Contacts of the helix formed by residues 1417 - 1432 (chain A) in PDB entry 5XA0
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 GLU1417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1415A ILE 3.3 4.0 + - - -
1416A PRO* 1.3 63.3 - - - +
1418A VAL* 1.3 59.2 + - + +
1419A LYS 3.4 1.1 - - - -
1420A ILE* 3.1 9.0 + - - +
1421A ALA* 2.7 33.6 + - - +
1454A LEU 5.4 0.4 - - - -
1455A VAL* 2.7 19.0 - - - +
1456A ASP 5.3 2.5 - - - +
1457A ILE* 4.3 2.0 - - - -
1458A CYS* 2.9 25.1 - - + +
1459A ARG 5.2 0.7 - - - +
1461A CYS* 2.6 26.8 + - - +
1462A ASN* 4.2 4.0 - - - +
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Residues in contact with VAL1418 (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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1416A PRO 2.7 12.1 + - - +
1417A GLU* 1.3 77.0 - - + +
1419A LYS* 1.3 57.4 + - - +
1421A ALA* 4.1 4.3 - - - +
1422A TYR* 2.7 29.6 + - - +
1456A ASP 5.6 2.2 - - - -
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Residues in contact with LYS1419 (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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1414A CYS* 3.7 5.8 - - + -
1415A ILE* 3.0 47.7 + - + +
1417A GLU 3.4 0.2 - - - -
1418A VAL* 1.3 75.7 - - - +
1420A ILE* 1.3 55.3 + - - +
1422A TYR* 2.7 9.3 + - - -
1423A ILE* 2.3 39.8 + - + +
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Residues in contact with ILE1420 (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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1413A ASP* 5.7 1.6 - - - -
1414A CYS* 3.9 14.6 - - + +
1415A ILE 3.1 16.5 + - - +
1417A GLU* 3.1 16.3 + - - +
1419A LYS* 1.3 74.1 - - - +
1421A ALA* 1.3 61.7 + - - +
1423A ILE* 3.5 1.4 + - - +
1424A ASN* 3.1 25.3 + - - +
1455A VAL* 4.3 15.0 - - + +
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Residues in contact with ALA1421 (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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1417A GLU 2.7 14.0 + - - +
1418A VAL* 4.1 3.8 - - - +
1420A ILE* 1.3 73.0 - - - +
1422A TYR* 1.3 52.7 + - - +
1425A PHE* 2.1 46.4 + - + +
1426A LEU* 2.4 15.5 + - - -
1455A VAL* 3.3 8.0 + - - +
1456A ASP* 3.1 38.6 - - + +
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Residues in contact with TYR1422 (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 ALA 4.9 4.7 - - - +
1383A VAL* 5.9 2.1 - - - +
1418A VAL 2.7 22.3 + - - +
1419A LYS* 2.7 15.8 + - - +
1421A ALA* 1.3 73.4 - - - +
1423A ILE* 1.3 60.8 + - - +
1426A LEU* 3.3 30.0 + - + +
1427A ASN 3.8 4.0 + - - -
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Residues in contact with ILE1423 (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 GLU 5.2 3.4 - - - +
1382A ALA* 2.9 43.1 - - + +
1383A VAL* 6.0 1.6 - - - -
1409A VAL* 5.3 5.5 - - + +
1413A ASP 5.2 2.7 - - - +
1414A CYS* 3.9 18.8 - - + -
1419A LYS* 2.3 29.2 + - + +
1420A ILE 4.0 2.5 - - - +
1422A TYR* 1.3 68.9 - - - +
1424A ASN* 1.3 60.4 + - + +
1427A ASN* 4.4 7.1 - - - +
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Residues in contact with ASN1424 (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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1409A VAL* 3.7 29.6 - - + +
1410A THR 5.6 0.2 - - - +
1420A ILE 3.1 12.4 + - - +
1423A ILE* 1.3 79.2 - - + +
1425A PHE* 1.3 63.1 + - - +
1426A LEU 3.5 1.6 - - - -
1427A ASN* 4.1 4.3 + - - +
1428A HIS* 3.6 16.8 + - - +
