Contacts of the helix formed by residues 1649 - 1664 (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 ASP1649 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1616B ARG* 5.6 11.3 - - - +
1619B TRP* 5.8 4.2 - - - -
1644B VAL* 3.9 23.3 - - + +
1645B SER 3.4 4.6 + - - +
1646B PRO 3.2 10.2 + - - +
1648B GLU* 1.3 76.5 - - - +
1650B MET* 1.3 62.1 + - - +
1651B ARG* 3.2 32.5 + - - +
1652B THR* 2.6 27.9 + - - +
1653B TRP* 3.3 20.1 + - + +
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Residues in contact with MET1650 (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 3.5 7.6 - - - +
1647B HIS* 3.5 38.1 - - + +
1648B GLU 3.7 2.2 + - - -
1649B ASP* 1.3 73.8 - - - +
1651B ARG* 1.3 60.5 + - - +
1653B TRP* 3.4 1.7 + - - +
1654B LEU* 2.9 42.6 + - + +
1676B LEU* 3.4 37.4 - - + +
1693B HIS* 3.9 28.9 - - + +
1696B VAL* 3.8 24.9 - - - -
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Residues in contact with ARG1651 (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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1616B ARG* 4.1 16.2 + - - +
1617B GLN* 4.9 6.7 - - - +
1620B TRP* 3.5 67.8 - - + +
1649B ASP* 3.2 21.4 + - - +
1650B MET* 1.3 78.2 - - - +
1652B THR* 1.3 58.9 + - - +
1654B LEU* 4.0 7.9 - - - +
1655B LYS* 3.2 27.7 + - - +
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Residues in contact with THR1652 (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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1619B TRP 6.1 0.6 - - - -
1620B TRP* 3.8 23.0 - - - +
1623B LEU* 3.7 19.1 - - + +
1637B LEU* 3.8 26.9 - - + -
1640B ARG* 4.5 9.2 - - - +
1649B ASP* 2.6 34.9 + - - +
1650B MET 3.2 0.6 - - - -
1651B ARG* 1.3 78.2 + - - +
1653B TRP* 1.3 63.3 + - + +
1655B LYS* 3.2 5.0 + - - +
1656B TYR* 2.9 26.9 + - - +
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Residues in contact with TRP1653 (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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1637B LEU* 4.3 30.5 - - + +
1638B MET* 5.5 2.7 - - + -
1640B ARG* 6.3 0.8 - - + +
1641B SER* 3.3 30.1 - - - -
1644B VAL* 4.9 3.2 + - - +
1645B SER 4.5 3.0 + - - -
1646B PRO* 3.6 38.6 - - + +
1649B ASP* 3.3 20.4 + - + +
1650B MET 3.4 2.1 + - - +
1652B THR* 1.3 84.8 - - + +
1654B LEU* 1.3 56.6 + - - +
1656B TYR* 3.8 19.2 - + - +
1657B ALA* 2.9 27.9 + - - +
1672B THR* 3.7 24.3 - - + +
1675B LEU* 4.9 15.0 - - + -
1676B LEU* 4.0 25.2 - - + +
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Residues in contact with LEU1654 (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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1650B MET* 2.9 30.4 + - + +
1651B ARG* 4.0 6.7 - - - +
1653B TRP* 1.3 75.2 - - - +
1655B LYS* 1.3 54.7 + - - +
1657B ALA* 3.7 2.8 - - - +
1658B SER* 2.8 33.4 + - - -
1673B LEU* 3.7 26.9 - - + -
1676B LEU* 4.3 7.4 - - + -
1695B GLN* 4.2 25.8 - - + +
1696B VAL* 4.1 34.1 - - + -
1699B ALA* 4.1 10.8 - - + -
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Residues in contact with LYS1655 (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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1620B TRP* 4.2 15.5 - - + -
1623B LEU* 4.1 19.7 - - + -
1624B GLN* 4.7 26.0 - - + +
1651B ARG 3.2 18.8 + - - +
1652B THR 3.2 4.7 + - - +
1654B LEU* 1.3 72.7 - - - +
1656B TYR* 1.3 64.1 + - - +
1658B SER* 3.5 11.3 + - - +
1659B LEU* 3.1 55.0 + - + +
1662B LYS* 4.9 10.7 - - - +
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Residues in contact with TYR1656 (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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1623B LEU* 6.0 0.4 - - + -
1630B VAL* 4.3 17.3 - - + -
