Contacts of the helix formed by residues 1418 - 1431 (chain A) in PDB entry 5IRC
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 THR1418 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1401A TRP* 3.5 32.7 - - + -
1407A PRO* 4.4 2.2 - - + -
1408A ASP 4.1 9.4 - - - +
1409A PHE* 3.9 15.7 - - + -
1414A ALA 3.2 18.2 - - - +
1415A LEU* 2.5 27.6 + - - +
1417A ALA* 1.3 78.6 - - - +
1419A ARG* 1.3 63.9 + - - +
1420A SER 3.1 2.5 - - - -
1421A TYR* 3.0 30.0 + - + +
1422A GLN* 3.2 9.7 + - - +
38F VAL* 5.9 0.3 - - - +
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Residues in contact with ARG1419 (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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1415A LEU 4.5 2.2 - - - +
1416A THR* 3.2 51.5 + - - +
1418A THR* 1.3 79.7 + - - +
1420A SER* 1.3 61.2 + - - +
1422A GLN* 3.5 12.0 + - - +
1423A THR* 3.1 24.7 + - - -
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Residues in contact with SER1420 (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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1342A VAL* 3.9 26.0 - - - +
1345A HIS* 4.3 16.8 - - - -
1416A THR 4.9 0.2 + - - -
1417A ALA 3.5 15.8 + - - -
1419A ARG* 1.3 77.8 - - - +
1421A TYR* 1.3 61.9 + - - +
1423A THR* 3.2 7.6 + - - -
1424A ILE* 2.9 40.3 + - - +
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Residues in contact with TYR1421 (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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1338A GLN* 4.2 30.1 + - + +
1339A ILE* 6.0 1.0 - - - +
1341A LEU* 6.4 0.2 - - + -
1342A VAL* 3.4 32.0 - - + +
1401A TRP* 3.5 36.1 - + + -
1405A MET* 3.8 18.6 - - + -
1407A PRO* 4.9 6.7 - - + -
1408A ASP 6.1 0.4 - - - -
1417A ALA* 3.9 15.0 - - + -
1418A THR* 3.0 32.3 + - + +
1420A SER* 1.3 74.8 + - - +
1422A GLN* 1.3 66.3 + - - +
1424A ILE* 3.3 7.4 + - + +
1425A ILE* 3.1 29.3 + - - +
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Residues in contact with GLN1422 (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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1394A GLU* 4.2 17.1 + - - +
1397A SER* 2.6 33.2 + - - +
1398A ILE* 3.4 36.6 - - + +
1401A TRP* 3.5 21.8 + - + +
1418A THR 3.2 6.3 + - - +
1419A ARG* 3.7 12.9 + - - +
1420A SER 3.3 0.2 - - - -
1421A TYR* 1.3 80.2 - - - +
1423A THR* 1.3 58.7 + - - +
1426A GLU* 3.0 21.6 + - - +
38F VAL* 4.5 12.8 - - - +
66F TYR* 5.0 0.3 + - - -
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Residues in contact with THR1423 (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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1345A HIS* 3.3 31.5 - - + +
1350A ARG* 6.3 0.2 - - - +
1419A ARG 3.1 13.4 + - - -
1420A SER* 3.2 8.3 + - - -
1422A GLN* 1.3 81.4 + - - +
1424A ILE* 1.3 57.7 + - - +
1426A GLU* 3.2 13.7 + - + +
1427A LEU* 2.9 36.0 + - + +
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Residues in contact with ILE1424 (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 LEU* 3.8 44.6 - - + +
1342A VAL* 4.0 12.8 - - + +
1345A HIS* 3.8 26.9 - - + -
1357A LEU* 4.5 8.2 - - + +
1405A MET* 4.6 6.7 - - + -
1420A SER* 2.9 26.5 + - - +
1421A TYR* 3.7 9.9 - - + +
1422A GLN 3.3 0.2 - - - -
1423A THR* 1.3 77.1 - - - +
1425A ILE* 1.3 64.0 + - - +
1427A LEU* 3.2 10.7 + - - +
1428A PHE* 3.0 46.0 + - + -
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Residues in contact with ILE1425 (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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1372A PHE* 3.9 32.3 - - + -
