Contacts of the helix formed by residues 1668 - 1681 (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 ASP1668 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1176B LEU* 3.4 6.7 - - + +
1177B PRO* 3.2 30.4 - - - +
1548B HIS* 3.1 14.7 + - - -
1659B TYR* 2.7 32.9 + - + -
1664B ALA 3.5 13.2 + - - +
1665B VAL 2.8 15.8 + - - +
1666B GLN 4.6 0.7 - - - -
1667B GLN* 1.3 73.0 - - - +
1669B THR* 1.3 59.5 + - - +
1670B GLU 3.5 4.3 + - - -
1671B LEU* 3.5 15.0 - - + +
1672B GLN* 3.0 32.9 + - - +
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Residues in contact with THR1669 (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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1177B PRO* 4.2 14.6 - - + +
1189B LYS* 5.1 11.2 - - - -
1667B GLN 3.2 10.1 + - - -
1668B ASP* 1.3 73.5 + - - +
1670B GLU* 1.3 76.1 - - + +
1672B GLN* 3.4 7.4 - - - +
1673B ALA* 3.2 21.0 + - - +
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Residues in contact with GLU1670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177B PRO* 3.8 12.7 - - + +
1188B ARG* 2.8 46.5 + - - +
1189B LYS* 4.6 12.8 - - - +
1192B PHE* 3.7 21.0 - - + -
1543B HIS 3.3 17.2 - - - +
1544B LEU* 4.0 3.6 - - + -
1545B SER 3.0 21.7 + - - -
1548B HIS* 3.4 15.4 - - + -
1668B ASP* 3.4 2.3 + - - +
1669B THR* 1.3 80.8 - - + +
1671B LEU* 1.3 55.4 + - - +
1673B ALA* 3.3 5.6 + - - +
1674B TRP* 2.8 35.7 + - - +
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Residues in contact with LEU1671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544B LEU* 4.0 6.1 - - + +
1548B HIS* 4.7 0.2 - - + -
1550B ILE* 4.0 23.1 - - + -
1659B TYR* 4.1 4.7 - - + +
1665B VAL* 3.7 28.0 - - + +
1668B ASP* 3.5 24.5 + - - +
1670B GLU* 1.3 76.8 - - - +
1672B GLN* 1.3 58.2 + - - +
1674B TRP* 3.5 23.1 - - + +
1675B TRP* 3.1 30.5 + - - +
1695B LYS* 3.5 27.4 - - + +
1701B LEU* 3.5 31.4 - - + -
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Residues in contact with GLN1672 (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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1665B VAL 2.9 25.8 - - - +
1666B GLN* 3.5 16.4 - - - +
1668B ASP 3.0 17.2 + - - +
1669B THR* 3.4 7.6 - - - +
1671B LEU* 1.3 78.7 - - - +
1673B ALA* 1.3 61.3 + - - +
1675B TRP* 4.2 2.6 - - - +
1676B LYS* 3.2 23.8 + - - +
1695B LYS* 3.3 38.2 + - - +
1696B GLN* 4.1 11.5 - - - +
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Residues in contact with ALA1673 (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* 6.2 0.9 - - - +
1543B HIS* 3.9 25.4 - - + +
1669B THR 3.2 11.1 + - - +
1670B GLU* 3.9 6.3 - - - +
1672B GLN* 1.3 74.0 - - - +
1674B TRP* 1.4 56.6 + - - +
1676B LYS* 3.2 9.0 + - + +
1677B GLU* 2.8 37.8 + - - +
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Residues in contact with TRP1674 (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* 4.3 4.8 + + - -
1539B ALA* 3.5 28.7 - - + +
1540B THR* 3.2 28.1 + - - +
1543B HIS* 3.9 13.4 - - + +
1544B LEU* 3.7 25.5 - - + +
1550B ILE* 4.6 4.3 - - + -
1554B LEU* 3.9 28.5 - - + -
1558B TYR* 4.8 0.2 - - - -
1670B GLU 2.8 22.5 + - - +
1671B LEU* 3.5 34.8 - - + +
1673B ALA* 1.4 70.9 - - - +
1675B TRP* 1.3 96.2 + + + +
1677B GLU* 3.8 1.9 - - - +
1678B ALA* 2.9 31.1 + - + +
1695B LYS* 4.2 12.6 - - - -
