Contacts of the helix formed by residues 1642 - 1660 (chain B) in PDB entry 3AU5
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 SER1642 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1604B ASP* 2.5 36.9 + - - -
1641B PRO* 1.3 74.8 - - - +
1643B ARG* 1.3 79.7 + - - +
1644B GLY* 3.1 9.9 + - - -
1645B ILE* 3.0 5.8 + - - +
1646B LEU* 2.6 34.0 + - - +
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Residues in contact with ARG1643 (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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1641B PRO 3.6 2.7 + - - +
1642B SER* 1.3 92.8 + - - +
1644B GLY* 1.3 59.4 + - - +
1646B LEU* 3.9 10.2 - - + +
1647B LYS* 3.1 32.9 + - + +
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Residues in contact with GLY1644 (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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1510B ILE* 5.4 3.6 - - - +
1642B SER* 3.1 8.0 + - - -
1643B ARG* 1.3 81.2 - - - +
1645B ILE* 1.3 66.4 + - - +
1647B LYS* 3.4 11.7 + - - +
1648B TYR* 3.2 20.1 + - - +
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Residues in contact with ILE1645 (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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1510B ILE* 4.3 16.4 - - + -
1545B LEU* 4.4 7.9 - - + -
1604B ASP* 3.4 39.9 - - + +
1607B TYR* 3.9 28.7 - - + -
1608B CYS* 4.0 26.9 - - - +
1611B ILE* 4.9 5.8 - - + -
1641B PRO* 4.1 6.1 - - + -
1642B SER* 3.0 5.6 + - - +
1644B GLY* 1.3 78.4 - - - +
1646B LEU* 1.3 55.7 + - - +
1648B TYR* 3.3 4.5 + - + +
1649B LEU* 2.7 32.7 + - - +
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Residues in contact with LEU1646 (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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1640B LEU* 4.8 17.3 - - + -
1641B PRO* 3.7 22.8 - - + +
1642B SER 2.6 21.0 + - - +
1643B ARG* 3.9 9.9 - - - +
1645B ILE* 1.3 72.7 - - - +
1647B LYS* 1.3 59.0 + - + +
1649B LEU* 3.3 2.8 + - + +
1650B LYS* 2.9 47.5 + - + +
1676B LEU* 3.7 37.0 - - + +
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Residues in contact with LYS1647 (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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1514B LYS* 6.4 2.9 - - - -
1643B ARG* 3.1 21.7 + - + +
1644B GLY* 3.5 11.4 - - - +
1646B LEU* 1.3 76.4 - - + +
1648B TYR* 1.3 60.3 + - - +
1650B LYS* 3.1 9.0 + - - +
1651B PHE* 2.8 30.6 + - - +
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Residues in contact with TYR1648 (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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1506B THR* 5.4 2.0 - - + -
1510B ILE* 3.4 52.7 - - + -
1513B ILE* 4.1 13.4 - - + +
1527B TYR* 2.6 44.0 + - - -
1533B LEU* 4.6 11.8 + - + +
1608B CYS* 5.1 6.5 - - - -
1611B ILE* 3.9 34.0 - - + +
1615B ASN* 5.2 0.2 + - - -
1644B GLY 3.2 10.5 + - - +
1645B ILE* 3.3 8.5 + - + +
1647B LYS* 1.3 79.6 - - - +
1649B LEU* 1.3 57.0 + - - +
1651B PHE* 3.4 20.9 + + - -
1652B HIS* 3.0 27.1 + - + +
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Residues in contact with LEU1649 (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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1607B TYR* 3.5 29.8 - - + -
1611B ILE* 3.5 30.9 - - + +
1632B LEU* 4.2 19.1 - - + -
1641B PRO* 4.4 9.6 - - + -
1645B ILE* 2.7 22.1 + - + +
1646B LEU* 3.5 4.7 - - + +
1647B LYS 3.2 0.2 - - - -
1648B TYR* 1.3 71.4 - - - +
1650B LYS* 1.3 54.0 + - - +
1652B HIS* 3.1 4.8 + - + +
1653B LEU* 2.7 62.1 + - + +
1672B THR* 4.9 1.8 - - + -
1676B LEU* 3.5 26.9 - - + -
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Residues in contact with LYS1650 (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 LEU* 2.9 45.1 + - + +
1647B LYS* 3.6 7.0 - - - +
1649B LEU* 1.3 71.9 - - - +
1651B PHE* 1.3 66.9 + - - +
1653B LEU* 3.6 11.0 - - + +
1654B LYS* 3.0 27.4 + - - +
1673B TYR* 3.3 45.3 + - + +
1676B LEU* 5.4 3.6 - - - -
1677B LYS* 5.4 6.8 - - - +
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Residues in contact with PHE1651 (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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1513B ILE* 3.7 23.1 - - + -
1517B CYS* 4.3 31.6 - - + -
1523B VAL* 3.9 13.0 - - + -
