Contacts of the helix formed by residues 1653 - 1669 (chain B) in PDB entry 5V7W
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 ASN1653 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1615B GLN 3.2 14.1 + - - +
1616B ASN 3.0 17.5 - - - +
1617B PHE* 3.9 4.0 - - + +
1651B ILE* 4.7 2.5 - - + -
1652B GLN* 1.3 74.1 - - - +
1654B PRO* 1.3 58.6 - - - +
1655B ASP 3.5 3.3 + - - -
1656B LEU* 3.3 28.3 + - + +
1657B TRP* 2.9 29.7 + - - +
1693B ASN 2.8 29.0 + - - +
1694B ARG 3.0 22.0 + - - -
1792B TYR* 2.9 17.1 + - + +
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Residues in contact with PRO1654 (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 ASN 3.7 13.5 - - - +
1617B PHE* 5.0 0.4 - - - -
1618B CYS* 6.4 0.4 - - - -
1652B GLN* 3.5 11.7 - - + +
1653B ASN* 1.3 82.9 - - - +
1655B ASP* 1.3 59.5 + - - +
1657B TRP* 3.7 7.3 - - + +
1658B ASN* 3.0 40.3 + - - +
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Residues in contact with ASP1655 (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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1613B LYS* 3.8 26.7 - - + +
1614B GLN* 3.8 10.2 + - - +
1615B GLN* 3.0 44.7 + - + -
1616B ASN 4.5 1.4 + - - -
1653B ASN* 3.4 1.4 + - - -
1654B PRO* 1.3 76.8 - - - +
1656B LEU* 1.3 66.7 + - - +
1658B ASN* 3.3 12.3 + - - +
1659B SER* 3.1 27.4 + - - -
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Residues in contact with LEU1656 (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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1615B GLN* 3.9 10.7 - - - +
1653B ASN* 3.3 33.1 + - + +
1655B ASP* 1.3 78.3 - - - +
1657B TRP* 1.3 61.6 + - - +
1659B SER* 3.7 3.5 + - - -
1660B TYR* 3.1 23.9 + - - +
1693B ASN 4.0 6.5 - - - +
1694B ARG 4.4 0.9 - - - +
1695B ASN 3.5 25.4 - - - +
1696B GLY* 3.8 18.6 - - - +
1789B TYR* 3.9 26.9 - - + -
1791B ALA 5.2 5.4 - - - +
1792B TYR* 3.9 13.0 - - + -
1793B PRO* 3.8 25.6 - - + -
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Residues in contact with TRP1657 (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 ASN 2.9 19.3 + - - +
1654B PRO* 3.7 7.9 - - + +
1656B LEU* 1.3 74.7 - - - +
1658B ASN* 1.3 77.7 + - - +
1660B TYR* 3.0 9.6 + + - +
1661B GLN* 2.9 60.6 + - + +
1742B ARG* 4.3 24.9 - - - -
1792B TYR* 3.5 51.5 - + + +
1794B GLU* 4.8 8.3 - - - -
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Residues in contact with ASN1658 (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 PRO* 3.0 27.2 + - - +
1655B ASP* 3.3 12.9 + - - +
1657B TRP* 1.3 89.3 - - - +
1659B SER* 1.3 62.0 + - - +
1661B GLN* 3.4 7.6 + - - +
1662B ALA* 3.0 23.7 + - - +
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Residues in contact with SER1659 (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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1613B LYS* 5.6 4.9 - - - +
1615B GLN* 4.6 1.9 + - - -
1655B ASP 3.1 17.3 + - - -
1656B LEU 3.8 1.3 - - - -
1658B ASN* 1.3 72.0 - - - +
1660B TYR* 1.3 67.7 + - - +
1662B ALA* 2.8 19.2 + - - +
1663B LYS* 3.0 12.8 + - - +
1789B TYR* 3.5 47.6 - - - -
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Residues in contact with TYR1660 (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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1656B LEU* 3.1 12.2 + - + +
1657B TRP* 3.0 12.2 + + - +
1659B SER* 1.3 77.5 - - - +
1661B GLN* 1.3 79.9 + - + +
1663B LYS* 3.3 2.9 + - - +
1664B LYS* 2.9 32.6 + - + +
1677B GLU* 2.4 43.2 + - - +
1742B ARG* 3.3 36.6 + - + +
1743B VAL 3.7 0.9 + - - -
1744B LEU* 3.8 17.2 - - + +
1789B TYR* 3.4 26.7 - - + +
1790B GLN 3.3 15.5 - - - -
1791B ALA 3.8 3.4 - - - +
1792B TYR* 3.8 25.8 - - + -
