Contacts of the helix formed by residues 1312 - 1328 (chain D) in PDB entry 3CMT
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 ASN1312 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1308D TRP* 2.8 56.0 + - + +
1309D LEU* 3.3 8.7 - - - +
1310D LYS 3.4 0.2 - - - -
1311D ASP* 1.3 87.6 - - - +
1313D PRO* 1.3 60.6 - - - +
1314D GLU* 3.2 5.8 - - + +
1315D THR* 3.2 21.0 + - - +
1316D ALA* 3.0 22.5 + - - +
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Residues in contact with PRO1313 (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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1271D TYR* 4.9 9.2 - - - +
1309D LEU 3.7 6.3 - - - +
1310D LYS 3.6 14.1 - - - +
1311D ASP 3.2 11.9 - - - +
1312D ASN* 1.3 83.6 - - - +
1314D GLU* 1.3 79.7 + - + +
1316D ALA* 3.4 5.6 + - + +
1317D LYS* 3.0 38.0 + - + +
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Residues in contact with GLU1314 (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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1312D ASN* 4.7 3.1 - - + -
1313D PRO* 1.3 99.8 - - + +
1315D THR* 1.3 63.1 + - - +
1317D LYS* 3.5 9.1 + - - +
1318D GLU* 3.3 20.1 + - - +
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Residues in contact with THR1315 (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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1293D TYR* 3.5 37.0 - - + +
1308D TRP* 4.0 19.1 - - + -
1312D ASN* 3.2 26.3 + - - +
1314D GLU* 1.3 76.5 - - - +
1316D ALA* 1.3 60.8 + - - +
1318D GLU* 3.2 12.1 + - - +
1319D ILE* 3.0 36.3 + - + +
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Residues in contact with ALA1316 (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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1271D TYR* 3.7 30.3 - - + +
1274D LEU* 3.7 13.6 - - + +
1309D LEU* 3.8 19.0 - - + +
1312D ASN 3.0 13.6 + - - +
1313D PRO* 3.5 10.5 - - + +
1314D GLU 3.3 0.2 - - - -
1315D THR* 1.3 77.1 - - - +
1317D LYS* 1.3 59.9 + - - +
1319D ILE* 3.3 1.7 + - - +
1320D GLU* 2.8 32.1 + - - +
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Residues in contact with LYS1317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1270D PHE* 4.9 9.9 - - - -
1271D TYR* 5.3 8.1 + - - -
1313D PRO* 3.0 27.3 + - + +
1314D GLU* 3.7 9.0 - - - +
1316D ALA* 1.3 78.7 - - - +
1318D GLU* 1.3 57.2 + - - +
1320D GLU* 2.9 27.4 + - - +
1321D LYS* 2.9 34.0 + - - +
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Residues in contact with GLU1318 (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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1293D TYR* 2.7 26.9 + - - +
1294D LYS* 3.7 16.8 + - - -
1314D GLU 3.3 10.6 + - - +
1315D THR* 3.2 15.5 + - - +
1316D ALA 3.2 0.4 - - - -
1317D LYS* 1.3 77.5 - - - +
1319D ILE* 1.3 64.4 + - - +
1321D LYS* 3.4 7.3 + - - +
1322D LYS* 3.3 45.7 + - - +
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Residues in contact with ILE1319 (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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1274D LEU* 4.3 13.5 - - + -
1278D GLY* 4.6 3.4 - - - -
1283D LEU* 4.1 22.7 - - + -
1284D ILE* 4.3 19.5 - - + -
1293D TYR* 3.8 46.2 - - + +
1298D ILE* 6.2 0.2 - - + -
1308D TRP* 5.3 0.9 - - + -
1309D LEU* 3.9 24.5 - - + -
1315D THR* 3.0 18.5 + - + +
1316D ALA 3.9 2.9 - - - +
1318D GLU* 1.3 72.4 - - - +
1320D GLU* 1.3 66.7 + - - +
1322D LYS* 3.2 8.1 + - - +
1323D VAL* 2.9 29.2 + - + +
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Residues in contact with GLU1320 (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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1045D LEU* 3.7 19.5 - - + +
1270D PHE* 3.7 23.1 - - + -
1274D LEU* 3.7 16.7 - - + +
1316D ALA 2.8 17.0 + - - +
1317D LYS* 2.9 36.4 + - - +
1319D ILE* 1.3 77.5 - - - +
1321D LYS* 1.3 58.1 + - - +