1527B TYR* 3.5 20.2 - - - -
1647B LYS 2.8 17.0 + - - +
1648B TYR* 3.4 25.1 - + - +
1650B LYS* 1.3 77.8 - - - +
1652B HIS* 1.3 62.7 + - - +
1654B LYS* 3.9 6.8 + - - +
1655B ARG* 3.3 51.7 + - + +
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Residues in contact with HIS1652 (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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1527B TYR* 4.8 7.3 + - - -
1611B ILE* 3.6 29.0 + - + +
1614B THR* 3.1 31.6 + - - -
1615B ASN* 3.5 40.7 + - + -
1629B TRP* 4.1 13.5 - + - -
1632B LEU* 5.4 0.7 - - + -
1648B TYR* 3.0 15.3 + - + +
1649B LEU* 3.3 11.9 - - + +
1651B PHE* 1.3 80.5 - - + +
1653B LEU* 1.3 68.5 + - + +
1655B ARG* 3.2 12.3 + - - +
1656B ILE* 3.1 36.1 + - + +
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Residues in contact with LEU1653 (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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1629B TRP* 3.7 30.3 - - + -
1649B LEU* 2.7 52.9 + - + +
1650B LYS* 3.2 15.0 + - - +
1652B HIS* 1.3 72.1 - - + +
1654B LYS* 1.3 67.0 + - - +
1656B ILE* 3.0 16.1 + - - +
1657B ARG* 3.3 15.4 + - - +
1669B ALA* 4.1 20.5 - - + +
1672B THR* 4.2 8.1 - - + -
1673B TYR* 4.0 35.9 - - + +
1676B LEU* 4.1 8.7 - - + -
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Residues in contact with LYS1654 (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 LYS 3.0 17.2 + - - +
1651B PHE* 4.0 6.7 - - - +
1653B LEU* 1.3 78.8 - - - +
1655B ARG* 1.3 66.3 + - + +
1656B ILE 3.1 0.3 + - - -
1657B ARG* 3.2 14.9 + - - +
1658B GLU* 2.8 48.1 + - + +
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Residues in contact with ARG1655 (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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1520B SER* 6.2 2.2 - - - +
1523B VAL* 5.2 3.2 - - - +
1524B GLU* 2.6 31.1 + - - +
1527B TYR* 3.8 18.8 + - - -
1615B ASN* 4.8 2.2 + - - -
1616B LYS* 3.5 21.2 - - - +
1651B PHE* 3.3 52.9 + - + +
1652B HIS* 3.2 13.6 + - - +
1654B LYS* 1.3 80.7 - - + +
1656B ILE* 1.3 63.5 + - + +
1658B GLU* 3.4 13.8 + - - +
1659B GLN* 3.1 52.8 + - - +
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Residues in contact with ILE1656 (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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1614B THR 3.9 20.6 - - - +
1615B ASN* 5.6 1.8 - - - +
1616B LYS 6.1 0.4 - - - +
1629B TRP* 3.6 32.3 - - + +
1652B HIS* 3.1 28.9 + - + +
1653B LEU 3.0 9.6 + - - +
1655B ARG* 1.3 76.2 - - + +
1657B ARG* 1.3 60.4 + - - +
1659B GLN 3.1 1.6 + - - -
1660B PHE* 2.8 60.4 + - + +
1665B MET* 4.1 24.7 - - + +
1666B GLU 4.4 0.9 - - - +
1669B ALA* 4.3 2.9 - - + -
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Residues in contact with ARG1657 (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 LEU 4.0 4.9 - - - +
1654B LYS* 3.2 9.9 + - - +
1656B ILE* 1.3 79.8 - - - +
1658B GLU* 1.3 60.4 + - + +
1661B PRO* 3.3 27.9 - - - +
1666B GLU* 2.5 55.4 + - + +
1669B ALA* 3.9 11.9 - - + -
1670B LEU* 3.0 51.1 - - - +
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Residues in contact with GLU1658 (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 LYS* 2.8 52.1 + - + +
1655B ARG* 3.7 19.5 - - - +
1656B ILE 3.1 0.2 - - - -
1657B ARG* 1.3 79.3 - - + +
1659B GLN* 1.3 67.3 + - + +
1660B PHE 3.5 0.2 - - - -
1661B PRO* 3.9 9.3 - - - +
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Residues in contact with GLN1659 (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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1524B GLU* 4.7 2.0 - - - +
1616B LYS* 3.6 22.5 + - - -
1655B ARG* 3.1 59.6 + - - +
1658B GLU* 1.3 82.0 + - + +
1660B PHE* 1.3 88.6 + - + +
1661B PRO* 3.6 5.1 - - - +
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Residues in contact with PHE1660 (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 LYS* 6.1 6.7 - - - -
1617B VAL* 6.1 2.7 - - + -
1620B PRO* 3.9 27.4 - - + -
1656B ILE* 2.8 53.4 + - + +
1657B ARG 3.7 3.4 - - - -
1659B GLN* 1.3 103.5 - - + +
1661B PRO* 1.3 63.7 - - - +
1663B THR* 2.5 38.6 + - + +
1665B MET* 4.4 17.7 - - + -
1666B GLU* 2.9 10.6 - - - +
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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