Contacts of the helix formed by residues 1424 - 1442 (chain A) in PDB entry 6XAF
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 GLY1424 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1420A ASP 4.6 0.3 - - - +
1421A LEU 3.3 11.0 + - - -
1422A SER 3.4 1.6 - - - -
1423A LYS* 1.3 76.2 - - - +
1425A GLN* 1.3 58.8 + - - -
1426A ALA 3.0 7.0 - - - -
1427A GLU* 2.9 26.0 + - - +
1461A GLN* 3.8 22.0 - - - -
1465A CYS* 3.9 10.9 - - - -
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Residues in contact with GLN1425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1424A GLY* 1.3 70.7 - - - -
1426A ALA* 1.3 63.3 + - - +
1427A GLU 3.1 0.4 - - - -
1428A VAL* 3.1 6.2 + - - +
1429A ASP* 3.0 19.7 + - - +
1461A GLN* 5.1 1.0 + - - +
1464A ALA* 3.6 42.1 - - + +
1465A CYS* 3.8 12.5 - - - -
1468A LYS* 3.7 32.9 - - + +
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Residues in contact with ALA1426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1423A LYS 4.3 12.1 - - - +
1425A GLN* 1.3 81.6 - - - +
1427A GLU* 1.3 63.4 + - - +
1429A ASP* 3.3 13.8 - - - +
1430A ALA* 2.9 24.6 + - - +
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Residues in contact with GLU1427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1342A ASN* 4.8 9.0 + - - +
1345A SER* 6.0 1.0 - - - -
1419A TYR* 4.0 20.3 - - + +
1420A ASP* 3.3 31.7 + - - +
1423A LYS* 3.4 43.2 + - + +
1424A GLY 2.9 10.6 + - - +
1426A ALA* 1.3 80.6 - - - +
1428A VAL* 1.3 66.5 + - - +
1430A ALA* 3.1 21.9 + - - +
1431A MET* 3.2 18.0 + - - +
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Residues in contact with VAL1428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1419A TYR* 3.8 20.9 - - + +
1425A GLN 3.1 7.7 + - - +
1427A GLU* 1.3 76.2 - - - +
1429A ASP* 1.3 58.3 + - - +
1431A MET* 2.9 31.2 + - - +
1432A LYS* 3.7 4.5 + - - +
1465A CYS* 3.6 40.8 - - + +
1468A LYS* 3.6 26.7 - - + -
1469A ILE* 3.9 20.6 - - + +
1473A LEU* 3.9 18.0 - - + +
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Residues in contact with ASP1429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1425A GLN 3.0 9.6 + - - +
1426A ALA* 3.3 15.5 - - - +
1428A VAL* 1.3 76.3 - - - +
1430A ALA* 1.3 59.3 + - - +
1432A LYS* 3.1 47.2 + - + +
1433A PRO* 3.6 4.3 - - - +
1468A LYS* 3.0 38.0 + - - +
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Residues in contact with ALA1430 (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 ASN* 4.0 21.1 + - - +
1426A ALA 2.9 14.2 + - - +
1427A GLU* 3.1 20.1 + - - +
1429A ASP* 1.3 75.3 - - - +
1431A MET* 1.3 65.1 + - + +
1432A LYS 3.2 0.2 - - - -
1433A PRO* 3.3 20.8 - - - +
1434A TRP* 3.7 12.3 - - - -
1398B HIS* 5.0 0.2 + - - -
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Residues in contact with MET1431 (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 GLY* 4.5 3.8 - - - -
1342A ASN* 4.9 5.2 - - - +
1417A ALA* 4.0 28.5 - - - +
1418A VAL 3.5 25.4 - - - +
1419A TYR* 3.9 26.9 - - + -
1427A GLU* 3.5 12.3 - - - +
1428A VAL* 2.9 14.5 + - + +
1430A ALA* 1.3 82.7 - - + +
1432A LYS* 1.3 65.0 + - - +
1433A PRO 3.5 0.2 - - - -
1434A TRP* 3.1 27.0 + - + +
1435A LEU* 2.9 28.6 + - + +
1449A LEU* 4.1 10.1 - - + -
1473A LEU* 4.4 13.7 - - + -
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Residues in contact with LYS1432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1428A VAL 4.5 0.9 - - - +
1429A ASP* 3.1 31.7 + - - +
1431A MET* 1.3 76.5 - - - +
1433A PRO* 1.3 70.7 - - + +
1435A LEU* 3.1 6.4 + - - +
1436A PHE* 3.0 35.5 + - + -
1468A LYS* 4.6 1.3 - - - +
1472A GLU* 2.8 43.2 + - - -
1473A LEU* 3.9 20.2 - - + -
1479A PHE* 3.9 18.3 - - + -
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Residues in contact with PRO1433 (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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1429A ASP 3.6 7.0 - - - +
1430A ALA* 3.3 20.9 - - - +
1432A LYS* 1.3 93.9 - - + +
1434A TRP* 1.3 58.4 + - - +
1436A PHE* 3.4 10.9 + - + +
1437A ASN* 3.0 32.7 + - - +
1398B HIS* 4.2 17.0 - - + +
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Residues in contact with TRP1434 (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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1340A VAL* 3.4 33.4 - - + -
