Contacts of the helix formed by residues 1377 - 1396 (chain A) in PDB entry 3MB3
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 SER1377 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1321A TRP* 3.8 11.0 - - - -
1375A TYR* 3.2 4.6 - - - +
1376A GLU* 1.3 91.8 + - - +
1378A PRO* 1.3 76.8 - - - +
1379A MET* 3.3 27.3 + - - +
1380A GLU* 2.9 33.1 + - - +
1381A LEU 3.7 2.3 + - - -
1425A TYR* 3.7 15.9 - - - -
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Residues in contact with PRO1378 (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 TRP* 3.6 50.3 - - + -
1325A CYS* 4.6 4.7 - - - -
1377A SER* 1.3 87.9 - - - +
1379A MET* 1.3 61.2 + - - +
1381A LEU* 3.2 7.6 + - + +
1382A CYS* 3.0 23.7 + - - +
1418A ILE* 5.5 1.5 - - + +
1421A VAL* 4.6 9.6 - - + -
1422A LEU* 4.0 16.2 - - + -
1425A TYR* 3.7 36.8 - - + -
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Residues in contact with MET1379 (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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1377A SER* 3.1 25.8 + - - +
1378A PRO* 1.3 76.2 - - - +
1380A GLU* 1.3 64.5 + - - +
1382A CYS* 3.2 9.5 + - - +
1383A LYS* 3.0 35.6 + - - +
1422A LEU* 4.1 18.2 - - + -
1425A TYR* 3.7 34.8 - - + +
1426A LYS* 4.3 24.7 - - - +
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Residues in contact with GLU1380 (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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1375A TYR* 3.6 25.8 - - + -
1376A GLU* 4.4 11.0 - - + +
1377A SER* 2.9 31.6 + - - +
1379A MET* 1.3 76.7 - - - +
1381A LEU* 1.3 65.5 + - - +
1383A LYS* 3.1 40.9 + - - +
1384A ASP* 3.2 18.0 + - - +
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Residues in contact with LEU1381 (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 TRP* 5.1 1.1 - - + -
1325A CYS* 4.0 35.9 - - + -
1329A LEU* 4.3 6.3 - - + -
1366A VAL* 3.9 17.3 - - + -
1370A LEU* 4.1 15.9 - - + -
1375A TYR* 3.5 39.2 - - + -
1377A SER 3.7 1.4 + - - -
1378A PRO* 3.2 15.5 + - + +
1380A GLU* 1.3 78.2 - - - +
1382A CYS* 1.3 67.3 + - - +
1384A ASP* 3.1 4.9 + - - +
1385A VAL* 2.9 39.6 + - + +
1414A PHE* 4.4 11.7 - - + -
1418A ILE* 4.8 2.9 - - + -
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Residues in contact with CYS1382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1378A PRO 3.0 15.2 + - - +
1379A MET* 3.3 11.9 - - - +
1381A LEU* 1.3 81.7 - - - +
1383A LYS* 1.3 57.5 + - + +
1385A VAL* 3.4 1.0 + - - +
1386A ARG* 2.9 51.4 + - - +
1414A PHE* 4.2 11.8 - - - -
1418A ILE* 3.4 37.5 - - - -
1422A LEU* 4.2 18.2 - - - -
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Residues in contact with LYS1383 (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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1379A MET* 3.0 19.5 + - - +
1380A GLU* 3.1 41.1 + - - +
1381A LEU 3.2 0.2 - - - -
1382A CYS* 1.3 77.9 - - - +
1384A ASP* 1.3 67.1 + - - +
1386A ARG* 3.4 7.5 + - - +
1387A LEU* 3.0 24.1 + - - +
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Residues in contact with ASP1384 (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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1361A MET* 3.4 33.6 - - + +
1366A VAL* 3.9 10.1 - - + -
1369A THR* 4.9 3.6 + - - +
1375A TYR* 2.7 37.4 + - - +
1380A GLU 3.2 7.8 + - - +
1381A LEU 3.1 6.4 + - - +
1383A LYS* 1.3 82.4 - - - +
1385A VAL* 1.3 63.0 + - - +
1387A LEU* 3.1 27.2 + - - +
1388A ILE 3.3 5.0 + - - -
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Residues in contact with VAL1385 (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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1329A LEU* 4.4 3.1 - - + -
1363A PHE* 3.9 22.0 - - + -
1366A VAL* 4.0 17.0 - - + -
1381A LEU* 2.9 41.5 + - + +
1382A CYS 4.0 0.2 - - - +
1384A ASP* 1.3 71.2 - - - +
1386A ARG* 1.3 62.0 + - - +
1388A ILE* 3.1 23.8 + - - +
1389A PHE* 3.4 18.9 - - + -
1414A PHE* 3.6 46.0 - - + -
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Residues in contact with ARG1386 (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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1382A CYS* 2.9 39.4 + - - +
1383A LYS* 3.9 6.7 - - - +
1385A VAL* 1.3 78.1 - - - +
1387A LEU* 1.3 57.2 + - - +
1389A PHE* 3.3 11.2 + - + +
1390A SER* 3.0 28.3 + - - -
1414A PHE* 4.8 5.9 - - + -
1415A GLU* 2.8 43.5 + - - +
1418A ILE* 4.6 8.3 - - - +
1422A LEU* 5.1 8.5 - - - +
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Residues in contact with LEU1387 (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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1359A THR* 3.9 38.6 - - + +
1361A MET* 4.1 17.0 - - + -
