Contacts of the helix formed by residues 1606 - 1614 (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 ALA1606 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1603B THR 3.6 16.4 + - - +
1605B GLN* 1.3 77.7 - - - +
1607B LEU* 1.4 65.7 + - - +
1608B PRO* 3.4 3.3 - - + -
1609B ALA* 3.4 9.0 + - + +
1610B ASP* 3.0 18.5 + - - +
1644B TRP* 3.4 36.1 - - + -
1703B GLN* 4.1 9.0 - - - +
1707B ILE* 4.0 10.3 - - + +
1710B TRP* 4.6 0.4 - - - -
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Residues in contact with LEU1607 (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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1605B GLN 3.7 3.3 + - - -
1606B ALA* 1.4 68.2 - - - +
1608B PRO* 1.3 70.8 - - + +
1610B ASP* 2.9 31.9 + - + +
1611B LEU* 2.9 34.2 + - + +
1636B TYR* 3.9 23.8 - - + +
1637B ALA* 3.6 11.4 - - - +
1640B GLY* 3.4 10.1 - - - -
1641B LEU* 3.3 43.3 - - + +
1644B TRP* 4.0 15.1 - - + -
1710B TRP* 3.4 24.0 - - + +
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Residues in contact with PRO1608 (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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1606B ALA* 3.6 4.7 - - + -
1607B LEU* 1.3 90.9 - - + +
1609B ALA* 1.4 52.6 - - + +
1611B LEU* 3.3 5.3 + - + +
1612B VAL* 3.0 40.9 + - - +
1619B GLU* 6.0 1.6 - - - +
1625B HIS* 6.0 1.6 - - + +
1627B LEU* 3.6 33.8 - - + +
1641B LEU* 4.4 3.8 - - + -
1644B TRP* 3.4 35.4 - - + +
1645B ASP* 5.9 0.2 - - - +
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Residues in contact with ALA1609 (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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1603B THR 4.0 18.4 - - - +
1604B HIS* 4.2 18.4 + - + +
1606B ALA* 3.5 14.8 - - + +
1608B PRO* 1.4 75.9 - - - +
1610B ASP* 1.3 64.3 + - - +
1612B VAL* 4.1 5.1 - - - +
1613B LYS* 3.1 25.1 + - - +
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Residues in contact with ASP1610 (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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1381B ASN* 4.1 13.3 - - - +
1604B HIS* 3.7 16.7 + - - +
1605B GLN 4.6 3.6 - - - +
1606B ALA 3.0 12.8 + - - +
1607B LEU* 2.9 26.4 + - + +
1609B ALA* 1.3 77.0 - - - +
1611B LEU* 1.4 60.7 + - - +
1612B VAL 3.3 0.9 + - - -
1613B LYS* 3.4 8.7 + - - +
1614B ARG* 2.8 62.8 + - - +
1636B TYR* 4.6 1.1 + - - -
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Residues in contact with LEU1611 (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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1607B LEU* 2.9 51.9 + - + +
1608B PRO* 3.3 5.1 + - + +
1610B ASP* 1.4 72.3 - - - +
1612B VAL* 1.3 59.3 + - - +
1614B ARG* 3.5 26.8 + - - +
1615B GLY 3.4 2.8 + - - -
1616B LEU* 3.0 32.2 + - + +
1617B ALA* 3.2 22.6 + - + +
1627B LEU* 5.0 0.4 - - + -
1629B LEU* 4.3 7.0 - - + -
1634B TYR* 4.0 9.4 - - + -
1636B TYR* 5.5 0.2 - - + -
1637B ALA* 3.8 26.5 - - + -
1641B LEU* 3.6 26.2 - - + -
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Residues in contact with VAL1612 (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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1608B PRO 3.0 19.5 + - - +
1609B ALA* 4.2 5.8 - - - +
1610B ASP 3.3 0.2 - - - -
1611B LEU* 1.3 75.1 - - - +
1613B LYS* 1.3 64.7 - - - +
1614B ARG 3.2 0.4 - - - -
1615B GLY* 3.4 10.4 + - - -
1617B ALA* 3.5 20.1 - - + +
1619B GLU* 4.0 26.7 - - + +
1627B LEU* 3.5 25.4 - - + -
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Residues in contact with LYS1613 (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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1384B ARG* 6.0 2.3 - - - +
1604B HIS* 3.7 38.5 - - + +
1609B ALA 3.1 19.1 + - - +
1610B ASP* 3.4 9.3 + - - +
1612B VAL* 1.3 78.2 - - - +
1614B ARG* 1.4 74.6 + - - +
1615B GLY 3.7 0.5 + - - -
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Residues in contact with ARG1614 (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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1381B ASN* 3.0 34.7 + - - +
1382B VAL 3.9 6.1 - - - -
1383B ILE* 2.8 45.5 + - - +
1384B ARG* 3.3 17.2 - - + +
1385B ARG* 2.8 27.4 + - - +
1387B GLN* 5.5 1.3 - - - -
1610B ASP* 2.8 47.7 + - - +
1611B LEU* 3.5 20.3 + - - +
1612B VAL 3.2 0.8 - - - -
1613B LYS* 1.4 90.7 - - - +
1615B GLY* 1.3 57.9 + - - +
1616B LEU* 3.3 10.8 - - + +
1634B TYR* 3.0 29.7 + - - -
1636B TYR* 4.5 2.2 - - - -
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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