1376A ILE* 4.4 7.9 - - + -
1379A LEU* 5.6 1.8 - - + -
1397A SER* 3.5 20.0 - - - +
1400A PHE* 5.8 0.2 - - + -
1401A TRP* 3.5 29.8 - - + +
1404A LEU* 4.8 8.5 - - + -
1405A MET* 3.6 28.5 - - + -
1421A TYR 3.1 10.0 + - - +
1424A ILE* 1.3 73.1 - - - +
1426A GLU* 1.3 66.2 + - - +
1428A PHE* 3.2 8.6 + - + +
1429A ILE* 3.0 40.2 + - + +
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Residues in contact with GLU1426 (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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1393A SER* 3.9 9.2 - - - -
1394A GLU* 3.5 47.4 + - - +
1397A SER* 3.5 12.0 + - - -
1422A GLN* 3.0 23.9 + - - +
1423A THR* 3.4 14.1 - - - +
1424A ILE 3.2 0.2 - - - -
1425A ILE* 1.3 75.8 - - - +
1427A LEU* 1.3 61.0 + - + +
1429A ILE* 3.3 3.3 + - - +
1430A GLN* 2.8 34.4 + - + +
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Residues in contact with LEU1427 (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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1345A HIS* 4.0 28.5 - - + +
1350A ARG* 3.3 33.9 - - - +
1353A LYS* 4.0 16.2 - - + -
1354A LEU* 4.4 5.4 - - + -
1357A LEU* 4.1 13.0 - - + -
1423A THR* 2.9 21.4 + - + +
1424A ILE* 3.5 8.3 - - - +
1426A GLU* 1.3 77.7 - - + +
1428A PHE* 1.3 60.4 + - + +
1430A GLN* 4.5 3.4 - - + +
1431A GLN* 2.8 48.8 + - + +
1435A PHE* 3.7 9.7 - - + -
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Residues in contact with PHE1428 (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 LEU* 3.9 27.6 - - + -
1357A LEU* 4.3 12.6 - - + -
1361A LEU* 3.6 32.5 - - + -
1372A PHE* 3.9 21.3 - + - -
1376A ILE* 3.3 25.7 - - + +
1424A ILE* 3.0 45.1 + - + -
1425A ILE* 3.2 9.4 + - + +
1427A LEU* 1.3 77.6 - - + +
1429A ILE* 1.3 57.4 + - - +
1432A CSX 3.1 27.7 + - - -
1435A PHE* 3.6 41.4 - + + -
1436A PHE* 4.3 8.1 - + - -
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Residues in contact with ILE1429 (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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1376A ILE* 3.8 21.5 - - + -
1379A LEU* 3.9 30.1 - - + +
1380A ASN* 2.8 50.6 + - - +
1383A SER* 4.6 1.1 - - - +
1393A SER* 3.4 25.6 - - - +
1396A LEU* 3.9 7.0 - - + -
1397A SER* 3.9 20.6 - - - +
1425A ILE* 3.0 30.5 + - + +
1426A GLU 3.7 3.6 - - - +
1428A PHE* 1.3 75.2 - - - +
1430A GLN* 1.3 62.6 + - - +
1432A CSX 3.3 6.9 + - - +
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Residues in contact with GLN1430 (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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1380A ASN* 4.0 8.5 + - - +
1383A SER* 5.2 1.4 + - - -
1393A SER* 2.9 26.7 + - - +
1426A GLU* 2.8 27.4 + - + +
1427A LEU* 4.2 3.8 - - + +
1429A ILE* 1.3 75.3 - - - +
1431A GLN* 1.3 84.7 + - + +
1432A CSX 3.3 1.8 + - - -
1433A PRO* 4.3 4.0 - - - +
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Residues in contact with GLN1431 (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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1350A ARG* 4.8 11.7 - - - +
1354A LEU* 4.5 19.7 - - + -
1427A LEU* 2.8 29.4 + - + +
1428A PHE 3.7 3.4 - - - -
1430A GLN* 1.3 102.7 - - + +
1432A CSX 1.3 64.3 + - - +
1433A PRO* 3.2 3.4 - - - -
1434A PHE* 3.0 16.3 + - + -
1435A PHE* 3.2 22.5 + - + -
1501A CL 3.3 22.4 - - + +
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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