Contacts of the helix formed by residues 1665 - 1678 (chain B) in PDB entry 5WBY
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 ARG1665 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1456B TRP* 4.0 14.8 - - - +
1457B GLU* 6.1 1.8 - - + +
1486B ALA 3.6 8.7 + - - -
1487B LEU* 3.1 54.6 + - + +
1630B VAL* 4.1 11.6 - - + +
1631B GLU* 2.9 40.2 + - - +
1634B GLN* 3.9 2.6 - - - +
1660B CYS* 2.8 18.5 + - + +
1663B SER* 4.9 5.2 - - - +
1664B GLY* 1.3 74.0 - - - +
1666B LEU* 1.3 58.8 + - - +
1667B ALA 3.4 2.0 - - - -
1668B LEU* 3.4 31.5 + - + +
1669B ALA* 2.9 27.9 + - - +
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Residues in contact with LEU1666 (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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1661B GLY* 4.5 20.6 - - - +
1664B GLY* 3.6 9.9 + - - +
1665B ARG* 1.3 72.4 - - - +
1667B ALA* 1.3 56.8 + - - +
1669B ALA* 3.6 4.0 - - - +
1670B HIS* 2.7 37.0 + - - +
1703B ASN* 3.3 25.8 + - - +
1706B LYS* 3.6 45.3 - - + +
1707B SER* 4.0 15.9 - - - +
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Residues in contact with ALA1667 (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 ARG 3.4 0.4 - - - -
1666B LEU* 1.3 77.7 - - - +
1668B LEU* 1.3 60.0 + - - +
1670B HIS* 3.9 6.8 + - - +
1671B LYS* 3.4 39.0 + - - +
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Residues in contact with LEU1668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1487B LEU 4.1 9.4 - - - +
1488B GLY 5.3 4.3 - - - +
1630B VAL* 3.6 31.4 - - + -
1634B GLN* 4.1 15.3 - - - +
1656B TYR* 3.9 21.3 - - - +
1660B CYS* 4.2 5.8 - - - -
1665B ARG* 3.4 36.4 + - + +
1666B LEU 3.2 0.2 - - - -
1667B ALA* 1.3 77.5 - - - +
1669B ALA* 1.3 59.2 + - - +
1670B HIS 3.2 0.2 - - - -
1671B LYS* 3.3 8.6 + - + +
1672B THR* 2.8 32.2 + - - +
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Residues in contact with ALA1669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1657B ALA* 3.7 13.8 - - - +
1660B CYS* 3.6 19.9 - - + +
1661B GLY* 3.9 7.4 - - - +
1665B ARG 2.9 17.8 + - - +
1666B LEU* 3.6 5.4 - - - +
1668B LEU* 1.3 72.9 - - - +
1670B HIS* 1.3 66.9 + - - +
1672B THR* 3.4 11.6 - - - -
1673B LEU* 3.3 25.8 + - + +
1703B ASN* 3.9 14.6 - - - +
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Residues in contact with HIS1670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1666B LEU 2.7 21.7 + - - +
1667B ALA* 3.9 9.1 + - - +
1669B ALA* 1.3 71.4 - - - +
1671B LYS* 1.3 69.6 + - + +
1673B LEU* 2.9 24.9 + - - +
1674B VAL* 3.0 32.1 + - + +
1681B PRO* 3.6 21.7 - - + +
1682B SER* 4.0 5.4 + - - -
1700B TYR* 3.4 43.9 + + - -
1703B ASN* 3.9 18.3 - - - +
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Residues in contact with LYS1671 (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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1489B GLU* 3.6 24.4 + - - +
1667B ALA* 3.4 26.2 + - - +
1668B LEU* 3.3 11.0 + - + +
1670B HIS* 1.3 88.6 - - + +
1672B THR* 1.3 61.6 + - - +
1674B VAL* 3.9 11.3 - - + +
1675B LEU* 3.6 18.4 + - - +
1681B PRO* 6.4 0.4 - - + -
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Residues in contact with THR1672 (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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1653B TRP* 3.7 30.7 - - + +
