Contacts of the helix formed by residues 1649 - 1658 (chain A) in PDB entry 4C6C
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1644A PHE 4.4 1.8 - - - +
1645A LEU* 3.3 29.3 - - + +
1646A SER* 2.8 37.0 + - - +
1648A ASP* 1.3 80.1 - - - +
1650A LEU* 1.3 58.3 + - - +
1651A GLU 3.3 3.1 - - - -
1652A ARG* 3.2 28.2 + - - +
1653A LEU* 3.0 35.3 + - + +
1777A GLN* 4.9 2.4 + - - -
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Residues in contact with LEU1650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1646A SER 4.4 2.2 - - - +
1647A HIS* 3.0 41.4 + - + +
1649A ASP* 1.3 75.5 - - - +
1651A GLU* 1.3 61.4 + - - +
1653A LEU* 4.4 2.5 - - + +
1654A GLY* 2.8 33.7 + - - +
1655A PRO* 6.0 1.3 - - + -
1658A GLY* 4.2 26.5 - - - +
1664A LEU* 4.1 22.7 - - + -
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Residues in contact with GLU1651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1647A HIS 4.6 1.0 + - - -
1648A ASP 4.5 7.9 + - - +
1649A ASP 3.3 0.6 - - - -
1650A LEU* 1.3 79.1 - - - +
1652A ARG* 1.3 63.3 + - - +
1654A GLY* 3.8 5.9 + - - -
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Residues in contact with ARG1652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1645A LEU* 3.5 22.6 - - - +
1648A ASP 5.2 0.6 + - - +
1649A ASP* 3.2 26.3 + - - +
1651A GLU* 1.3 83.3 - - - +
1653A LEU* 1.3 77.0 + - - +
1654A GLY 3.5 0.2 + - - -
1657A LYS* 5.5 2.4 + - - -
1772A THR 5.2 0.2 + - - -
1773A PRO 3.0 29.9 + - - -
1774A PHE* 4.9 0.2 - - - +
1775A GLU* 3.3 28.0 + - - +
1777A GLN* 4.6 7.0 - - - +
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Residues in contact with LEU1653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1645A LEU* 4.7 5.2 - - + -
1649A ASP* 3.0 26.4 + - + +
1650A LEU* 4.2 2.9 - - + +
1652A ARG* 1.3 91.9 - - - +
1654A GLY* 1.3 65.6 + - - +
1657A LYS* 3.3 44.3 + - + +
1658A GLY* 4.1 16.6 - - - +
1664A LEU* 4.0 26.5 - - + -
1704A PHE* 4.7 1.8 - - + -
1771A TRP* 4.8 1.1 - - + -
1772A THR 5.2 0.4 - - - +
1773A PRO* 3.6 45.5 - - + +
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Residues in contact with GLY1654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1650A LEU* 2.8 21.2 + - - +
1651A GLU 3.8 4.4 + - - -
1652A ARG 3.3 3.2 + - - -
1653A LEU* 1.3 77.5 - - - +
1655A PRO* 1.3 71.6 - - - +
1656A GLY 3.3 2.9 - - - -
1658A GLY* 3.0 26.7 + - - -
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Residues in contact with PRO1655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1650A LEU* 6.0 2.0 - - + -
1654A GLY* 1.3 83.1 - - - +
1656A GLY* 1.3 61.0 + - - +
1658A GLY* 4.1 1.7 - - - -
1659A GLU* 3.2 29.6 + - - +
1700A PRO* 4.8 1.6 - - - +
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Residues in contact with GLY1656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1654A GLY 3.3 0.6 - - - -
1655A PRO* 1.3 80.5 - - - +
1657A LYS* 1.3 65.6 + - - +
1658A GLY 3.1 1.1 - - - -
1659A GLU* 3.1 16.5 + - - +
1695A LYS* 3.1 34.5 - - - +
1696A CYS* 5.1 2.9 - - - -
1700A PRO* 3.8 15.2 - - - +
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Residues in contact with LYS1657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1652A ARG 5.5 3.2 + - - -
1653A LEU* 3.3 35.7 + - + +
1654A GLY 4.0 0.4 + - - -
1656A GLY* 1.3 75.5 - - - +
1658A GLY* 1.3 58.2 + - - +
1659A GLU 3.1 1.3 + - - -
1692A LEU* 3.9 24.9 - - + -
1695A LYS* 3.6 18.7 + - + +
1696A CYS* 4.6 10.0 - - - +
1704A PHE* 3.1 22.9 - - - -
1771A TRP* 3.4 43.2 - - + -
1772A THR 5.4 3.1 + - - -
1775A GLU* 4.5 13.9 + - - -
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Residues in contact with GLY1658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1650A LEU* 4.2 19.6 - - - +
1653A LEU* 4.1 17.4 - - - +
1654A GLY 3.0 21.3 + - - -
1655A PRO* 4.4 2.2 - - - -
1656A GLY 3.1 0.6 - - - -
1657A LYS* 1.3 76.0 - - - +
1659A GLU* 1.3 62.3 + - - +
1660A VAL* 3.2 14.0 + - - +
1663A GLU* 6.0 0.3 - - - +
1664A LEU* 4.7 3.1 + - - +
1704A PHE* 4.1 4.1 - - - -
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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