1323D VAL* 3.1 4.5 + - - +
1324D ARG* 2.8 64.6 + - - +
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Residues in contact with LYS1321 (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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1317D LYS 2.9 19.3 + - - +
1318D GLU* 3.7 8.7 - - - +
1320D GLU* 1.3 76.7 - - - +
1322D LYS* 1.3 57.9 + - + +
1324D ARG* 3.5 9.9 + - - +
1325D GLU* 3.0 48.2 + - + +
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Residues in contact with LYS1322 (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 LEU* 3.7 27.8 - - + -
1293D TYR* 4.5 5.4 + - - +
1294D LYS* 5.8 2.0 - - - +
1318D GLU* 3.3 41.9 + - + +
1319D ILE* 3.2 9.5 + - - +
1321D LYS* 1.3 78.0 - - + +
1323D VAL* 1.3 60.5 + - - +
1325D GLU* 3.3 16.5 + - - +
1326D LEU* 2.9 34.9 + - + +
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Residues in contact with VAL1323 (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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1045D LEU* 4.2 7.9 - - + -
1049D ILE* 4.1 19.3 - - + -
1274D LEU* 4.5 5.2 - - + -
1277D LEU* 4.0 24.9 - - + +
1278D GLY* 4.4 16.6 - - - +
1281D GLU* 5.1 2.7 - - + -
1283D LEU* 3.8 17.0 - - + -
1319D ILE* 2.9 26.8 + - + +
1320D GLU* 3.5 9.4 - - - +
1322D LYS* 1.3 75.4 - - - +
1324D ARG* 1.3 58.0 + - - +
1326D LEU* 3.3 7.1 + - - +
1327D LEU* 2.9 38.3 + - + +
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Residues in contact with ARG1324 (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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1041D SER* 4.4 7.7 + - - -
1045D LEU* 3.8 18.1 - - + +
1048D ASP* 2.7 37.2 + - - +
1049D ILE* 5.4 3.8 - - + -
1054D GLY* 3.3 32.3 + - - -
1270D PHE* 5.5 1.2 - - - -
1320D GLU* 2.8 49.7 + - - +
1321D LYS* 3.7 8.1 - - - +
1323D VAL* 1.3 76.5 - - - +
1325D GLU* 1.3 58.1 + - - +
1327D LEU* 5.3 0.4 - - - -
1328D LEU* 2.8 61.4 + - + +
1331D PRO* 5.7 0.6 - - - +
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Residues in contact with GLU1325 (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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1321D LYS* 3.0 45.0 + - + +
1322D LYS* 3.3 16.1 + - - +
1324D ARG* 1.3 76.2 - - + +
1326D LEU* 1.3 62.9 + - + +
1328D LEU 4.5 6.1 + - - +
1331D PRO* 5.5 8.7 - - - +
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Residues in contact with LEU1326 (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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4282A LYS* 5.7 1.8 - - - +
1281D GLU* 3.8 42.6 - - + +
1283D LEU* 4.4 19.5 - - + -
1322D LYS* 2.9 23.7 + - + +
1323D VAL* 3.6 4.5 - - - +
1325D GLU* 1.3 79.8 - - + +
1327D LEU* 1.3 66.0 + - + +
1328D LEU 5.2 0.8 - - - +
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Residues in contact with LEU1327 (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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1049D ILE* 3.8 31.7 - - + +
1256D LYS* 5.2 2.9 + - - -
1277D LEU* 3.8 28.7 - - + -
1280D LYS* 5.2 8.3 - - - +
1281D GLU* 3.6 41.1 - - + +
1323D VAL* 2.9 25.8 + - + +
1326D LEU* 1.3 83.1 - - - +
1328D LEU* 1.3 63.2 + - - +
1329D SER* 3.4 4.3 + - - -
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Residues in contact with LEU1328 (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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1048D ASP 3.4 26.7 - - - +
1049D ILE* 3.6 21.5 - - + +
1052D GLY 3.8 9.6 - - - +
1053D ALA 4.5 3.8 - - - +
1054D GLY* 3.8 15.5 - - - +
1324D ARG* 2.8 62.4 + - + +
1325D GLU 4.6 4.7 - - - +
1326D LEU 5.2 0.7 - - - +
1327D LEU* 1.3 70.1 - - - +
1329D SER* 1.3 63.7 + - - +
1330D ASN 3.2 2.2 + - - +
1331D PRO* 3.6 30.1 - - + +
1332D ASN 5.5 1.6 - - - +
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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