1383A LYS 3.0 13.8 + - - +
1384A ASP* 3.2 20.4 - - - +
1386A ARG* 1.3 76.5 - - - +
1388A ILE* 1.3 62.8 + - - -
1389A PHE 3.1 0.4 - - - -
1390A SER* 3.3 15.2 + - - +
1391A ASN* 2.9 43.8 + - - +
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Residues in contact with ILE1388 (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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1341A PHE* 3.9 33.7 - - + -
1361A MET* 3.7 37.5 - - + +
1362A ASP 3.5 29.4 - - - +
1363A PHE* 3.6 34.8 - - + +
1366A VAL* 4.3 6.5 - - + -
1384A ASP 3.7 3.8 - - - +
1385A VAL* 3.1 9.6 + - - +
1387A LEU* 1.3 76.5 - - - +
1389A PHE* 1.3 66.0 + - + +
1391A ASN* 3.6 4.0 - - - +
1392A SER* 3.1 25.1 + - - -
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Residues in contact with PHE1389 (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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1341A PHE* 5.0 2.5 - + - -
1363A PHE* 3.8 23.1 - + - -
1385A VAL* 3.4 32.7 + - + -
1386A ARG* 3.3 13.3 + - + +
1387A LEU 3.1 0.4 - - - -
1388A ILE* 1.3 84.6 - - + +
1390A SER* 1.3 58.7 + - - +
1392A SER* 3.3 3.6 + - - -
1393A LYS* 2.9 28.1 + - - +
1407A SER* 3.7 35.9 + - - +
1410A LEU* 4.0 23.1 - - + -
1411A SER* 3.6 41.3 - - - +
1414A PHE* 4.1 11.0 - + + -
1415A GLU* 5.4 0.2 - - - -
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Residues in contact with SER1390 (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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1386A ARG 3.0 15.0 + - - -
1387A LEU* 3.3 24.3 + - - +
1389A PHE* 1.3 72.5 - - - +
1391A ASN* 1.3 69.0 + - - +
1393A LYS* 3.4 8.7 + - - +
1394A ALA* 3.0 25.5 + - - +
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Residues in contact with ASN1391 (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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1353A TYR* 3.6 17.7 + - - +
1357A ILE* 3.6 25.6 - - + +
1358A ASP 5.6 0.2 + - - -
1359A THR 2.8 27.0 + - - +
1360A PRO* 3.5 14.3 - - - +
1361A MET 3.5 10.3 + - - +
1387A LEU* 2.9 37.8 + - - +
1388A ILE* 3.6 4.9 - - - +
1390A SER* 1.3 78.5 + - - +
1392A SER* 1.3 59.0 + - - +
1394A ALA* 3.0 4.4 + - - +
1395A TYR* 2.8 31.2 + - - +
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Residues in contact with SER1392 (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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1A MB3 4.7 9.9 + - - -
1341A PHE* 3.7 24.7 - - - -
1353A TYR* 4.8 1.1 + - - -
1388A ILE 3.1 12.4 + - - -
1389A PHE 3.3 7.4 + - - -
1391A ASN* 1.3 79.7 - - - +
1393A LYS* 1.3 53.6 + - - +
1395A TYR* 4.5 1.1 - - - +
1396A THR* 2.7 39.4 + - - +
1403A ILE* 4.3 10.4 + - - +
1404A TYR* 5.3 1.0 - - - -
1407A SER* 3.7 24.0 + - - -
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Residues in contact with LYS1393 (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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1389A PHE 2.9 16.3 + - - +
1390A SER* 3.9 8.3 - - - +
1391A ASN 3.2 0.4 - - - -
1392A SER* 1.3 77.1 - - - +
1394A ALA* 1.3 59.9 + - - +
1396A THR 4.0 5.4 - - - -
1397A PRO* 3.4 24.0 - - + +
1404A TYR* 4.6 29.4 - - + -
1407A SER* 5.1 1.0 + - - +
1408A LEU* 6.4 2.9 - - + -
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Residues in contact with ALA1394 (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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1356A ILE* 3.9 15.0 - - + +
1357A ILE* 4.0 14.4 - - + -
1390A SER 3.0 17.5 + - - +
1391A ASN* 3.6 3.1 - - - +
1393A LYS* 1.3 80.0 - - - +
1395A TYR* 1.3 60.3 + - - +
1397A PRO* 4.0 9.4 - - - +
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Residues in contact with TYR1395 (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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1A MB3 4.0 10.5 - - - +
1350A TYR* 3.7 33.6 - + - +
1352A ASP* 2.9 28.1 + - - -
1353A TYR* 3.7 51.4 - + + -
1356A ILE* 3.8 31.9 - - + -
1357A ILE* 4.2 4.5 - - + -
1391A ASN 2.8 15.4 + - - +
1392A SER 4.2 1.3 - - - +
1394A ALA* 1.3 79.7 - - - +
1396A THR* 1.3 66.6 + - - +
1397A PRO* 3.4 7.7 - - - +
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Residues in contact with THR1396 (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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1A MB3 4.0 19.0 + - - -
1392A SER* 2.7 28.4 + - - +
1393A LYS* 3.8 2.8 - - - +
1395A TYR* 1.3 88.9 + - - +
1397A PRO* 1.3 62.8 - - - +
1398A SER* 3.4 2.2 + - - +
1401A SER* 3.4 34.5 - - - +
1403A ILE* 4.1 13.8 - - + +
1404A TYR* 3.7 18.5 - - - +
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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