1656B TYR* 3.6 41.5 + - + -
1657B ALA* 3.8 9.7 - - + +
1660B CYS* 4.7 0.3 - - - -
1668B LEU* 2.8 21.1 + - - +
1669B ALA* 3.4 11.0 + - - -
1670B HIS 3.2 0.2 - - - -
1671B LYS* 1.3 77.0 - - - +
1673B LEU* 1.3 60.6 + - - +
1675B LEU* 3.4 11.5 + - - +
1676B LEU* 3.4 22.1 + - + +
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Residues in contact with LEU1673 (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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1654B LEU* 3.7 20.4 - - + -
1657B ALA* 3.9 18.6 - - + +
1669B ALA* 3.5 15.7 - - + +
1670B HIS* 2.9 8.7 + - - +
1672B THR* 1.3 76.7 - - - +
1674B VAL* 1.3 63.9 + - - +
1676B LEU* 3.3 10.4 + - + +
1677B LEU* 3.0 30.0 + - - +
1696B VAL* 4.4 9.2 - - + -
1699B ALA* 3.7 26.0 - - + +
1700B TYR* 3.6 42.2 - - + +
1703B ASN* 4.3 13.0 - - + -
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Residues in contact with VAL1674 (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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1670B HIS* 3.0 47.3 + - + +
1671B LYS* 3.9 11.0 - - + +
1672B THR 3.3 0.4 - - - -
1673B LEU* 1.3 76.4 - - - +
1675B LEU* 1.3 57.9 + - - +
1677B LEU* 3.4 2.1 + - - -
1678B GLY* 3.0 23.9 + - - -
1679B VAL 3.4 17.3 + - - +
1680B ASP 3.3 25.6 - - - +
1681B PRO* 3.7 21.5 - - + -
1700B TYR* 4.7 1.3 - - + -
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Residues in contact with LEU1675 (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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1646B PRO* 3.9 28.7 - - + -
1647B HIS* 3.3 31.0 - - + +
1653B TRP* 4.9 15.0 - - + -
1671B LYS 3.6 8.3 + - - +
1672B THR* 3.4 13.2 + - - +
1673B LEU 3.3 0.2 - - - -
1674B VAL* 1.3 80.6 - - - +
1676B LEU* 1.3 61.4 + - + +
1678B GLY* 3.3 10.2 + - - -
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Residues in contact with LEU1676 (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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1646B PRO* 3.8 30.3 - - + +
1647B HIS* 4.2 5.2 + - - -
1650B MET* 3.4 46.2 - - + +
1653B TRP* 4.0 41.3 - - + +
1654B LEU* 4.2 8.3 - - + +
1672B THR* 3.4 17.0 + - + +
1673B LEU* 3.3 25.6 + - + +
1675B LEU* 1.3 79.4 - - + +
1677B LEU* 1.3 60.7 + - - +
1678B GLY 3.5 0.3 + - - -
1693B HIS* 4.0 5.9 + - - -
1696B VAL* 3.8 15.7 - - + -
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Residues in contact with LEU1677 (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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1673B LEU 3.0 20.7 + - - +
1674B VAL 3.8 0.2 - - - +
1676B LEU* 1.3 75.3 - - - +
1678B GLY* 1.3 58.0 + - - +
1679B VAL* 3.3 34.2 + - + +
1680B ASP* 4.7 6.3 - - + +
1689B LEU* 5.5 1.8 - - + -
1690B PRO* 4.3 22.2 - - + +
1692B VAL* 4.4 11.4 - - + +
1693B HIS* 4.3 16.1 + - + +
1696B VAL* 3.5 24.5 - - + -
1697B THR* 4.0 21.3 - - + +
1700B TYR* 4.0 34.5 - - + -
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Residues in contact with GLY1678 (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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1647B HIS* 5.0 7.4 - - - -
1674B VAL 3.0 6.9 + - - -
1675B LEU* 3.3 10.9 + - - -
1676B LEU 3.2 3.4 - - - -
1677B LEU* 1.3 76.1 - - - +
1679B VAL* 1.3 68.8 + - - +
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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