Contacts of the helix formed by residues 1656 - 1669 (chain B) in PDB entry 3ZQK
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 THR1656 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1651B ILE* 3.9 13.0 - - + -
1652B GLN* 4.5 10.8 - - + +
1653B ASP* 2.8 32.6 + - - -
1654B PHE 3.1 0.2 - - - -
1655B GLU* 1.3 78.7 + - - +
1657B LEU* 1.3 64.2 + - - +
1658B PRO 3.5 0.4 - - - -
1659B ARG* 3.1 13.9 + - + +
1660B GLU* 3.0 48.9 + - + +
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Residues in contact with LEU1657 (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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1516B ARG 4.0 2.5 - - - +
1517B SER* 3.8 37.2 - - - +
1520B PHE* 3.7 19.9 - - + -
1607B VAL* 4.1 10.8 - - + -
1628B ILE* 3.9 23.3 - - + -
1630B VAL* 4.0 9.0 - - + -
1651B ILE* 3.6 10.7 - - + +
1653B ASP 3.2 9.5 + - - +
1654B PHE* 3.1 22.1 + - + +
1656B THR* 1.3 75.5 - - - +
1658B PRO* 1.3 65.4 - - + +
1661B ALA* 2.9 53.9 + - + +
1662B PRO* 3.5 0.7 - - - +
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Residues in contact with PRO1658 (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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1516B ARG* 3.8 21.8 - - + +
1519B GLU* 4.4 8.5 - - + +
1520B PHE* 4.0 21.3 - - + +
1523B GLU* 2.6 40.5 - - - +
1654B PHE 3.1 12.8 - - - +
1655B GLU 3.7 8.3 - - - +
1657B LEU* 1.3 99.4 - - + +
1659B ARG* 1.3 64.8 + - + +
1662B PRO* 3.4 9.4 - - + +
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Residues in contact with ARG1659 (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 GLU* 2.8 61.4 + - - +
1656B THR* 3.1 13.9 + - - +
1658B PRO* 1.3 84.2 - - + +
1660B GLU* 1.3 68.7 + - + +
1662B PRO* 4.3 2.0 - - - +
1663B ASP* 5.3 5.5 + - - +
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Residues in contact with GLU1660 (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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1651B ILE* 4.6 9.0 - - + -
1656B THR* 3.0 33.5 + - + +
1659B ARG* 1.3 85.2 - - + +
1661B ALA* 1.3 67.7 + - - +
1662B PRO* 3.5 2.1 - - - -
1663B ASP* 3.6 12.0 + - - +
1664B LEU* 3.5 23.8 + - + +
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Residues in contact with ALA1661 (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 PHE* 3.6 20.2 - - + -
1628B ILE* 4.9 4.3 - - + -
1649B ILE* 5.0 3.1 - - + -
1651B ILE* 4.0 17.2 - - + +
1656B THR 4.3 0.2 + - - -
1657B LEU* 2.9 34.5 + - + +
1660B GLU* 1.3 78.3 - - - +
1662B PRO* 1.4 65.1 - - - +
1664B LEU* 2.9 7.2 + - - +
1665B VAL* 2.9 27.0 + - + +
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Residues in contact with PRO1662 (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 PHE* 3.9 11.6 - - + -
1523B GLU* 3.7 27.4 - - + +
1524B VAL* 4.1 20.6 - - + +
1527B ARG* 3.9 18.4 - - - +
1657B LEU 3.5 5.6 - - - +
1658B PRO 3.4 26.0 - - - +
1659B ARG 4.3 2.2 - - - +
1660B GLU 3.5 3.8 - - - +
1661B ALA* 1.4 91.8 - - + +
1663B ASP* 1.3 62.2 + - - +
1665B VAL* 3.3 1.0 + - + +
1666B LEU* 2.9 32.4 + - + +
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Residues in contact with ASP1663 (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 ARG* 2.7 41.1 + - - +
1659B ARG 5.3 5.2 - - - +
1660B GLU* 3.6 8.8 + - - +
1661B ALA 3.3 0.6 - - - -
1662B PRO* 1.3 80.6 - - - +
1664B LEU* 1.3 65.7 + - + +
1667B GLN* 3.0 28.6 + - - +
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Residues in contact with LEU1664 (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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1649B ILE* 3.8 35.0 - - + -
1650B LEU 5.6 1.3 - - - +
1651B ILE* 4.1 13.7 - - + -
1660B GLU* 3.5 24.0 - - + +
1661B ALA* 2.9 6.5 + - - +
1663B ASP* 1.3 81.2 - - + +
1665B VAL* 1.3 63.9 + - - +
1667B GLN* 3.8 6.6 + - - +
1668B ARG* 3.7 22.4 + - - +
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Residues in contact with VAL1665 (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 PHE* 4.2 7.0 - - + -
1524B VAL* 4.5 12.3 - - + -
1605B TYR* 3.1 49.7 + - + +
1626B VAL* 5.9 0.2 - - - -
1628B ILE* 4.1 18.8 - - + -
1649B ILE* 3.8 22.0 - - + -
1661B ALA* 2.9 18.0 + - + +
1662B PRO* 3.8 4.9 - - + +
1664B LEU* 1.3 77.9 - - - +
1666B LEU* 1.3 67.9 + - + +
1668B ARG* 3.1 21.7 + - - +
1669B CYS* 3.3 10.9 + - - +
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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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1524B VAL* 4.2 19.1 - - + +
1527B ARG* 3.3 56.1 - - + +
1528B MET* 3.6 31.9 - - + +
1662B PRO* 2.9 22.3 + - + +
1663B ASP 4.4 1.3 - - - +
1665B VAL* 1.3 78.4 - - + +
1667B GLN* 1.3 63.8 + - - +
1668B ARG 3.1 2.0 - - - -
1669B CYS* 2.9 23.8 - - - +
1670B CYS* 4.6 16.5 - - + +
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Residues in contact with GLN1667 (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 ASP 3.0 19.0 + - - +
1664B LEU* 4.2 5.8 - - - +
1665B VAL 3.2 0.4 - - - -
1666B LEU* 1.3 79.6 - - - +
1668B ARG* 1.3 61.7 + - + +
1669B CYS 4.9 0.2 - - - +
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Residues in contact with ARG1668 (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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1626B VAL* 4.5 14.1 - - + +
1646B ASN* 4.9 6.7 - - - +
1647B ALA* 3.0 42.7 + - - +
1648B PRO 4.5 2.8 + - - -
1649B ILE* 3.5 31.3 - - - +
1664B LEU* 3.7 16.7 + - - +
1665B VAL* 3.1 9.8 + - - +
1666B LEU 3.1 0.2 - - - -
1667B GLN* 1.3 81.9 - - + +
1669B CYS* 1.3 60.9 + - + +
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Residues in contact with CYS1669 (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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1603B LEU* 3.9 11.2 - - + -
1605B TYR* 3.0 26.0 - - - +
1665B VAL 3.3 8.0 + - - +
1666B LEU* 2.9 22.8 - - - +
1667B GLN 4.7 0.3 - - - +
1668B ARG* 1.3 82.7 - - + +
1670B CYS* 1.3 112.1 + - - +
1671B SER* 3.6 1.4 + - - -
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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