Contacts of the helix formed by residues 1690 - 1700 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38G SER* 5.9 3.4 - - - +
41G ASP* 4.4 21.3 - - + -
42G ARG 5.8 0.2 - - - +
1686H CYS* 4.0 7.0 - - - -
1687H SER 5.1 1.5 + - - +
1688H HIS 3.5 6.3 + - - +
1689H VAL* 1.3 81.8 - - - +
1691H GLN* 1.3 67.0 + - + +
1692H ALA* 3.2 6.3 - - + +
1693H GLN* 3.3 20.7 + - + +
1694H LEU* 3.6 8.3 + - - +
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Residues in contact with GLN1691 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G ASP 4.5 1.3 + - - +
42G ARG* 2.6 50.0 + - + +
44G LYS* 5.6 1.2 - - - +
1686H CYS* 4.9 9.4 - - - -
1690H ASP* 1.3 74.5 - - - +
1692H ALA* 1.3 64.3 + - - +
1694H LEU* 3.6 6.9 + - - +
1695H LEU* 3.4 27.2 + - - +
1719H HIS* 4.5 10.6 - - + +
1781H PRO* 4.9 10.8 - - - +
1802H SER 4.0 10.7 - - - +
1803H ILE* 3.3 32.8 - - + +
1804H PRO* 4.3 13.8 - - - +
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Residues in contact with ALA1692 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G ASP* 3.4 32.8 - - + +
637H LEU* 4.8 8.4 - - + +
1690H ASP* 3.2 2.5 - - + +
1691H GLN* 1.3 80.4 - - + +
1693H GLN* 1.3 60.0 + - - +
1695H LEU* 3.3 7.9 + - - +
1696H HIS* 2.9 29.6 + - - +
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Residues in contact with GLN1693 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635H THR* 5.1 9.9 - - - +
636H ASN* 6.1 1.8 - - - -
637H LEU* 3.9 25.4 - - + +
1689H VAL* 4.3 13.7 - - + -
1690H ASP* 3.3 19.7 + - + +
1692H ALA* 1.3 78.7 - - - +
1694H LEU* 1.3 56.7 + - - +
1696H HIS* 3.3 3.1 + - - +
1697H ALA* 2.9 31.0 + - - +
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Residues in contact with LEU1694 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1689H VAL* 4.9 8.1 - - + +
1690H ASP 3.6 7.8 + - - +
1691H GLN* 3.8 11.7 - - - +
1692H ALA 3.2 0.2 - - - -
1693H GLN* 1.3 79.2 - - - +
1695H LEU* 1.3 58.9 + - + +
1697H ALA* 3.3 5.3 + - - +
1698H LEU* 2.9 38.1 + - + +
1711H TYR* 5.6 7.2 - - + +
1715H LEU* 4.0 31.4 - - + -
1719H HIS* 6.0 0.4 - - - +
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Residues in contact with LEU1695 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1691H GLN 3.4 16.3 + - - +
1692H ALA* 3.3 10.6 + - - +
1694H LEU* 1.3 83.7 - - + +
1696H HIS* 1.3 57.8 + - - +
1698H LEU* 3.3 9.1 + - + +
1699H GLU* 2.9 31.4 + - - +
1715H LEU* 5.3 2.5 - - + -
1803H ILE* 5.2 4.7 - - + -
1804H PRO* 6.3 1.1 - - + -
1807H ALA* 4.9 17.0 - - + +
1808H LEU* 3.8 39.0 - - + -
1811H LYS* 5.2 10.5 - - + -
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Residues in contact with HIS1696 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637H LEU* 4.0 25.3 - - + +
1635H THR* 3.5 22.2 + - - -
1636H MET* 3.8 3.7 - - - -
1637H MET* 3.5 39.7 - - + +
1651H LEU* 5.6 8.1 - - + -
1692H ALA 2.9 17.4 + - - +
1693H GLN* 3.7 7.1 + - - +
1695H LEU* 1.3 77.8 - - - +
1697H ALA* 1.3 64.2 + - - +
1699H GLU* 3.5 6.6 + - + +
1700H ASP* 3.3 23.4 + - + +
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Residues in contact with ALA1697 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1693H GLN 2.9 16.8 + - - +
1694H LEU* 3.8 5.2 - - - +
1696H HIS* 1.3 78.2 + - - +
1698H LEU* 1.3 65.8 + - - +
1700H ASP* 3.3 19.5 + - - +
1703H LEU* 3.5 16.7 - - + +
1708H ARG* 4.1 3.5 + - - +
1711H TYR* 3.6 41.3 - - + -
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Residues in contact with LEU1698 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1694H LEU* 2.9 29.7 + - + +
1695H LEU* 3.3 9.8 + - + +
1697H ALA* 1.3 79.3 - - - +
1699H GLU* 1.3 59.1 + - - +
1700H ASP 3.7 1.0 - - - +
1708H ARG* 3.3 24.2 + - + +
1711H TYR* 4.9 13.0 - - + +
1712H TYR* 3.5 51.1 + - + +
1715H LEU* 4.0 25.6 - - + -
1808H LEU* 4.9 11.2 - - + -
1811H LYS* 5.6 12.1 - - + -
1812H ALA* 6.5 0.4 - - - -
1815H MET* 5.5 3.6 - - - +
1845H LEU* 6.2 0.4 - - + -
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Residues in contact with GLU1699 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1695H LEU 2.9 17.2 + - - +
1696H HIS* 3.9 7.6 - - + +
1697H ALA 3.3 0.2 - - - -
1698H LEU* 1.3 74.1 - - - +
1700H ASP* 1.3 63.4 + - - +
1701H ALA* 3.7 2.6 + - - +
1814H ARG* 3.9 30.9 + - - +
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Residues in contact with ASP1700 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1651H LEU* 5.0 15.7 - - + -
1696H HIS* 3.3 15.8 + - + +
1697H ALA* 3.5 15.7 - - - +
1698H LEU 3.2 2.3 - - - +
1699H GLU* 1.3 81.0 - - - +
1701H ALA* 1.3 59.6 + - - +
1702H HIS 4.6 0.7 - - - +
1703H LEU* 4.3 22.4 + - + +
1708H ARG* 3.6 20.8 + - - -
1831H 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