Contacts of the helix formed by residues 1686 - 1694 (chain B) in PDB entry 5EK0
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 ILE1686 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1662B TRP* 4.3 12.3 - - + -
1663B PHE* 3.7 35.2 - - + -
1672B THR* 3.9 18.8 - - + -
1675B GLN* 3.4 37.5 - - + +
1676B VAL* 4.2 18.2 - - + -
1681B SER 3.4 11.5 + - - +
1682B TRP* 3.5 7.2 + - - +
1683B SER 3.5 0.2 + - - -
1685B GLY* 1.4 80.0 - - - +
1687B VAL* 1.3 68.7 + - + +
1688B ARG 3.4 2.0 - - - -
1689B PRO* 3.2 13.1 - - - +
1690B LEU* 3.2 22.4 + - + +
1701B PHE* 4.9 1.3 - - + -
1684C MET* 3.7 10.1 - - + -
1688C ARG* 4.7 0.7 - - - +
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Residues in contact with VAL1687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1671A TYR* 3.4 22.2 - - + +
1676B VAL* 5.0 2.7 - - + -
1682B TRP* 2.8 44.2 + - + +
1686B ILE* 1.3 75.3 - - + +
1688B ARG* 1.3 58.0 + - - +
1690B LEU* 3.6 7.4 - - - +
1691B MET* 3.2 26.7 + - + +
1697B ALA 4.7 0.7 - - - -
1698B TRP* 4.2 18.2 - - - +
1701B PHE* 3.6 47.8 - - + -
1702B ILE* 5.5 0.2 - - + -
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Residues in contact with ARG1688 (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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1661A GLU 4.2 7.9 + - - -
1662A TRP* 3.2 32.5 - - - +
1668A GLU* 4.8 3.8 + - - -
1671A TYR* 3.7 23.9 - - + +
1672A THR* 2.8 33.7 + - - +
1675A GLN* 3.0 28.3 + - - -
1686A ILE* 4.2 1.2 - - - +
1802A PX4 5.7 2.0 - - - -
1683B SER* 2.7 31.5 + - - +
1684B MET* 3.8 24.0 - - - +
1687B VAL* 1.3 68.7 - - - +
1689B PRO* 1.4 59.6 - - + +
1690B LEU 3.1 4.0 - - - -
1691B MET* 3.0 30.2 + - + +
1692B GLU* 3.5 12.9 + - - +
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Residues in contact with PRO1689 (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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1659B PHE* 3.4 18.3 - - + -
1662B TRP* 3.7 15.9 - - + -
1684B MET 3.2 20.4 - - - +
1685B GLY 3.3 18.2 - - - +
1686B ILE 3.2 16.6 - - - +
1688B ARG* 1.4 88.8 - - + +
1690B LEU* 1.3 57.1 + - - -
1692B GLU* 3.4 26.3 - - + +
1693B VAL* 4.4 0.3 - - - +
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Residues in contact with LEU1690 (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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1655B PHE* 3.7 20.4 - - + -
1659B PHE* 3.6 30.3 - - + -
1662B TRP* 3.6 27.6 - - + -
1663B PHE* 3.7 12.1 - - + -
1686B ILE* 3.2 25.1 + - + +
1687B VAL 3.6 6.7 - - - +
1688B ARG 3.1 0.2 - - - -
1689B PRO* 1.3 76.2 - - - +
1691B MET* 1.3 52.8 + - - +
1692B GLU 3.2 1.8 - - - -
1693B VAL* 3.4 2.3 + - - +
1694B TYR* 2.8 40.6 + - - +
1697B ALA* 4.2 4.9 - - + -
1701B PHE* 3.4 38.4 - - + -
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Residues in contact with MET1691 (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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1671A TYR* 3.4 37.9 - - + +
1802A PX4 3.7 31.4 - - - -
1687B VAL* 3.2 19.7 - - + +
1688B ARG* 3.0 17.3 + - + +
1690B LEU* 1.3 75.7 - - - +
1692B GLU* 1.3 62.5 + - - +
1693B VAL 3.3 0.2 - - - -
1694B TYR 3.3 6.3 - - - +
1695B PRO* 3.2 28.6 - - - +
1697B ALA* 3.8 14.4 - - + -
1698B TRP* 3.5 36.8 - - - -
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Residues in contact with GLU1692 (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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1688B ARG* 3.9 10.6 - - - +
1689B PRO* 3.4 20.9 - - + +
1690B LEU 3.2 0.2 - - - -
1691B MET* 1.3 81.1 - - - +
1693B VAL* 1.3 64.0 + - + +
1695B PRO* 4.7 2.4 - - - +
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Residues in contact with VAL1693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1658B ARG* 3.6 45.5 - - + +
1659B PHE* 3.5 32.1 - - + -
1689B PRO 4.4 2.0 - - - +
1690B LEU 3.4 1.4 + - - -
1692B GLU* 1.3 82.4 - - + +
1694B TYR* 1.3 80.4 + - + +
1695B PRO* 3.4 9.1 - - - +
1801B PX4 5.3 0.7 + - - -
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Residues in contact with TYR1694 (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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1599A ARG* 3.3 42.5 + - - -
1654B LEU 3.5 15.0 + - - -
1655B PHE* 3.6 31.9 + + - -
1657B GLU* 4.4 3.1 - - - +
1658B ARG* 3.3 38.5 + - + +
1659B PHE* 3.6 25.8 - + - -
1690B LEU* 2.8 26.4 + - + +
1691B MET* 3.3 5.3 - - - -
1693B VAL* 1.3 85.3 - - + +
1695B PRO* 1.4 65.7 - - - +
1696B TYR 3.0 3.8 + - - -
1697B ALA* 3.1 11.2 + - + +
1801B PX4 3.4 28.3 - - - +
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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
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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