Contacts of the helix formed by residues 1690 - 1700 (chain F) in PDB entry 6X34
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 ASP1690 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E SER* 5.9 3.6 - - - +
41E ASP* 4.4 20.9 - - + -
42E ARG* 5.8 0.7 - - - +
1686F CYS* 4.0 6.7 - - - -
1687F SER 5.6 0.7 - - - +
1688F HIS 3.5 6.1 + - - +
1689F VAL* 1.3 80.9 - - - +
1691F GLN* 1.3 66.3 + - + +
1692F ALA* 3.2 6.3 - - + +
1693F GLN* 3.3 21.2 + - + +
1694F LEU* 3.6 8.7 + - - +
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Residues in contact with GLN1691 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ASP 4.5 1.1 + - - +
42E ARG* 2.6 50.2 + - + +
44E LYS* 5.6 1.2 - - - +
1686F CYS* 4.9 9.2 - - - -
1689F VAL 3.9 0.4 + - - -
1690F ASP* 1.3 73.5 - - - +
1692F ALA* 1.3 62.8 + - - +
1694F LEU* 3.6 7.8 + - - +
1695F LEU* 3.4 27.8 + - + +
1719F HIS* 4.5 11.2 - - + +
1781F PRO* 4.9 10.7 - - - +
1802F SER 4.0 10.2 - - - +
1803F ILE* 3.3 33.0 - - + +
1804F PRO* 4.3 14.0 - - - +
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Residues in contact with ALA1692 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ASP* 3.4 33.7 - - + +
637F LEU* 4.8 9.3 - - + +
1690F ASP* 3.2 2.3 - - + +
1691F GLN* 1.3 81.0 - - - +
1693F GLN* 1.3 60.0 + - - +
1695F LEU* 3.3 8.9 + - - +
1696F HIS* 2.9 28.6 + - - +
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Residues in contact with GLN1693 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635F THR* 5.1 9.9 - - - +
636F ASN* 6.1 2.0 - - - -
637F LEU* 3.9 26.3 - - + +
1689F VAL* 4.3 14.6 - - + -
1690F ASP* 3.3 19.5 + - + +
1692F ALA* 1.3 79.3 - - - +
1694F LEU* 1.3 56.1 + - - +
1696F HIS* 3.3 3.0 + - - +
1697F ALA* 2.9 30.3 + - - +
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Residues in contact with LEU1694 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1689F VAL* 4.9 7.0 - - + +
1690F ASP 3.6 8.7 + - - +
1691F GLN* 3.8 11.0 - - - +
1692F ALA 3.2 0.4 - - - -
1693F GLN* 1.3 78.5 - - - +
1695F LEU* 1.3 56.9 + - + +
1697F ALA* 3.3 5.1 + - - +
1698F LEU* 2.9 39.4 + - + +
1711F TYR* 5.6 7.2 - - + +
1715F LEU* 4.0 31.2 - - + -
1719F HIS* 6.0 0.4 - - - +
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Residues in contact with LEU1695 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1691F GLN 3.4 15.7 + - - +
1692F ALA* 3.3 11.3 + - - +
1694F LEU* 1.3 83.3 - - + +
1696F HIS* 1.3 57.9 + - - +
1698F LEU* 3.3 9.8 + - + +
1699F GLU* 2.9 31.4 + - - +
1715F LEU* 5.3 3.1 - - + -
1803F ILE* 5.2 5.2 - - + -
1804F PRO* 6.3 1.6 - - + -
1807F ALA* 4.9 17.0 - - + +
1808F LEU* 3.8 39.0 - - + -
1811F LYS* 5.2 11.2 - - + -
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Residues in contact with HIS1696 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637F LEU* 4.0 27.2 - - + +
1635F THR* 3.5 21.9 + - - -
1636F MET* 3.8 4.2 - - + -
1637F MET* 3.5 38.7 - - + +
1651F LEU* 5.6 8.5 - - + -
1692F ALA 2.9 17.0 + - - +
1693F GLN* 3.7 6.6 + - - +
1695F LEU* 1.3 77.5 - - - +
1697F ALA* 1.3 63.2 + - - +
1699F GLU* 3.5 7.2 + - + +
1700F ASP* 3.3 23.0 + - + +
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Residues in contact with ALA1697 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1693F GLN 2.9 17.8 + - - +
1694F LEU* 3.8 4.3 - - - +
1696F HIS* 1.3 78.9 + - - +
1698F LEU* 1.3 67.4 + - - +
1700F ASP* 3.3 20.2 + - - +
1703F LEU* 3.5 16.9 - - + +
1708F ARG* 4.1 3.1 + - - +
1711F TYR* 3.6 41.7 - - + -
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Residues in contact with LEU1698 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1694F LEU* 2.9 28.7 + - + +
1695F LEU* 3.7 9.6 - - + +
1697F ALA* 1.3 79.9 - - - +
1699F GLU* 1.3 60.4 + - - +
1700F ASP 3.7 0.7 - - - +
1708F ARG* 3.3 26.0 + - + +
1711F TYR* 4.9 14.4 - - + +
1712F TYR* 3.5 49.8 + - + +
1715F LEU* 4.0 26.5 - - + -
1808F LEU* 4.9 10.3 - - + -
1811F LYS* 5.5 12.3 - - + -
1812F ALA* 6.5 0.4 - - - -
1815F MET* 5.5 4.0 - - - +
1845F LEU* 6.2 0.2 - - + -
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Residues in contact with GLU1699 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1695F LEU 2.9 17.3 + - - +
1696F HIS* 3.9 7.4 - - + +
1697F ALA 3.3 0.2 - - - -
1698F LEU* 1.3 75.4 - - - +
1700F ASP* 1.3 63.1 + - - +
1701F ALA* 3.7 2.9 + - - +
1814F ARG* 3.9 30.8 + - - +
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Residues in contact with ASP1700 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1651F LEU* 5.0 15.0 - - + -
1696F HIS* 3.3 16.8 + - + +
1697F ALA* 3.5 15.0 - - - +
1698F LEU 3.2 1.9 - - - +
1699F GLU* 1.3 80.8 - - - +
1701F ALA* 1.3 60.1 + - - +
1702F HIS 4.6 0.7 - - - +
1703F LEU* 4.3 21.5 + - + +
1708F ARG* 3.6 21.0 + - - -
1831F VAL* 5.0 1.6 - - - +
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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