1701B LEU* 4.4 2.7 - - + -
1704B SER* 5.5 1.6 - - - -
1705B CYS* 4.7 6.7 - - - -
1708B ILE* 4.4 11.9 - - + -
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Residues in contact with TRP1675 (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* 3.9 28.3 - + - -
1602B PHE* 4.1 13.9 - + + -
1671B LEU 3.1 14.2 + - - +
1672B GLN 4.3 2.2 - - - +
1674B TRP* 1.3 107.7 - + + +
1676B LYS* 1.3 65.9 + - - +
1678B ALA* 4.2 5.2 - - + -
1679B VAL* 3.1 50.3 + - + +
1692B TRP* 4.5 7.0 - + - -
1693B PRO* 2.9 51.0 + - + -
1694B LYS* 4.4 4.5 - - - -
1695B LYS* 3.5 29.8 - - + -
1704B SER* 4.0 20.2 - - - -
1708B ILE* 4.8 4.9 - - + -
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Residues in contact with LYS1676 (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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1672B GLN 3.2 19.0 + - - +
1673B ALA* 3.2 9.0 + - - +
1675B TRP* 1.3 79.1 - - - +
1677B GLU* 1.3 58.7 + - - +
1679B VAL* 3.8 1.5 - - - -
1680B GLU* 2.8 67.6 + - - +
1681B LYS* 4.3 12.1 - - - +
1692B TRP* 5.0 7.8 - - + -
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Residues in contact with GLU1677 (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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1212B TYR* 2.9 21.3 + - - +
1539B ALA* 3.8 2.0 - - + -
1542B ARG* 2.8 45.8 + - - +
1543B HIS* 2.8 33.4 + - + +
1673B ALA 2.8 17.4 + - - +
1674B TRP 3.9 1.6 - - - +
1676B LYS* 1.3 77.9 - - - +
1678B ALA* 1.3 58.6 + - - +
1681B LYS* 3.0 39.6 + - + +
1682B GLY 2.8 25.3 + - - -
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Residues in contact with ALA1678 (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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1212B TYR* 4.5 0.2 - - - -
1535B PRO* 4.3 2.5 - - - +
1536B PHE* 3.9 27.4 - - + -
1539B ALA* 3.8 19.4 - - + +
1674B TRP* 2.9 21.3 + - - +
1675B TRP* 3.8 14.1 - - + +
1676B LYS 3.4 0.2 - - - -
1677B GLU* 1.3 73.7 - - - +
1679B VAL* 1.3 57.6 + - - +
1682B GLY* 3.2 8.3 - - - -
1683B HIS* 2.9 32.2 + - - +
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Residues in contact with VAL1679 (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* 5.9 0.9 - - + -
1602B PHE* 3.4 35.4 - - + -
1675B TRP* 3.1 49.2 + - + +
1676B LYS 3.9 1.6 - - - +
1678B ALA* 1.3 77.8 - - - +
1680B GLU* 1.3 60.4 + - + +
1683B HIS* 3.1 32.7 - - - +
1687B LYS* 3.6 17.5 - - + +
1692B TRP* 3.5 28.3 - - + -
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Residues in contact with GLU1680 (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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1676B LYS* 2.8 47.3 + - + +
1679B VAL* 1.3 76.7 - - + +
1681B LYS* 1.3 84.9 + - + +
1684B GLY* 3.1 19.8 - - - -
1687B LYS* 3.9 42.2 + - + +
1692B TRP* 3.8 21.1 - - + -
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Residues in contact with LYS1681 (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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1212B TYR* 4.1 14.1 - - + -
1240B LEU* 3.2 23.8 - - + +
1676B LYS* 4.3 17.6 - - - +
1677B GLU* 3.0 39.3 + - + +
1680B GLU* 1.3 102.1 + - + +
1682B GLY* 1.3 68.2 + - - +
1684B GLY* 3.1 12.0 + - - -
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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