1633B TRP* 4.2 32.9 - + + -
1634B GLN* 3.5 27.1 + - + +
1637B LEU* 3.4 33.4 - - + -
1652B THR 2.9 16.0 + - - +
1653B TRP* 3.8 13.5 - + - +
1654B LEU 3.3 0.2 - - - -
1655B LYS* 1.3 74.7 - - - +
1657B ALA* 1.3 62.7 + - - +
1659B LEU* 3.2 5.2 + - + +
1660B CYS* 3.0 45.2 + - - -
1668B LEU* 3.9 17.3 - - - +
1672B THR* 3.6 34.5 - - + -
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Residues in contact with ALA1657 (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 2.9 20.3 + - - +
1654B LEU 3.7 4.0 - - - +
1655B LYS 3.4 0.2 - - - -
1656B TYR* 1.3 75.8 - - - +
1658B SER* 1.3 62.7 + - - +
1660B CYS* 3.4 10.3 + - - +
1661B GLY* 3.2 17.0 + - - -
1669B ALA* 3.7 9.8 - - - +
1672B THR* 3.8 23.1 - - + -
1673B LEU* 3.9 28.9 - - + +
1699B ALA* 6.1 0.2 - - + -
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Residues in contact with SER1658 (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 2.8 22.7 + - - -
1655B LYS* 3.5 18.0 + - - +
1657B ALA* 1.3 73.2 - - - +
1659B LEU* 1.3 57.1 + - - +
1661B GLY* 3.2 4.0 + - - -
1662B LYS* 3.0 45.3 + - - +
1702B LYS* 6.2 0.5 - - - -
1706B LYS* 5.8 0.9 + - - -
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Residues in contact with LEU1659 (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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1623B LEU 5.0 0.9 - - - +
1630B VAL* 4.9 2.4 - - + +
1633B TRP* 3.3 41.5 - - + -
1655B LYS* 3.1 40.6 + - - +
1656B TYR* 3.2 7.2 + - + +
1658B SER* 1.3 76.2 - - - +
1660B CYS* 1.3 60.8 + - - +
1662B LYS* 3.7 20.2 - - + +
1663B SER* 2.9 31.7 + - - -
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Residues in contact with CYS1660 (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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1630B VAL* 3.7 20.0 - - + -
1656B TYR* 3.0 53.6 + - - -
1657B ALA* 3.5 10.3 - - - +
1658B SER 3.3 0.2 - - - -
1659B LEU* 1.3 76.0 - - - +
1661B GLY* 1.3 55.8 + - - +
1663B SER* 3.2 7.2 + - - -
1664B GLY 3.1 6.9 + - - -
1665B ARG* 2.8 37.6 + - + +
1668B LEU* 4.2 9.4 - - + -
1669B ALA* 3.6 18.4 - - + -
1672B THR* 4.7 0.2 - - - -
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Residues in contact with GLY1661 (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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1657B ALA 3.2 7.0 + - - -
1658B SER 3.2 7.8 + - - -
1660B CYS* 1.3 78.0 - - - +
1662B LYS* 1.3 63.5 + - - +
1664B GLY* 3.3 11.8 + - - -
1666B LEU* 4.5 18.8 - - - +
1669B ALA* 3.9 8.9 - - - +
1703B ASN* 5.0 2.0 - - - -
1706B LYS* 4.7 17.0 - - - +
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Residues in contact with LYS1662 (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 LYS* 4.9 10.0 - - - +
1658B SER* 3.0 30.4 + - - +
1659B LEU* 3.4 25.5 + - + +
1661B GLY* 1.3 77.0 - - - +
1663B SER* 1.3 61.4 + - - +
1664B GLY* 4.5 0.3 - - - -
1706B LYS* 5.3 8.5 - - - +
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Residues in contact with SER1663 (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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1630B VAL* 3.2 28.8 - - - +
1659B LEU 2.9 18.6 + - - -
1660B CYS 3.2 8.8 + - - -
1662B LYS* 1.3 75.7 - - - +
1664B GLY* 1.3 57.0 + - - +
1665B ARG* 4.3 3.2 + - - +
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Residues in contact with GLY1664 (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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1660B CYS 3.1 4.4 + - - -
1661B GLY* 3.3 11.2 + - - -
1662B LYS 3.3 3.9 - - - -
1663B SER* 1.3 78.7 - - - +
1665B ARG* 1.3 63.9 + - - +
1666B LEU* 3.6 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