Contacts of the helix formed by residues 1356 - 1368 (chain A) in PDB entry 4C2A
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 SER1356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1321A TYR* 3.5 12.6 - - - +
1322A HIS 2.9 15.9 + - - +
1323A ASP 4.7 1.6 - - - -
1354A VAL* 4.0 2.1 - - - +
1355A ALA* 1.3 69.7 - - - +
1357A THR* 1.3 62.3 + - - +
1358A SER* 4.0 2.3 - - - -
1359A GLU* 3.2 36.8 + - - +
1360A VAL 3.3 15.8 + - - -
1389A GLU* 2.7 24.0 + - - -
1393A MET* 3.6 23.3 - - - +
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Residues in contact with THR1357 (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 TYR* 4.0 20.4 - - + +
1355A ALA 3.3 6.3 + - - +
1356A SER* 1.3 69.9 - - - +
1358A SER* 1.3 66.3 + - - +
1360A VAL* 3.2 10.2 - - - +
1361A LEU* 3.1 28.2 + - - +
1383A LEU* 4.6 8.3 - - + -
1385A MET* 3.9 24.7 - - + -
1387A SER* 5.5 5.4 - - - +
1388A GLN* 6.4 0.2 - - - -
1389A GLU* 3.1 12.6 + - + +
1397A PHE* 3.9 7.6 - - - -
1421A ASN* 5.7 0.4 - - + -
1424A GLN* 2.4 34.5 + - - +
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Residues in contact with SER1358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1356A SER* 4.0 1.3 - - - -
1357A THR* 1.3 80.7 + - - +
1359A GLU* 1.3 58.8 + - - +
1361A LEU* 3.9 1.2 - - - +
1362A LYS* 2.9 29.3 + - - +
1389A GLU* 2.6 24.5 + - - -
1393A MET 3.2 23.6 + - - -
1394A SER* 3.6 0.4 - - - -
1397A PHE* 3.4 34.3 - - - +
1400A TYR* 3.5 15.0 - - - -
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Residues in contact with GLU1359 (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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1322A HIS 5.7 0.2 - - - +
1323A ASP 4.3 12.3 - - - +
1324A GLY* 5.4 6.1 - - - -
1325A SER* 4.8 1.6 - - - +
1356A SER* 3.2 28.7 + - - +
1358A SER* 1.3 78.3 - - - +
1360A VAL* 1.3 57.3 + - - +
1362A LYS* 3.2 9.4 + - - +
1363A TYR* 2.8 29.9 + - - +
1393A MET* 4.2 15.5 - - + +
199B PHE* 5.3 1.2 - - - -
225B GLU* 4.7 5.4 - - - +
228B TYR* 2.7 33.2 + - - -
241B SER* 3.6 24.3 + - - -
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Residues in contact with VAL1360 (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 LEU* 3.8 27.6 - - + -
1319A VAL* 4.3 3.8 - - + -
1321A TYR* 3.6 34.1 - - + -
1325A SER* 3.5 21.3 - - - +
1356A SER 3.3 9.0 + - - +
1357A THR* 3.2 17.7 - - - +
1359A GLU* 1.3 79.7 - - - +
1361A LEU* 1.3 56.7 + - + +
1363A TYR* 3.6 1.9 - - + +
1364A THR* 2.6 37.0 + - - -
1383A LEU* 3.9 22.7 - - + -
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Residues in contact with LEU1361 (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 LEU* 4.2 21.8 - - + -
1357A THR 3.1 16.3 + - - +
1358A SER* 4.0 3.8 - - - +
1360A VAL* 1.3 75.6 - - + +
1362A LYS* 1.3 60.5 + - - +
1364A THR* 3.7 4.0 - - - +
1365A LEU* 2.9 31.7 + - - +
1381A ALA* 5.3 2.2 - - + -
1383A LEU* 4.3 20.0 - - + -
1397A PHE* 3.6 33.7 - - + +
1400A TYR* 4.2 13.0 - - + -
1401A VAL* 4.0 19.5 - - + -
1404A LEU* 4.0 22.9 - - + +
1411A VAL* 4.7 10.3 - - + -
1428A ILE* 4.8 3.1 - - + -
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Residues in contact with LYS1362 (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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1358A SER 2.9 19.0 + - - +
