Contacts of the helix formed by residues 1435 - 1447 (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 TYR1435 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1379B ASN* 3.1 17.8 + - - -
1382B VAL* 3.3 19.2 - - + +
1433B LEU* 3.6 27.4 - - + -
1434B ASP* 1.3 76.5 + - - +
1436B GLN* 1.3 64.2 + - - +
1437B ASP 3.4 2.7 - - - +
1438B ALA* 4.2 5.6 - - + +
1439B PHE* 3.2 42.6 + + + +
1456B ALA* 4.0 0.3 - - - +
1457B THR* 3.4 24.9 + - - +
1512B VAL 5.0 0.7 - - - -
1515B ASN* 3.7 26.0 - - + +
1516B ASP* 2.9 43.5 + - + -
1519B TYR* 3.4 37.5 - + + +
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Residues in contact with GLN1436 (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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1393B SER* 4.2 4.9 - - - +
1395B LEU* 4.7 0.7 - - + -
1403B GLN* 3.2 26.4 + - - +
1434B ASP* 3.1 16.9 + - - +
1435B TYR* 1.3 76.9 - - - +
1437B ASP* 1.3 60.2 + - - +
1440B ILE* 3.0 40.8 + - - +
1456B ALA* 3.4 19.3 + - - +
1457B THR 4.7 0.4 - - - +
1458B ARG* 3.1 46.8 + - - +
1475B GLU* 4.5 0.4 + - - -
1477B SER* 2.9 36.1 + - - -
1488B PRO* 4.1 4.2 - - - +
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Residues in contact with ASP1437 (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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1392B LYS 5.2 0.5 - - - +
1393B SER* 2.7 28.9 + - - -
1394B THR* 3.1 31.0 + - - +
1395B LEU* 3.6 17.9 - - + +
1434B ASP* 4.0 20.3 - - - +
1435B TYR 3.4 0.6 - - - -
1436B GLN* 1.3 79.2 - - - +
1438B ALA* 1.3 56.5 + - - +
1441B PRO* 3.1 25.3 - - - +
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Residues in contact with ALA1438 (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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1435B TYR* 3.7 7.8 + - + +
1436B GLN 3.5 0.4 - - - -
1437B ASP* 1.3 78.6 - - - +
1439B PHE* 1.3 76.2 + - + +
1441B PRO* 3.8 3.1 - - - +
1442B TYR* 3.8 14.6 - - - -
1519B TYR* 4.3 23.3 - - + -
1592B MET* 3.7 22.1 - - + +
1596B VAL* 4.7 10.5 - - + +
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Residues in contact with PHE1439 (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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1435B TYR* 3.2 40.4 + + + +
1438B ALA* 1.3 82.9 - - + +
1440B ILE* 1.3 60.0 + - - +
1441B PRO 3.3 2.0 - - - -
1442B TYR* 2.9 24.0 + - - +
1443B LEU* 2.9 15.4 + - + +
1446B ILE* 4.3 17.5 - - + -
1455B TYR 4.4 4.0 - - - +
1456B ALA* 3.9 13.9 - - + -
1514B VAL 5.2 0.4 - - - -
1515B ASN* 3.5 47.1 - - - -
1518B GLY* 4.8 4.9 - - - -
1519B TYR* 4.2 12.3 - - + -
1584B LEU* 4.3 15.3 - - + -
1585B PRO* 4.8 6.5 - - + -
1592B MET* 3.9 28.3 - - + -
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Residues in contact with ILE1440 (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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1395B LEU* 3.6 22.2 - - + -
1400B TYR* 4.1 15.3 - - + -
1403B GLN* 3.7 28.0 - - - +
1436B GLN* 3.0 24.1 + - - +
1439B PHE* 1.3 73.8 - - - +
1441B PRO* 1.3 57.8 - - + +
1442B TYR 3.0 5.4 + - - -
1443B LEU* 3.3 11.5 + - + +
1444B THR 4.6 1.4 + - - -
1456B ALA* 3.5 19.5 - - + +
1477B SER* 4.3 11.7 - - - +
1478B LYS 4.1 9.2 - - - -
1479B PRO* 3.9 39.8 - - + +
1488B PRO* 4.4 4.0 - - + -
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Residues in contact with PRO1441 (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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1395B LEU* 3.9 20.2 - - + -
