Contacts of the helix formed by residues 1438 - 1451 (chain F) in PDB entry 1IV4
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 ASP1438 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1419F TYR* 3.3 19.5 - - + +
1420F LEU* 3.4 5.9 + - - -
1421F CYS 3.0 15.3 + - - -
1422F GLY* 2.8 30.8 + - - -
1436F ASP* 3.0 22.6 + - - +
1437F GLY* 1.3 72.1 - - - +
1439F ALA* 1.3 63.5 + - - +
1440F ALA 3.2 4.3 + - - -
1441F MET* 3.0 30.1 + - + +
1442F HIS* 3.0 28.2 + - - -
1473F SER* 3.8 7.5 - - - +
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Residues in contact with ALA1439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1408F ASP* 3.4 28.8 - - + +
1410F HIS* 4.1 10.3 - - + -
1420F LEU* 4.3 4.6 - - + +
1437F GLY 3.0 6.0 + - - -
1438F ASP* 1.3 73.8 + - - +
1440F ALA* 1.3 58.2 + - - +
1443F ALA* 2.9 24.4 + - - +
1498F LEU* 5.7 0.2 - - + -
1542F VAL* 4.2 26.2 - - + +
1544F ALA* 3.3 25.1 - - + +
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Residues in contact with ALA1440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1420F LEU* 4.1 6.1 - - + +
1421F CYS* 3.7 32.3 - - - +
1438F ASP* 3.2 8.6 + - - +
1439F ALA* 1.3 81.5 - - - +
1441F MET* 1.3 63.1 + - - +
1443F ALA* 3.5 1.2 + - - +
1444F LEU* 3.0 33.0 + - + +
1496F LEU* 4.0 8.0 - - + +
1498F LEU* 3.8 17.7 - - + -
1544F ALA* 4.0 10.0 - - - +
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Residues in contact with MET1441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1421F CYS* 3.7 10.5 - - - -
1422F GLY* 3.7 20.2 - - - +
1438F ASP* 3.0 29.3 + - + +
1440F ALA* 1.3 77.3 - - - +
1442F HIS* 1.3 54.5 + - - +
1444F LEU* 3.4 5.4 + - + +
1445F THR* 2.7 38.6 + - - -
1473F SER* 3.7 22.4 - - - +
1474F GLU* 3.8 12.3 - - - +
1477F LEU* 3.3 45.9 - - + +
1516F LEU* 4.7 7.9 - - + -
1519F LEU* 3.8 18.8 - - + -
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Residues in contact with HIS1442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1332E LYS* 5.1 0.2 - - - +
1407F GLU 5.0 0.2 - - - -
1408F ASP* 2.8 21.4 + - + +
1410F HIS* 3.2 7.7 + - - -
1435F SER* 3.7 26.8 - - - -
1438F ASP 3.0 18.4 + - - +
1441F MET* 1.3 74.0 - - - +
1443F ALA* 1.3 65.8 + - - +
1445F THR* 3.2 6.9 + - - -
1446F ASP* 2.9 28.2 + - - +
1457F ILE* 3.7 25.7 - - + +
1473F SER* 2.9 31.5 + - - -
1476F PHE* 4.6 14.6 - + + -
1566F MG 1.9 31.1 - - - -
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Residues in contact with ALA1443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1406F GLY* 3.7 21.3 - - - +
1407F GLU 3.9 20.4 - - - +
1408F ASP* 3.9 1.0 - - - +
1439F ALA 2.9 19.4 + - - +
1440F ALA 4.0 2.0 - - - +
1442F HIS* 1.3 77.2 - - - +
1444F LEU* 1.3 57.4 + - - +
1446F ASP* 3.5 0.6 + - - -
1447F ALA* 2.9 29.6 + - - +
1496F LEU* 5.6 0.4 - - + -
1544F ALA* 3.8 20.6 - - + +
1546F ALA* 4.1 10.0 - - + +
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Residues in contact with LEU1444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1440F ALA 3.0 24.3 + - - +
1441F MET* 3.8 6.7 - - - +
1443F ALA* 1.3 76.1 - - - +
1445F THR* 1.3 57.6 + - - +
1447F ALA* 3.3 3.1 + - - +
1448F LEU* 3.0 32.7 + - + +
1477F LEU* 3.9 16.8 - - + -
1494F ALA* 3.8 14.6 - - + -
1496F LEU* 4.1 20.6 - - + -
1516F LEU* 3.7 30.3 - - + -
1520F MET* 3.6 28.3 - - + -
1546F ALA* 3.9 18.8 - - + -
1548F VAL* 4.3 8.9 - - + +
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Residues in contact with THR1445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1441F MET 2.7 23.0 + - - -
