Contacts of the helix formed by residues 1713 - 1721 (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 SER1713 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1647B ILE* 3.7 11.4 - - - +
1709B VAL* 2.7 24.9 + - - -
1710B TRP 3.7 0.3 + - - -
1712B ALA* 1.3 76.6 - - - +
1714B ALA* 1.3 66.1 + - - +
1715B LEU 3.7 0.2 - - - -
1716B HIS* 4.1 0.2 - - - +
1717B ALA* 3.1 29.3 + - - +
1790B LEU* 3.5 31.2 - - - +
1858B ILE* 3.6 5.1 - - - +
1859B PRO* 3.3 21.3 - - - +
1860B ASN 3.4 7.0 - - - -
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Residues in contact with ALA1714 (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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1643B ILE* 4.1 7.6 - - + -
1710B TRP* 3.0 37.3 + - + -
1713B SER* 1.3 79.3 + - - +
1715B LEU* 1.3 62.1 + - - +
1716B HIS 3.3 1.1 - - - -
1717B ALA* 4.1 1.8 - - - -
1718B ALA* 3.3 23.6 + - - +
1845B LEU* 3.4 18.9 - - + +
1858B ILE* 4.0 15.7 - - + -
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Residues in contact with LEU1715 (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* 3.6 23.8 - - - +
1524B SER 5.2 2.9 - - - +
1528B ASN* 3.4 31.2 - - + +
1529B THR* 3.6 8.3 - - - +
1605B GLN* 4.2 14.8 - - - +
1636B TYR* 3.7 12.3 - - - +
1710B TRP* 2.8 34.6 + - + +
1711B THR* 3.6 26.7 - - + +
1714B ALA* 1.3 72.0 - - - +
1716B HIS* 1.3 66.9 + - - +
1718B ALA* 3.5 3.0 + - - +
1719B VAL* 3.2 35.3 + - + +
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Residues in contact with HIS1716 (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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1525B HIS* 3.5 5.8 + + - -
1529B THR* 3.1 32.8 - - + -
1530B HIS* 3.4 0.6 + - - -
1711B THR 3.4 16.8 + - - +
1712B ALA 3.6 12.6 - - - +
1714B ALA 3.3 0.2 - - - -
1715B LEU* 1.3 77.5 - - - +
1717B ALA* 1.3 65.9 + - - +
1719B VAL* 2.9 7.0 + - - +
1720B ASN* 2.8 49.9 + - + +
1721B PHE* 4.3 5.6 - + - -
1859B PRO* 5.3 1.0 - - - +
1861B SER 4.1 8.5 + - - -
1862B ILE* 3.5 19.7 - - + +
1863B SER* 4.5 1.5 + - - -
1864B ILE* 2.6 24.2 + - + -
1901B FE 2.3 26.8 - - - -
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Residues in contact with ALA1717 (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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1713B SER 3.1 18.3 + - - +
1714B ALA 4.3 1.8 - - - +
1716B HIS* 1.3 77.7 + - - +
1718B ALA* 1.3 56.0 + - - +
1721B PHE* 3.2 43.2 + - - +
1844B LEU* 4.4 8.5 - - - +
1857B GLY 3.6 22.4 - - - +
1858B ILE* 3.8 13.9 - - + -
1859B PRO* 3.6 12.6 - - + -
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Residues in contact with ALA1718 (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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1378B VAL* 3.5 10.9 - - - +
1380B PRO* 4.3 5.4 - - - +
1636B TYR* 3.8 28.5 - - + -
1714B ALA 3.3 18.9 + - - +
1715B LEU 3.7 3.8 - - - +
1716B HIS 3.1 1.0 + - - -
1717B ALA* 1.3 77.3 - - - +
1719B VAL* 1.3 59.6 + - + +
1720B ASN 3.6 0.2 - - - -
1721B PHE 5.1 0.4 - - - -
1722B GLY 5.3 0.3 + - - -
1842B TYR* 4.2 3.8 - - - +
1844B LEU* 3.6 28.1 - - - +
1845B LEU* 3.9 14.5 - - + +
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Residues in contact with VAL1719 (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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1378B VAL* 3.3 21.1 - - - +
1380B PRO* 3.9 15.7 - - + -
1381B ASN* 4.6 15.0 - - - +
1520B HIS* 2.6 42.5 + - + +
1524B SER* 3.8 24.0 - - - +
1525B HIS* 4.0 15.1 - - + +
1529B THR* 4.5 2.7 - - - +
1636B TYR* 5.9 0.7 - - - +
1715B LEU* 3.2 23.5 + - + +
1716B HIS* 2.9 17.5 + - - +
1718B ALA* 1.3 76.5 - - + +
1720B ASN* 1.3 59.8 + - - +
1722B GLY 5.0 0.2 - - - -
1723B GLN* 4.5 0.2 - - - +
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Residues in contact with ASN1720 (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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1525B HIS* 3.4 9.6 + - + +
1716B HIS* 2.8 29.5 + - + +
1719B VAL* 1.3 80.3 - - - +
1721B PHE* 1.4 82.0 + - - +
1722B GLY 3.2 4.7 - - - -
1723B GLN* 3.0 42.8 - - - +
1780B LEU* 3.2 25.5 + - - +
1781B SER* 3.6 3.1 + - - -
1864B ILE* 3.8 4.1 - - - +
1901B FE 3.0 21.0 - - - -
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Residues in contact with PHE1721 (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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1716B HIS* 4.3 5.2 - + - -
1717B ALA* 3.2 31.6 + - - +
1720B ASN* 1.4 91.6 - - - +
1722B GLY* 1.3 56.4 + - - +
1723B GLN 3.5 0.4 - - - -
1725B PRO* 3.3 21.3 - - - +
1780B LEU 4.0 1.8 - - - -
1781B SER* 3.3 36.6 - - - +
1782B ARG 4.0 3.8 - - - -
1783B HIS* 3.1 46.2 - + + -
1844B LEU* 3.9 11.4 - - + -
1854B THR 4.5 5.1 - - - +
1855B PHE* 3.9 8.6 - - - -
1856B LYS 4.7 5.6 - - - +
1857B GLY 4.0 7.0 - - - +
1859B PRO* 3.7 21.5 - - + -
1863B SER* 5.0 0.2 - - - -
1864B ILE* 3.7 18.2 - - + -
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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