Contacts of the helix formed by residues 1312 - 1328 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1308A TRP* 2.8 55.9 + - + +
1309A LEU* 3.3 8.2 - - - +
1310A LYS 3.4 0.2 - - - -
1311A ASP* 1.3 88.2 - - - +
1313A PRO* 1.3 60.3 - - - +
1314A GLU* 3.2 6.1 + - + -
1315A THR* 3.2 21.3 + - - +
1316A ALA 3.0 22.3 + - - -
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Residues in contact with PRO1313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1271A TYR* 4.8 8.7 - - - +
1309A LEU 3.9 6.7 - - - +
1310A LYS 3.6 13.7 - - - +
1311A ASP 3.2 11.9 - - - +
1312A ASN* 1.3 84.9 - - - +
1314A GLU* 1.3 78.2 + - + +
1315A THR 3.4 0.2 - - - -
1316A ALA* 3.5 5.8 - - + +
1317A LYS* 3.0 37.4 + - + +
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Residues in contact with GLU1314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1312A ASN* 4.7 2.7 - - + -
1313A PRO* 1.3 101.1 - - + +
1315A THR* 1.3 63.7 + - - +
1317A LYS* 3.5 8.5 + - - +
1318A GLU* 3.3 20.1 + - - +
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Residues in contact with THR1315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1293A TYR* 3.4 37.9 - - + +
1308A TRP* 4.0 18.0 - - + -
1312A ASN* 3.2 26.6 + - - +
1314A GLU* 1.3 76.6 - - - +
1316A ALA* 1.3 62.1 + - - +
1318A GLU* 3.2 12.0 + - - +
1319A ILE* 3.0 31.9 + - + +
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Residues in contact with ALA1316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270A PHE* 6.3 0.2 - - + -
1271A TYR* 3.7 29.8 - - + +
1274A LEU* 3.7 14.0 - - + +
1309A LEU* 3.8 20.4 - - + +
1312A ASN 3.0 13.2 + - - +
1313A PRO* 3.5 10.1 - - + +
1315A THR* 1.3 76.7 - - - +
1317A LYS* 1.3 61.2 + - - +
1319A ILE* 3.2 1.5 + - - -
1320A GLU* 2.8 32.0 + - - +
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Residues in contact with LYS1317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270A PHE* 4.8 10.1 - - - -
1271A TYR* 5.3 8.6 + - - -
1313A PRO* 3.0 25.6 + - + +
1314A GLU* 3.7 8.7 - - - +
1315A THR 3.3 0.2 - - - -
1316A ALA* 1.3 80.7 - - - +
1318A GLU* 1.3 58.6 + - - +
1320A GLU* 2.9 27.2 + - - +
1321A LYS* 2.9 33.3 + - - +
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Residues in contact with GLU1318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1293A TYR* 2.7 26.5 + - - +
1294A LYS* 3.7 17.8 + - - -
1314A GLU 3.3 10.8 + - - +
1315A THR* 3.2 15.2 + - - +
1316A ALA 3.2 0.6 - - - -
1317A LYS* 1.3 77.2 - - - +
1319A ILE* 1.3 64.0 + - - +
1321A LYS* 3.5 8.4 + - - +
1322A LYS* 3.3 46.4 + - - +
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Residues in contact with ILE1319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1274A LEU* 4.3 12.8 - - + -
1278A GLY* 4.6 2.7 - - - -
1283A LEU* 4.1 22.9 - - + -
1284A ILE* 4.3 19.7 - - + -
1293A TYR* 3.8 45.8 - - + +
1298A ILE* 6.2 0.4 - - + -
1308A TRP* 5.3 0.9 - - + -
1309A LEU* 3.9 24.5 - - + -
1315A THR* 3.0 19.2 + - + +
1316A ALA 3.8 2.7 - - - +
1318A GLU* 1.3 72.0 - - - +
1320A GLU* 1.3 67.3 + - - +
1322A LYS* 3.2 8.2 + - - +
1323A VAL* 2.9 28.4 + - + +
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Residues in contact with GLU1320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045A LEU* 3.8 18.2 - - + -
1270A PHE* 3.7 21.9 - - + -
1274A LEU* 3.7 17.9 - - + +
1316A ALA 2.8 17.4 + - - +
1317A LYS* 2.9 36.5 + - - +
1319A ILE* 1.3 76.3 - - - +
1321A LYS* 1.3 55.7 + - - +
1323A VAL* 3.1 3.9 + - - +
