Contacts of the helix formed by residues 1529 - 1544 (chain B) in PDB entry 2IUK
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 THR1529 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1524B SER 4.1 5.1 + - - -
1525B HIS* 2.9 22.4 - - + +
1527B LEU 3.2 1.0 - - - -
1528B ASN* 1.3 81.1 + - - +
1530B HIS* 1.3 77.2 + - + +
1531B ALA 3.6 0.4 - - - -
1532B VAL* 4.4 0.7 - - - +
1533B MET* 3.1 25.5 + - - +
1711B THR* 3.8 9.6 + - - -
1715B LEU* 3.6 15.9 - - - +
1716B HIS* 3.1 43.5 - - + -
1719B VAL* 4.5 0.7 - - - +
1862B ILE* 3.7 12.3 - - + -
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Residues in contact with HIS1530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1525B HIS* 3.0 24.6 + + - -
1526B TRP* 3.3 35.5 + + + +
1529B THR* 1.3 90.6 - - + +
1531B ALA* 1.3 68.3 + - - +
1533B MET* 3.5 3.0 + - - +
1534B GLU 3.4 9.2 + - - -
1561B THR* 4.4 1.8 - - - +
1564B ILE* 3.3 21.9 - - + +
1565B ASN* 2.9 37.0 + - - +
1716B HIS* 3.4 1.8 + - - -
1862B ILE* 3.5 9.6 - - + +
1864B ILE* 3.1 16.5 + - - -
1901B FE 2.3 30.3 - - - -
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Residues in contact with ALA1531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1215B TYR* 4.4 13.5 + - - +
1238B TYR* 4.4 5.4 - - + +
1239B PRO* 3.8 12.3 - - + +
1240B LEU 4.6 0.5 - - - +
1526B TRP* 2.9 39.2 + - + +
1527B LEU* 3.7 19.7 - - + +
1529B THR 3.6 0.2 - - - -
1530B HIS* 1.3 72.3 - - - +
1532B VAL* 1.3 56.0 + - - +
1534B GLU* 2.9 27.4 + - - +
1535B PRO* 3.2 10.0 - - - +
1565B ASN* 4.9 1.6 - - - -
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Residues in contact with VAL1532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1239B PRO* 3.7 14.5 - - + +
1527B LEU* 2.9 35.7 - - + +
1528B ASN 4.0 17.5 - - - +
1529B THR 4.4 1.1 - - - +
1531B ALA* 1.3 73.6 - - - +
1533B MET* 1.3 63.7 + - + +
1535B PRO* 3.4 2.3 - - - +
1536B PHE* 3.2 12.7 - - + -
1597B TYR* 4.4 1.3 - - + -
1600B TRP* 3.3 49.4 - - + +
1683B HIS* 3.1 27.3 - - - +
1711B THR* 5.8 4.5 - - + -
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Residues in contact with MET1533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1529B THR 3.1 19.4 + - - +
1530B HIS 3.7 3.1 - - - +
1531B ALA 3.1 0.6 - - - -
1532B VAL* 1.3 80.8 - - + +
1534B GLU* 1.3 67.7 + - - +
1536B PHE* 3.2 23.1 + - + +
1537B ALA* 3.4 9.1 + - + +
1557B HIS 4.5 5.6 - - - +
1558B TYR* 3.4 37.7 - - + -
1561B THR* 3.9 20.6 - - + -
1708B ILE* 3.7 22.7 - - + +
1711B THR* 3.1 30.7 - - - +
1712B ALA* 4.3 6.7 - - - +
1862B ILE* 4.0 10.1 - - + -
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Residues in contact with GLU1534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215B TYR* 4.1 5.6 + - - +
1240B LEU 4.2 5.2 - - - +
1241B ARG* 4.1 8.0 - - - +
1242B VAL* 3.6 28.5 + - - +
1530B HIS 3.4 2.8 + - - -
1531B ALA* 2.9 16.4 + - - +
1533B MET* 1.3 77.7 - - - +
1535B PRO* 1.4 62.2 - - + +
1536B PHE 3.1 1.4 + - - -
1537B ALA* 3.1 15.2 + - - +
1538B ILE* 3.3 20.3 + - + +
1561B THR* 5.0 2.4 - - - +
1562B ILE* 3.6 32.0 - - + +
1565B ASN* 3.1 36.5 - - - +
1569B ARG* 3.9 11.5 + - - -
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Residues in contact with PRO1535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212B TYR* 3.4 19.0 + - + -
1239B PRO* 3.7 11.7 - - + -
1240B LEU 3.9 9.8 - - - +
1531B ALA 3.2 12.8 - - - +
1532B VAL 3.4 8.5 - - - +
1534B GLU* 1.4 87.6 - - + +
1536B PHE* 1.3 61.3 + - + +
1538B ILE* 4.8 0.4 - - + -
1539B ALA* 3.1 23.7 + - - +
1678B ALA* 4.3 3.2 - - - +
1682B GLY* 3.1 33.9 - - - +
1683B HIS* 3.5 27.1 - - + +
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Residues in contact with PHE1536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1532B VAL* 3.2 30.1 - - + -
1533B MET* 3.2 18.6 + - + +
1534B GLU 3.1 1.2 + - - -
1535B PRO* 1.3 75.3 - - - +
1537B ALA* 1.3 55.2 + - - +
1539B ALA* 3.4 4.0 + - - +
1540B THR* 2.6 38.9 + - - -
1558B TYR* 3.9 18.8 - - + +
1600B TRP* 4.6 11.9 - + - -
1602B PHE* 5.3 9.0 - + + -
