Contacts of the helix formed by residues 1690 - 1700 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A SER* 5.9 2.9 - - - +
41A ASP* 4.4 21.1 - - + -
42A ARG 5.8 0.4 - - - +
1686B CYS* 4.0 6.7 - - - -
1687B SER 5.6 1.6 - - - +
1688B HIS 3.5 5.8 + - - +
1689B VAL* 1.3 80.5 - - - +
1691B GLN* 1.3 66.3 + - + +
1692B ALA* 3.2 6.5 - - + +
1693B GLN* 3.3 20.2 + - + +
1694B LEU* 3.6 9.2 + - - +
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Residues in contact with GLN1691 (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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41A ASP 4.5 0.9 + - - +
42A ARG* 2.6 50.6 + - + +
44A LYS* 5.6 1.2 - - - +
1686B CYS* 4.9 9.8 - - - -
1689B VAL 3.9 0.4 + - - -
1690B ASP* 1.3 73.2 - - + +
1692B ALA* 1.3 64.1 + - + +
1694B LEU* 3.6 7.6 + - - +
1695B LEU* 3.4 27.0 + - - +
1719B HIS* 4.5 10.7 - - + +
1781B PRO* 4.9 10.6 - - - +
1802B SER 4.0 10.2 - - - +
1803B ILE* 3.3 33.4 - - + +
1804B PRO* 4.3 13.9 - - - +
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Residues in contact with ALA1692 (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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41A ASP* 3.4 33.4 + - + +
637B LEU* 4.8 9.1 - - + +
1690B ASP* 3.2 2.3 - - + +
1691B GLN* 1.3 81.2 - - + +
1693B GLN* 1.3 59.6 + - - +
1695B LEU* 3.3 8.3 + - - +
1696B HIS* 2.9 28.6 + - - +
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Residues in contact with GLN1693 (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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635B THR* 5.1 9.9 - - - +
636B ASN* 6.1 2.0 - - - -
637B LEU* 3.9 26.3 - - + +
1689B VAL* 4.3 13.7 - - + -
1690B ASP* 3.3 19.5 + - + +
1692B ALA* 1.3 80.1 - - - +
1694B LEU* 1.3 55.4 + - - +
1696B HIS* 3.3 2.9 + - - +
1697B ALA* 2.9 30.5 + - - +
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Residues in contact with LEU1694 (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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1689B VAL* 4.9 7.7 - - + +
1690B ASP 3.6 8.5 + - - +
1691B GLN* 3.8 12.1 - - - +
1692B ALA 3.2 0.6 - - - -
1693B GLN* 1.3 79.0 - - - +
1695B LEU* 1.3 57.7 + - + +
1697B ALA* 3.3 4.7 + - - +
1698B LEU* 2.9 38.6 + - + +
1711B TYR* 5.6 7.4 - - + +
1715B LEU* 4.0 31.4 - - + -
1719B HIS* 6.0 0.2 - - - +
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Residues in contact with LEU1695 (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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1691B GLN 3.4 15.2 + - - +
1692B ALA* 3.3 10.6 + - - +
1694B LEU* 1.3 83.6 - - + +
1696B HIS* 1.3 56.9 + - - +
1698B LEU* 3.3 8.6 + - + +
1699B GLU* 2.9 30.7 + - - +
1715B LEU* 5.3 3.1 - - + -
1803B ILE* 5.2 4.9 - - + -
1804B PRO* 6.3 1.1 - - + -
1807B ALA* 4.9 17.0 - - + +
1808B LEU* 3.8 39.5 - - + -
1811B LYS* 5.2 10.5 - - + -
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Residues in contact with HIS1696 (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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637B LEU* 4.0 26.4 - - + +
1635B THR* 3.5 21.8 + - - -
1636B MET* 3.8 4.6 - - + -
1637B MET* 3.5 39.1 - - + +
1651B LEU* 5.6 8.1 - - + -
1692B ALA 2.9 17.2 + - - +
1693B GLN* 3.7 6.4 + - - +
1695B LEU* 1.3 77.8 - - - +
1697B ALA* 1.3 64.4 + - - +
1699B GLU* 3.5 7.3 + - + +
1700B ASP* 3.3 23.0 + - + +
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Residues in contact with ALA1697 (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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1693B GLN 2.9 16.9 + - - +
1694B LEU* 3.8 5.2 - - - +
1696B HIS* 1.3 77.9 + - - +
1698B LEU* 1.3 65.7 + - - +
1700B ASP* 3.3 19.9 + - - +
1703B LEU* 3.5 16.4 - - + +
1708B ARG* 4.1 3.1 + - - +
1711B TYR* 3.6 40.6 - - + -
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Residues in contact with LEU1698 (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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1694B LEU* 2.9 30.4 + - + +
1695B LEU* 3.3 9.4 + - + +
1697B ALA* 1.3 78.9 - - - +
1699B GLU* 1.3 59.8 + - - +
1700B ASP 3.7 0.7 - - - +
1708B ARG* 3.3 24.0 + - + +
1711B TYR* 4.9 13.7 - - + +
1712B TYR* 3.5 48.7 - - + +
1715B LEU* 4.0 27.1 - - + -
1808B LEU* 4.9 10.1 - - + -
1811B LYS* 5.6 12.3 - - + -
1812B ALA* 6.5 0.2 - - - -
1815B MET* 5.5 4.0 - - - +
1845B LEU* 6.2 0.2 - - + -
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Residues in contact with GLU1699 (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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1695B LEU 2.9 16.8 + - - +
1696B HIS* 3.9 7.6 - - + +
1697B ALA 3.3 0.2 - - - -
1698B LEU* 1.3 74.3 - - - +
1700B ASP* 1.3 62.7 - - - +
1701B ALA* 3.7 2.6 + - - +
1814B ARG* 3.9 30.4 + - - +
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Residues in contact with ASP1700 (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 LEU* 5.0 15.7 - - + -
1696B HIS* 3.3 15.4 + - + +
1697B ALA* 3.5 15.3 - - - +
1698B LEU 3.2 2.1 - - - +
1699B GLU* 1.3 80.0 - - - +
1701B ALA* 1.3 60.7 + - - +
1702B HIS 4.6 0.9 - - - +
1703B LEU* 4.3 22.0 + - + +
1708B ARG* 3.6 21.3 + - - -
1831B VAL* 5.0 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