1359A GLU* 3.2 9.8 + - - +
1361A LEU* 1.3 77.2 - - - +
1363A TYR* 1.3 63.0 + - - +
1365A LEU* 3.3 1.8 + - - +
1366A PHE* 3.0 33.9 + - + +
1400A TYR* 3.4 45.9 + - + +
198B PRO* 2.9 38.0 + - - -
199B PHE* 3.6 19.7 - - + -
225B GLU* 3.4 7.7 + - - +
226B ASN* 3.3 15.5 + - - -
228B TYR* 2.8 29.0 + - - +
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Residues in contact with TYR1363 (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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1319A VAL* 4.4 13.7 - - + -
1325A SER* 3.6 29.4 - - - +
1327A ALA* 3.7 20.0 - - + +
1359A GLU 2.8 19.9 + - - +
1360A VAL* 3.6 6.1 - - + +
1362A LYS* 1.3 74.2 - - - +
1364A THR* 1.3 56.7 + - - +
1367A GLN* 2.7 62.6 + - + +
1368A ILE* 3.4 29.1 + - + +
199B PHE* 4.0 11.8 - + + -
237B LYS* 4.4 16.2 + - - +
239B VAL* 3.7 40.2 - - + +
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Residues in contact with THR1364 (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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1279A VAL* 4.9 3.6 - - + -
1281A LEU* 3.7 23.6 - - - +
1360A VAL* 2.6 21.8 + - - +
1361A LEU* 3.7 8.7 - - - -
1362A LYS 3.3 0.2 - - - -
1363A TYR* 1.3 77.5 - - - +
1365A LEU* 1.3 58.1 + - - +
1368A ILE* 3.3 21.1 + - + +
1369A PHE* 2.9 57.6 + - + +
1381A ALA* 4.4 14.1 - - + -
1404A LEU* 4.1 10.3 - - + -
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Residues in contact with LEU1365 (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 LEU 2.9 17.5 + - - +
1362A LYS 3.7 3.6 - - - +
1364A THR* 1.3 80.6 - - - +
1366A PHE* 1.3 89.6 + - + +
1369A PHE* 3.6 3.7 - - - +
1370A SER* 3.5 18.0 + - - -
1399A ARG 4.7 0.7 - - - +
1400A TYR* 4.0 20.9 - - + +
1403A GLY* 3.5 44.9 - - - +
1404A LEU* 3.7 16.5 - - + +
1407A LYS* 3.9 19.0 - - + -
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Residues in contact with PHE1366 (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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1362A LYS* 3.0 27.3 + - + +
1365A LEU* 1.3 102.7 - - + +
1367A GLN* 1.3 66.0 + - - +
1370A SER* 3.2 8.8 - - - -
1400A TYR* 4.3 18.4 - + - -
152B LYS* 2.8 30.3 + - - -
175B ASP* 3.6 36.8 - - + +
198B PRO* 3.9 22.0 - - + -
199B PHE* 3.7 25.4 - + + -
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Residues in contact with GLN1367 (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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1363A TYR* 2.7 61.1 + - + +
1366A PHE* 1.3 79.0 - - - +
1368A ILE* 1.3 61.3 + - - +
1370A SER* 4.6 4.2 + - - -
152B LYS* 3.7 15.7 - - - +
176B THR* 2.9 32.0 + - - +
199B PHE* 3.3 33.5 - - + +
201B PHE* 5.5 3.5 - - - -
239B VAL* 5.8 1.3 - - + -
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Residues in contact with ILE1368 (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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1279A VAL* 3.9 38.1 - - + -
1317A ALA* 4.8 7.4 - - + -
1319A VAL* 4.2 11.2 - - + -
1331A LEU* 4.0 30.2 - - + +
1363A TYR* 3.8 32.3 - - + +
1364A THR* 3.3 21.9 + - + +
1367A GLN* 1.3 83.9 - - - +
1369A PHE* 1.3 67.2 + - + +
1370A SER* 3.4 5.8 + - - -
1371A LYS 5.0 3.6 + - - +
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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