 62.3 + - - +
1361D VAL* 3.5 8.5 + - + +
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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