1400B TYR* 3.5 31.8 + - + +
1437B ASP 3.1 26.2 - - - +
1438B ALA 3.8 2.2 - - - +
1439B PHE 3.5 2.7 - - - -
1440B ILE* 1.3 92.5 - - + +
1442B TYR* 1.3 73.3 - - + +
1444B THR 5.5 0.4 - - - -
1445B ARG* 5.4 4.0 - - - +
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Residues in contact with TYR1442 (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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1438B ALA 3.8 15.3 - - - -
1439B PHE* 2.9 9.2 + - - +
1441B PRO* 1.3 91.9 - - + +
1443B LEU* 1.3 53.0 + - - +
1444B THR 3.4 2.5 - - - -
1445B ARG* 3.1 15.4 + - + +
1446B ILE* 2.7 45.9 + - + +
1588B TYR* 4.1 37.0 - + + -
1591B GLU* 3.0 37.1 + - - -
1592B MET* 3.6 30.1 - - + -
1595B SER* 2.8 32.0 + - - -
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Residues in contact with LEU1443 (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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1439B PHE* 2.9 22.2 + - + +
1440B ILE* 3.3 8.7 + - + +
1442B TYR* 1.3 75.7 - - - +
1444B THR* 1.3 54.4 + - - +
1446B ILE* 3.5 28.3 - - + -
1447B ASN* 2.6 44.0 + - - +
1454B ALA* 4.1 12.8 - - + +
1455B TYR* 3.7 28.0 - - - +
1456B ALA* 3.9 1.3 - - + +
1477B SER 3.5 24.9 - - - +
1478B LYS* 3.7 5.8 - - + -
1479B PRO* 3.6 27.6 - - + -
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Residues in contact with THR1444 (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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1440B ILE 4.6 1.8 + - - -
1441B PRO 5.5 0.2 - - - -
1442B TYR 3.4 0.8 - - - -
1443B LEU* 1.3 75.7 - - - +
1445B ARG* 1.3 77.8 + - - +
1447B ASN* 4.0 2.2 - - - -
1448B SER* 3.2 25.1 + - - -
1479B PRO* 3.4 28.9 - - - +
1480B HIS 5.0 2.3 + - - +
1483B GLY* 5.6 2.4 + - - -
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Residues in contact with ARG1445 (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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1441B PRO 5.4 2.9 - - - +
1442B TYR* 3.1 20.1 + - + +
1444B THR* 1.3 93.2 + - - +
1446B ILE* 1.3 60.5 + - - +
1448B SER* 2.7 56.9 + - - -
1449B LEU 5.1 0.5 - - - +
1588B TYR* 3.4 55.4 + - + -
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Residues in contact with ILE1446 (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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1439B PHE* 4.3 13.9 - - + -
1442B TYR* 2.7 36.4 + - + +
1443B LEU* 3.5 29.8 - - + -
1445B ARG* 1.3 70.6 - - - +
1447B ASN* 1.4 64.3 + - - +
1448B SER 3.2 1.3 + - - -
1449B LEU 3.7 8.8 + - - +
1452B ALA* 3.2 20.7 - - + +
1454B ALA* 4.9 0.2 - - + -
1584B LEU* 3.6 37.6 - - + +
1585B PRO* 3.6 33.7 - - + +
1588B TYR* 4.1 15.5 - - + -
1592B MET* 6.0 0.2 - - - -
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Residues in contact with ASN1447 (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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1443B LEU* 2.6 33.6 + - - +
1444B THR* 4.0 3.4 - - - +
1446B ILE* 1.4 70.7 - - - +
1448B SER* 1.4 54.6 + - - +
1449B LEU* 2.8 28.4 + - - +
1452B ALA* 4.0 5.1 - - - +
1453B LYS* 3.5 9.6 + - - +
1454B ALA* 2.8 50.3 + - - +
1478B LYS* 4.7 10.1 - - - +
1479B PRO* 5.7 0.8 - - - +
1740B PHE* 3.4 20.5 - - + -
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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