1448A LYS* 4.5 8.7 - - + +
1451A GLU* 5.5 4.7 - - + -
1455A VAL* 6.0 1.1 - - + -
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Residues in contact with PHE1425 (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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1421A ALA* 2.1 49.1 + - + +
1424A ASN* 1.3 72.8 - - - +
1426A LEU* 1.3 56.5 + - - -
1428A HIS* 3.0 10.8 - - - +
1429A CYS* 2.9 24.7 + - - +
1448A LYS* 5.1 2.5 - - - +
1451A GLU* 3.7 24.1 - - + +
1452A ASN* 5.2 0.7 - - + +
1456A ASP* 4.4 7.6 - - + -
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Residues in contact with LEU1426 (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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1421A ALA 2.4 19.2 + - - -
1422A TYR* 3.3 29.4 - - + +
1424A ASN 3.5 0.2 - - - -
1425A PHE* 1.3 63.7 - - - +
1427A ASN* 1.3 66.9 + - - +
1428A HIS 3.0 1.3 - - - -
1429A CYS* 3.2 9.0 + - - +
1430A TYR* 2.9 25.8 + - - +
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Residues in contact with ASN1427 (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 ALA* 4.5 12.8 - - - +
1422A TYR 3.8 4.6 + - - +
1423A ILE 4.4 14.8 - - - +
1424A ASN 4.1 4.4 + - - +
1425A PHE 3.5 0.4 - - - -
1426A LEU* 1.3 77.5 - - - +
1428A HIS* 1.4 49.3 + - - +
1430A TYR* 4.0 4.3 - - - +
1431A VAL* 2.7 42.2 + - + +
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Residues in contact with HIS1428 (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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1424A ASN 3.6 12.1 + - - +
1425A PHE* 3.0 15.5 + - - +
1426A LEU 3.0 0.4 - - - -
1427A ASN* 1.4 76.8 - - - +
1429A CYS* 1.3 58.5 + - - +
1431A VAL* 4.3 3.6 - - - -
1432A ASP* 2.7 35.4 + - - +
1448A LYS* 4.0 21.5 - - + +
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Residues in contact with CYS1429 (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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1425A PHE 2.9 11.5 + - - +
1426A LEU* 3.2 9.4 + - - +
1428A HIS* 1.3 74.5 - - - +
1430A TYR* 1.3 70.5 + - - +
1432A ASP* 3.3 11.6 + - - +
1433A THR 4.6 1.0 + - - -
1481A ILE* 5.4 6.7 - - + +
1485A ILE* 4.4 22.8 - - + +
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Residues in contact with TYR1430 (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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1426A LEU 2.9 15.7 + - - +
1427A ASN* 4.0 5.8 - - - +
1429A CYS* 1.3 79.2 - - - +
1431A VAL* 1.3 64.1 + - - +
1432A ASP 3.1 0.7 + - - -
1433A THR* 3.8 10.9 + - - -
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Residues in contact with VAL1431 (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 ASN* 5.4 12.1 - - + -
1390A VAL* 5.5 13.1 - - + +
1427A ASN* 2.7 26.8 + - + +
1428A HIS* 4.1 4.3 - - - +
1430A TYR* 1.3 73.8 - - - +
1432A ASP* 1.3 58.1 + - - +
1433A THR* 2.8 10.1 + - - -
1434A GLU* 4.0 7.4 + - - +
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Residues in contact with ASP1432 (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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1428A HIS 2.7 20.2 + - - +
1429A CYS* 3.3 9.6 + - - +
1430A TYR 3.1 2.2 + - - -
1431A VAL* 1.3 76.9 - - - +
1433A THR* 1.3 65.3 + - - +
1434A GLU 2.9 3.2 + - - -
1435A VAL* 3.5 12.7 + - - +
1485A ILE* 6.3 1.1 - - + -
1489A PHE* 5.2 4.6 - - - +
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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