1674B TRP* 4.3 3.4 + + + -
1675B TRP* 3.9 27.8 - + - -
1678B ALA* 3.9 21.3 - - + -
1679B VAL* 5.9 1.6 - - + -
1683B HIS* 3.5 22.4 - + - -
1708B ILE* 4.0 27.6 - - + -
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Residues in contact with ALA1537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210B TYR* 4.7 0.2 - - - -
1267B GLU* 5.3 1.1 - - - +
1533B MET* 3.4 5.4 + - + +
1534B GLU* 3.1 8.3 + - - +
1536B PHE* 1.3 75.9 - - - +
1538B ILE* 1.3 63.1 + - - +
1540B THR* 3.7 0.9 + - - -
1541B ASN* 2.8 31.4 + - - +
1558B TYR* 3.8 39.9 - - + +
1561B THR* 5.6 2.9 - - - -
1562B ILE* 3.7 27.1 - - + -
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Residues in contact with ILE1538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1210B TYR* 3.8 10.8 - - + -
1211B ASP 3.4 33.9 - - - +
1212B TYR* 3.7 23.3 - - + -
1241B ARG* 3.7 10.1 - - - +
1242B VAL* 3.6 26.9 - - + +
1534B GLU* 3.3 18.7 + - + +
1535B PRO* 4.0 0.9 - - + +
1537B ALA* 1.3 73.3 - - - +
1539B ALA* 1.3 58.9 + - - +
1541B ASN* 3.1 4.7 + - - +
1542B ARG* 2.9 55.1 + - - +
1562B ILE* 4.1 15.7 - - + -
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Residues in contact with ALA1539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212B TYR* 3.0 23.1 + - - +
1535B PRO 3.1 12.3 + - - +
1536B PHE 3.6 4.5 - - - +
1537B ALA 3.4 0.2 - - - -
1538B ILE* 1.3 76.1 - - - +
1540B THR* 1.3 62.5 + - - +
1542B ARG* 3.9 0.5 - - - +
1543B HIS* 3.2 23.2 + - - +
1674B TRP* 3.5 20.5 - - + +
1677B GLU* 3.8 7.4 - - - +
1678B ALA* 3.8 25.6 - - + +
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Residues in contact with THR1540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1536B PHE 2.6 22.9 + - - -
1537B ALA 4.0 2.9 - - - -
1538B ILE 3.3 0.2 - - - -
1539B ALA* 1.3 73.3 - - - +
1541B ASN* 1.3 59.2 + - - +
1544B LEU* 3.0 51.9 + - + +
1550B ILE 4.8 2.9 - - - +
1551B TYR* 4.3 21.2 - - + +
1554B LEU* 4.9 3.1 - - + -
1555B TYR* 5.3 1.8 - - - +
1558B TYR* 3.1 35.3 + - + +
1674B TRP* 3.2 16.1 + - + +
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Residues in contact with ASN1541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192B PHE* 3.6 7.1 - - - -
1195B LEU* 3.3 29.4 - - + +
1210B TYR* 3.7 46.5 + - + -
1267B GLU* 4.0 8.6 + - - +
1537B ALA* 2.8 20.1 + - - +
1538B ILE 3.1 7.6 + - - +
1540B THR* 1.3 77.5 - - - +
1542B ARG* 1.3 63.6 + - - +
1543B HIS 3.3 1.0 + - - -
1544B LEU 4.2 2.7 - - - +
1551B TYR* 4.0 24.7 + - - -
1558B TYR* 5.2 4.5 - - - +
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Residues in contact with ARG1542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192B PHE* 3.8 6.6 - - - -
1195B LEU* 4.8 4.5 - - - -
1196B ARG* 3.0 80.8 + - + +
1210B TYR* 2.8 47.8 + - + +
1211B ASP* 4.1 13.3 + - - +
1212B TYR* 3.6 7.6 - - - -
1538B ILE* 2.9 34.8 + - - +
1539B ALA 3.9 1.3 - - - +
1541B ASN* 1.3 75.4 - - - +
1543B HIS* 1.4 58.2 + - + +
1677B GLU* 2.8 46.6 + - - +
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Residues in contact with HIS1543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1189B LYS* 5.0 4.4 + - - +
1192B PHE* 3.2 17.1 - - - -
1196B ARG* 3.1 38.1 + - - +
1539B ALA 3.2 13.9 + - - +
1541B ASN 3.3 0.4 - - - -
1542B ARG* 1.4 76.2 + - - +
1544B LEU* 1.3 59.0 + - - +
1670B GLU* 3.3 23.7 - - - +
1673B ALA* 3.9 24.7 + - + +
1674B TRP* 3.9 15.7 - - - +
1677B GLU* 2.8 56.6 + - + +
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Residues in contact with LEU1544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192B PHE* 3.2 7.5 - - - -
1195B LEU* 5.8 0.3 - - - +
1540B THR* 3.0 42.8 + - + +
1541B ASN 4.2 2.4 - - - +
1543B HIS* 1.3 70.9 - - - +
1545B SER* 1.3 64.6 + - - +
1546B VAL 3.8 0.3 + - - -
1548B HIS* 4.2 20.2 - - + +
1550B ILE* 3.9 17.5 - - + -
1551B TYR* 3.4 36.3 - - + +
1670B GLU* 3.7 2.9 - - - -
1671B LEU* 4.0 22.4 - - + +
1674B TRP* 3.7 39.3 - - + +
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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