Contacts of the helix formed by residues 1688 - 1700 (chain A) in PDB entry 3RYT
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 LEU1688 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1301A LEU* 4.4 4.7 - - + -
1462A LEU* 5.4 1.1 - - + -
1465A ALA* 4.0 35.9 - - + +
1466A ILE* 3.4 27.4 - - + -
1469A GLN* 4.7 7.4 - - + -
1470A MET* 5.5 2.0 - - + -
1486A LEU* 4.6 12.3 - - + -
1684A THR* 3.1 36.6 + - + +
1685A LYS* 4.2 1.6 - - - +
1687A THR* 1.3 85.9 - - + +
1689A GLN* 1.3 64.8 + - - +
1690A LYS 2.9 4.4 + - - -
1691A PHE* 3.1 23.9 + - + -
1692A VAL* 3.3 22.9 + - + +
1800A TYR* 6.0 1.8 - - - +
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Residues in contact with GLN1689 (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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1685A LYS* 3.3 40.4 + - - +
1686A GLY* 3.1 22.0 + - - +
1688A LEU* 1.3 77.4 - - - +
1690A LYS* 1.3 58.7 + - - +
1692A VAL* 3.9 3.6 + - - +
1693A ASP* 2.9 59.2 + - - +
1800A TYR* 4.4 5.8 - - - -
1803A ASP* 4.1 13.3 + - - +
1807A TYR* 3.9 11.6 + - - -
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Residues in contact with LYS1690 (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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1298A PHE* 3.5 45.1 - - + -
1302A GLN* 4.7 7.9 - - - +
1686A GLY 4.5 0.8 + - - +
1687A THR 4.3 1.0 + - - +
1688A LEU* 3.0 0.6 - - - +
1689A GLN* 1.3 77.1 - - - +
1691A PHE* 1.3 68.5 + - - +
1692A VAL 2.9 3.1 + - - -
1693A ASP* 3.3 7.5 + - + +
1694A ASP* 3.2 26.9 + - + +
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Residues in contact with PHE1691 (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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1298A PHE* 3.6 35.0 - + - -
1301A LEU* 4.4 25.4 - - + -
1302A GLN* 4.8 6.1 - - + -
1305A ILE* 4.5 10.8 - - + -
1458A PRO 4.4 7.6 - - - +
1461A MET* 3.7 51.1 - - + -
1462A LEU* 4.0 21.6 - - + +
1465A ALA* 3.6 20.9 - - + -
1687A THR 4.3 2.7 - - - -
1688A LEU* 3.1 20.5 + - + +
1690A LYS* 1.3 80.2 - - + +
1692A VAL* 1.3 62.2 + - - +
1694A ASP* 3.6 15.9 - - - +
1695A LEU* 3.6 8.1 + - - +
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Residues in contact with VAL1692 (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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1462A LEU* 4.2 18.4 - - + -
1688A LEU* 3.3 20.4 + - + +
1689A GLN* 4.2 3.6 - - - +
1690A LYS 3.0 1.0 - - - -
1691A PHE* 1.3 74.3 - - - +
1693A ASP* 1.3 59.5 + - - +
1694A ASP 2.9 4.3 - - - -
1695A LEU* 2.7 28.3 + - - +
1696A PHE* 2.9 46.2 + - + -
1774A VAL* 4.3 22.0 - - + -
1777A THR* 6.5 0.2 - - + -
1800A TYR* 5.2 13.5 - - + +
1807A TYR* 4.3 13.5 - - + +
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Residues in contact with ASP1693 (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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1689A GLN* 2.9 38.5 + - - +
1690A LYS* 3.3 9.1 + - + +
1692A VAL* 1.3 74.3 - - - +
1694A ASP* 1.3 61.3 + - - +
1696A PHE* 4.6 1.1 - - - -
1697A GLU* 3.0 29.2 + - - +
1807A TYR* 2.8 28.5 + - - -
1810A TRP* 4.0 22.8 - - + -
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Residues in contact with ASP1694 (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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1458A PRO* 4.2 11.0 - - + -
1690A LYS* 3.2 19.9 + - + +
1691A PHE* 3.6 14.4 - - - +