1324A ARG* 2.8 62.2 + - - +
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Residues in contact with LYS1321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1317A LYS 2.9 19.8 + - - +
1318A GLU* 3.7 8.1 - - - +
1320A GLU* 1.3 74.6 - - - +
1322A LYS* 1.3 58.4 + - + +
1324A ARG* 3.5 10.0 + - - +
1325A GLU* 3.0 48.1 + - + +
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Residues in contact with LYS1322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283A LEU* 3.7 27.4 - - + -
1293A TYR* 4.5 5.0 + - - +
1294A LYS* 5.8 2.2 - - - +
1318A GLU* 3.3 41.5 + - - +
1319A ILE* 3.2 9.7 + - - +
1321A LYS* 1.3 77.1 - - + +
1323A VAL* 1.3 60.9 + - - +
1325A GLU* 3.6 15.1 - - - +
1326A LEU* 2.9 35.5 + - + +
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Residues in contact with VAL1323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045A LEU* 4.3 8.7 - - + -
1049A ILE* 4.2 14.4 - - + -
1274A LEU* 4.6 5.2 - - + -
1277A LEU* 4.0 24.0 - - + +
1278A GLY* 4.4 15.7 - - - +
1281A GLU* 5.0 2.7 - - + -
1283A LEU* 3.8 17.5 - - + -
1319A ILE* 2.9 27.0 + - + +
1320A GLU* 3.6 8.7 - - - +
1322A LYS* 1.3 73.8 - - - +
1324A ARG* 1.3 58.0 + - - +
1326A LEU* 3.3 7.9 + - - +
1327A LEU* 2.9 43.7 + - + +
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Residues in contact with ARG1324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041A SER* 4.6 7.7 + - - -
1045A LEU* 3.6 21.9 - - + +
1048A ASP* 2.9 32.7 + - - +
1049A ILE* 5.4 2.2 - - + -
1054A GLY* 3.6 19.6 + - - -
1270A PHE* 5.5 1.8 - - - -
1320A GLU* 2.8 48.2 + - - +
1321A LYS* 3.7 7.9 - - - +
1323A VAL* 1.3 74.5 - - - +
1325A GLU* 1.3 61.1 + - + +
1327A LEU* 5.2 0.7 - - - -
1328A LEU* 2.8 71.4 + - + +
1331A PRO* 5.7 0.2 - - - +
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Residues in contact with GLU1325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1321A LYS* 3.0 45.6 + - + +
1322A LYS* 3.6 14.8 - - - +
1324A ARG* 1.3 76.4 - - + +
1326A LEU* 1.3 62.3 + - + +
1327A LEU 3.6 0.2 + - - -
1328A LEU 4.5 6.2 + - - +
1331A PRO* 5.6 5.1 - - - +
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Residues in contact with LEU1326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1281A GLU* 3.9 42.4 - - + +
1283A LEU* 4.4 19.3 - - + -
1322A LYS* 2.9 23.3 + - + +
1323A VAL* 3.6 4.9 - - - +
1325A GLU* 1.3 80.0 - - + +
1327A LEU* 1.3 67.0 + - + +
1328A LEU 5.3 0.6 - - - +
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Residues in contact with LEU1327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049A ILE* 3.8 32.1 - - + +
1256A LYS* 5.3 2.3 + - - -
1277A LEU* 3.8 28.7 - - + -
1280A LYS* 5.2 8.1 - - - +
1281A GLU* 3.6 40.8 - - + +
1323A VAL* 2.9 21.3 + - + +
1326A LEU* 1.3 86.0 - - - +
1328A LEU* 1.3 64.5 + - - +
1329A SER* 3.4 5.4 + - - -
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Residues in contact with LEU1328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048A ASP 3.6 25.1 - - - +
1049A ILE* 3.7 22.0 - - + +
1052A GLY 4.0 7.4 - - - +
1053A ALA 4.9 3.1 - - - +
1054A GLY* 3.8 17.5 - - - +
1324A ARG* 2.8 61.2 + - + +
1325A GLU 4.5 5.0 - - - +
1326A LEU 5.3 0.5 - - - -
1327A LEU* 1.3 72.2 - - - +
1329A SER* 1.3 62.2 + - - +
1331A PRO* 3.6 32.5 - - + +
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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
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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