1341A GLY* 3.1 30.8 - - - -
1342A ASN* 2.9 20.6 + - - -
1417A ALA* 5.3 2.9 - - + -
1430A ALA 3.7 16.8 - - - -
1431A MET* 3.1 30.1 + - + +
1433A PRO* 1.3 74.9 - - - +
1435A LEU* 1.3 61.3 + - + +
1437A ASN* 3.1 6.4 + - + +
1438A ILE* 2.8 43.1 + - + +
1395B PHE* 5.3 1.1 - - + -
1397B GLY 3.7 8.5 - - - -
1398B HIS* 3.3 56.5 + + - -
1401B PHE* 3.7 31.4 - + + -
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Residues in contact with LEU1435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1417A ALA* 4.9 7.4 - - + -
1431A MET* 2.9 20.7 + - + +
1432A LYS 3.5 5.8 - - - +
1434A TRP* 1.3 76.4 - - - +
1436A PHE* 1.3 57.3 + - - +
1438A ILE* 3.3 7.4 + - + -
1439A LYS* 2.9 25.6 + - - +
1447A VAL* 4.2 25.4 - - + -
1449A LEU* 5.2 3.4 - - + -
1473A LEU* 3.9 38.1 - - + -
1479A PHE* 3.5 29.6 - - + -
1480A PRO* 3.3 24.3 - - + +
1482A ILE* 4.1 17.0 - - + -
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Residues in contact with PHE1436 (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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1432A LYS* 3.0 32.4 + - + -
1433A PRO* 3.8 9.9 - - + +
1435A LEU* 1.3 75.8 - - - +
1437A ASN* 1.3 63.1 + - - +
1439A LYS* 3.5 4.7 + - + +
1440A ALA* 3.1 23.9 + - - +
1478A GLY* 3.8 20.4 - - - -
1479A PHE* 3.4 31.4 - + - -
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Residues in contact with ASN1437 (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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1433A PRO* 3.0 21.1 + - - +
1434A TRP* 3.5 9.9 - - + +
1436A PHE* 1.3 76.1 - - - +
1438A ILE* 1.3 63.5 + - - +
1440A ALA* 3.4 6.0 + - - +
1441A ARG* 3.0 26.2 + - - +
1398B HIS* 3.4 30.1 + - - -
1401B PHE* 4.3 21.3 - - + -
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Residues in contact with ILE1438 (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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1340A VAL* 3.9 19.7 - - + -
1415A TYR* 3.7 54.3 - - + -
1417A ALA* 4.8 4.5 - - + -
1434A TRP* 2.8 35.1 + - + +
1435A LEU* 3.8 11.9 - - + +
1437A ASN* 1.3 72.8 - - - +
1439A LYS* 1.3 55.7 + - - +
1441A ARG* 4.5 4.0 - - - -
1442A ALA 2.7 38.9 + - - +
1445A SER* 4.8 1.1 - - - -
1447A VAL* 4.0 14.8 - - + -
1480A PRO* 3.6 16.6 - - + -
1401B PHE* 4.9 6.5 - - + -
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Residues in contact with LYS1439 (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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1435A LEU 2.9 17.6 + - - +
1436A PHE 3.8 4.3 - - - +
1438A ILE* 1.3 76.9 - - - +
1440A ALA* 1.3 62.8 + - - +
1442A ALA 4.4 3.1 - - - -
1443A SER* 3.0 56.2 + - - +
1478A GLY* 3.4 31.9 - - - +
1479A PHE 3.9 23.5 + - - +
1480A PRO* 3.8 12.5 - - + +
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Residues in contact with ALA1440 (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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1436A PHE 3.1 17.2 + - - +
1437A ASN* 3.8 6.7 - - - +
1438A ILE 3.2 0.2 - - - -
1439A LYS* 1.3 78.5 - - - +
1441A ARG* 1.3 62.0 + - - +
1443A SER* 5.1 1.9 + - - -
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Residues in contact with ARG1441 (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 MET* 5.7 2.8 - - + +
1409A MET* 5.1 5.7 + - - +
1410A THR* 3.2 37.6 - - + +
1415A TYR* 4.1 9.9 - - - +
1437A ASN 3.0 17.4 + - - +
1438A ILE 3.8 1.8 - - - +
1440A ALA* 1.3 79.0 - - - +
1442A ALA* 1.3 57.2 + - + +
1443A SER 4.0 1.5 + - - -
1401B PHE* 2.9 59.9 + - + -
1402B TYR* 3.9 6.9 + - - +
1404B THR* 3.0 29.5 + - - -
1405B HIS* 3.6 32.6 - - - +
1406B PRO* 4.1 17.7 - - - -
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Residues in contact with ALA1442 (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 MET 5.3 0.2 - - - +
1410A THR* 3.0 27.8 - - - +
1413A ALA* 5.3 0.2 - - + -
1415A TYR* 3.7 22.7 - - + +
1438A ILE* 2.7 18.8 + - - +
1439A LYS* 4.2 1.2 - - - +
1441A ARG* 1.3 73.1 - - - +
1443A SER* 1.3 59.2 + - - +
1444A SER 3.2 2.5 - - - -
1445A SER* 2.9 41.1 + - - +
1480A PRO* 5.6 0.9 - - - +
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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