1692A VAL 2.8 1.4 + - - -
1693A ASP* 1.3 78.3 - - - +
1695A LEU* 1.3 56.7 + - - +
1697A GLU* 3.6 7.1 - - - +
1698A THR* 3.0 35.6 + - + +
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Residues in contact with LEU1695 (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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1455A ALA* 4.5 8.5 - - + +
1458A PRO* 3.7 30.0 - - + +
1459A LEU* 4.1 29.6 - - + +
1462A LEU* 3.9 23.8 - - + -
1691A PHE 3.6 6.9 + - - +
1692A VAL* 2.7 14.7 + - - +
1694A ASP* 1.3 70.6 - - - +
1696A PHE* 1.3 61.8 + - + +
1697A GLU 3.0 4.6 + - - -
1698A THR* 3.1 4.0 + - - +
1699A ILE* 2.8 58.0 + - + +
1748A TRP* 5.9 2.0 - - + -
1752A ILE* 4.6 16.4 - - + -
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Residues in contact with PHE1696 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1692A VAL* 2.9 35.0 + - + +
1695A LEU* 1.3 84.1 - - + +
1697A GLU* 1.3 59.0 + - - +
1699A ILE* 4.0 7.1 - - + +
1700A PHE* 3.2 37.8 + + + +
1752A ILE* 4.5 8.7 - - + -
1774A VAL* 3.9 23.6 - - + -
1777A THR* 4.6 7.2 - - + -
1778A PHE* 3.6 55.4 - + + -
1781A SER* 4.6 2.0 - - - -
1807A TYR* 3.8 33.2 - + + -
1810A TRP* 3.7 21.5 - - + -
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Residues in contact with GLU1697 (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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1693A ASP 3.0 20.4 + - - +
1694A ASP* 3.6 9.1 - - - +
1695A LEU 3.0 0.4 - - - -
1696A PHE* 1.3 75.5 - - - +
1698A THR* 1.3 63.5 + - + +
1699A ILE 3.1 4.0 - - - -
1700A PHE* 3.3 6.0 - - - +
1701A SER* 3.1 30.0 + - - -
1704A HIS* 5.1 8.2 + - + -
1810A TRP* 3.9 14.7 - - + -
1813A ARG* 4.7 13.4 + - - +
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Residues in contact with THR1698 (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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1450A PHE* 3.8 20.1 - - - -
1454A CYS* 5.7 0.7 - - - -
1455A ALA* 4.4 10.0 - - - +
1458A PRO* 3.3 29.4 - - + +
1694A ASP* 3.0 15.9 - - + +
1695A LEU* 3.1 10.9 + - - +
1697A GLU* 1.3 80.1 - - + +
1699A ILE* 1.3 59.5 + - - +
1701A SER* 3.4 18.6 + - - -
1704A HIS* 3.2 39.7 - - + +
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Residues in contact with ILE1699 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1450A PHE* 5.3 3.2 - - - -
1455A ALA* 5.8 0.7 - - + -
1695A LEU* 2.8 52.0 + - + +
1696A PHE* 4.1 7.9 - - + +
1697A GLU 3.1 0.2 - - - -
1698A THR* 1.3 82.2 - - - +
1700A PHE* 1.3 74.7 + - + +
1701A SER 3.2 5.9 + - - +
1709A LEU* 5.9 0.2 - - - +
1713A ILE* 5.9 0.2 - - - +
1748A TRP* 3.9 58.0 + - + +
1752A ILE* 4.2 13.2 - - + -
1778A PHE* 4.1 22.0 - - + -
1814A TYR* 3.8 17.2 + - - -
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Residues in contact with PHE1700 (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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1696A PHE* 3.2 32.6 + + + +
1697A GLU 3.3 5.2 + - - -
1699A ILE* 1.3 90.7 - - + +
1701A SER* 1.3 54.2 + - - +
1744A PRO* 4.7 12.8 - - + -
1748A TRP* 5.9 0.2 - + - -
1778A PHE* 3.9 25.4 - + - -
1781A SER* 5.5 3.6 - - - -
1782A CYS* 4.2 9.6 - - - -
1807A TYR 4.1 14.1 - - - -
1810A TRP* 3.9 19.1 - + + +
1811A VAL* 3.8 26.0 - - + -
1813A ARG* 2.9 33.7 + - - +
1814A TYR* 3.4 44.5 - + + +
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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