1442F HIS* 3.2 6.9 + - - -
1444F LEU* 1.3 73.8 - - - +
1446F ASP* 1.3 64.8 + - - +
1448F LEU* 3.1 7.8 + - - +
1449F LEU* 2.9 24.2 + - + +
1457F ILE* 3.4 23.8 - - + -
1461F PHE* 3.9 12.1 - - + -
1473F SER 4.7 0.9 + - - -
1476F PHE* 3.9 22.7 - - + +
1477F LEU* 3.4 27.0 + - - +
1480F ALA* 4.0 7.9 - - + -
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Residues in contact with ASP1446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1330E THR* 4.0 13.7 + - + +
1332E LYS* 3.5 28.2 + - - +
1406F GLY* 4.1 12.8 - - - -
1407F GLU 3.9 3.2 + - - +
1442F HIS 2.9 17.4 + - - +
1443F ALA* 3.8 4.7 - - - +
1445F THR* 1.3 76.0 - - - +
1447F ALA* 1.3 58.3 + - - +
1449F LEU* 3.8 4.9 - - - +
1450F SER* 2.8 31.4 + - - -
1456F ASP* 3.3 15.7 - - - +
1457F ILE* 2.8 41.9 + - - +
1606F C5P 4.9 0.2 + - - -
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Residues in contact with ALA1447 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1404F GLY* 3.4 22.9 - - - +
1405F TYR 3.8 13.2 - - - +
1406F GLY* 3.6 15.6 - - - +
1443F ALA 2.9 19.3 + - - +
1444F LEU* 3.6 6.5 - - - +
1445F THR 3.2 0.4 - - - -
1446F ASP* 1.3 78.2 - - - +
1448F LEU* 1.3 62.1 + - - +
1450F SER 3.4 0.2 + - - -
1451F ALA 3.1 18.0 + - - -
1546F ALA 4.0 6.7 - - - +
1548F VAL* 3.6 17.3 - - + +
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Residues in contact with LEU1448 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1444F LEU 3.0 19.8 + - - +
1445F THR 3.1 5.6 + - - +
1447F ALA* 1.3 76.2 - - - +
1449F LEU* 1.3 64.6 + - - +
1451F ALA* 3.2 16.6 + - - +
1452F TYR 3.8 0.5 + - - -
1477F LEU* 3.9 24.0 - - + -
1480F ALA* 4.1 21.1 - - + -
1481F MET* 4.5 19.1 - - + +
1484F VAL* 3.7 26.6 - - + +
1491F LEU* 4.1 33.9 - - + -
1520F MET* 5.4 2.9 - - - -
1548F VAL* 4.1 14.6 - - + -
1550F LEU* 4.2 15.9 - - + +
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Residues in contact with LEU1449 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1445F THR* 2.9 30.4 + - + +
1446F ASP* 3.8 3.8 - - - +
1448F LEU* 1.3 77.0 - - - +
1450F SER* 1.3 63.3 + - - +
1452F TYR 3.0 8.7 + - - -
1454F LEU* 3.0 42.7 + - + +
1455F GLY 3.5 13.5 - - - +
1456F ASP* 3.7 28.7 - - - +
1457F ILE 4.0 2.9 - - - +
1460F LEU* 3.3 37.0 - - + -
1461F PHE* 4.2 4.9 - - + -
1480F ALA* 3.7 25.4 - - + +
1483F LEU* 4.3 1.1 - - + -
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Residues in contact with SER1450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1293E GLN* 4.2 3.3 - - - +
1295E SER* 2.8 28.4 + - - -
1296E LEU 4.9 0.2 + - - -
1325E ASP 4.8 0.3 - - - +
1326E ARG 5.7 0.2 - - - -
1327E ILE 4.5 0.2 - - - -
1328E GLY* 3.0 43.4 + - - -
1329E LEU 3.8 0.6 + - - +
1330E THR* 4.2 7.7 - - - +
1403F ILE 4.8 0.2 - - - +
1405F TYR 3.9 10.0 + - - -
1446F ASP 2.8 23.0 + - - -
1447F ALA 3.5 5.2 - - - -
1449F LEU* 1.3 73.8 - - - +
1451F ALA* 1.3 61.6 + - - +
1452F TYR 3.0 1.6 + - - -
1453F GLY* 3.0 10.4 + - - +
1455F GLY 4.2 5.7 + - - -
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Residues in contact with ALA1451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1293E GLN* 2.9 16.9 - - - +
1325E ASP 3.8 0.4 - - - +
1402F ARG* 3.0 21.0 + - + -
1403F ILE 3.5 25.1 - - - +
1404F GLY* 3.9 0.4 - - - -
1447F ALA 3.1 12.6 + - - +
1448F LEU 3.5 11.9 - - - +
1449F LEU 3.2 0.6 - - - -
1450F SER* 1.3 76.2 - - - +
1452F TYR* 1.3 61.0 + - + +
1550F LEU* 3.6 30.1 - - + -
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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