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Residues in contact with GLN1661 (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 TRP* 2.9 70.5 + - + +
1658B ASN* 3.7 6.7 - - - +
1660B TYR* 1.3 86.0 - - - +
1662B ALA* 1.3 60.4 + - - +
1664B LYS* 3.4 21.2 + - - +
1665B LYS* 2.9 27.5 + - - +
1677B GLU* 5.0 1.6 + - - -
1742B ARG* 5.8 0.2 - - - +
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Residues in contact with ALA1662 (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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1658B ASN 3.0 12.4 + - - +
1659B SER* 2.8 18.3 + - - +
1661B GLN* 1.3 69.2 - - - +
1663B LYS* 1.3 64.2 + - - +
1665B LYS* 3.1 9.3 + - - +
1666B THR* 3.0 25.6 + - - -
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Residues in contact with LYS1663 (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 SER 3.0 10.2 + - - +
1660B TYR 3.7 6.3 - - - +
1662B ALA* 1.3 76.2 - - - +
1664B LYS* 1.3 57.4 + - - +
1666B THR* 3.5 11.9 + - + -
1667B MET* 3.1 50.2 + - - +
1670B LYS* 5.9 1.4 - - - +
1744B LEU* 3.7 15.3 - - + -
1771B ASP* 4.8 7.1 + - - +
1787B TYR* 4.3 24.9 - - + +
1788B ASP 5.0 4.5 - - - +
1789B TYR* 3.9 20.4 - - + +
1790B GLN* 4.8 14.1 - - - +
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Residues in contact with LYS1664 (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 TYR* 2.9 21.4 + - + +
1661B GLN* 3.6 23.1 + - - +
1662B ALA 3.2 0.2 - - - -
1663B LYS* 1.3 75.8 - - - +
1665B LYS* 1.3 55.2 + - - +
1667B MET* 3.1 2.7 + - - +
1668B ASP* 2.7 66.3 + - - +
1677B GLU* 3.9 42.0 - - - +
1744B LEU* 3.7 27.0 - - + +
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Residues in contact with LYS1665 (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 GLN 2.9 14.9 + - - +
1662B ALA* 3.1 11.6 + - - +
1664B LYS* 1.3 76.9 - - - +
1666B THR* 1.3 61.9 + - - +
1668B ASP* 3.5 5.6 + - - +
1669B ALA* 3.3 24.0 + - + +
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Residues in contact with THR1666 (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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1662B ALA 3.0 14.9 + - - -
1663B LYS* 3.6 15.2 - - + -
1665B LYS* 1.3 76.3 - - - +
1667B MET* 1.3 61.6 + - - +
1669B ALA* 3.6 4.9 + - - +
1670B LYS* 3.3 28.5 + - + +
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Residues in contact with MET1667 (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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1663B LYS* 3.1 32.3 + - - +
1664B LYS* 3.1 8.2 + - - +
1666B THR* 1.3 77.2 - - - +
1668B ASP* 1.3 64.7 + - - +
1670B LYS* 3.1 9.8 + - - +
1671B ASN* 3.0 34.7 + - - +
1676B ASN* 3.4 17.2 + - + +
1744B LEU* 3.4 34.8 - - + +
1746B GLY* 3.0 42.6 - - - +
1771B ASP* 3.5 22.7 - - - +
1790B GLN* 5.2 0.2 - - - -
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Residues in contact with ASP1668 (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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1664B LYS* 2.7 53.0 + - - +
1665B LYS* 4.0 5.7 - - - +
1667B MET* 1.3 74.6 - - - +
1669B ALA* 1.3 61.0 + - - +
1670B LYS 3.3 0.7 + - - -
1671B ASN 3.8 5.7 + - - -
1672B GLY* 3.9 15.4 + - - +
1674B THR 4.9 1.2 - - - +
1676B ASN* 2.6 37.7 + - - +
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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
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1665B LYS* 3.3 15.2 + - + +
1666B THR* 4.1 4.0 - - - +
1667B MET 3.3 0.2 - - - -
1668B ASP* 1.3 78.0 - - - +
1670B LYS* 1.3 58.8 + - - +
1672B GLY* 4.9 2.1 + - - -
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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