Contacts of the helix formed by residues 1690 - 1700 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C SER* 5.9 3.1 - - - +
41C ASP* 4.4 21.8 - - + -
1686D CYS* 4.0 7.0 - - - -
1687D SER 5.6 0.9 - - - +
1688D HIS 3.5 5.4 + - - +
1689D VAL* 1.3 82.1 - - - +
1691D GLN* 1.3 65.9 + - + +
1692D ALA 3.2 6.5 - - - +
1693D GLN* 3.3 21.3 + - + +
1694D LEU* 3.6 8.5 + - - +
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Residues in contact with GLN1691 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ASP 4.5 0.7 - - - +
42C ARG* 2.6 49.7 + - + +
44C LYS* 5.6 1.4 - - - +
1686D CYS* 4.9 10.6 - - - -
1690D ASP* 1.3 74.6 - - + +
1692D ALA* 1.3 63.4 + - - +
1693D GLN 3.4 0.2 - - - -
1694D LEU* 3.6 7.5 + - - +
1695D LEU* 3.4 27.2 + - - +
1719D HIS* 4.5 9.5 - - + +
1781D PRO* 4.9 10.8 - - - +
1802D SER 4.0 10.2 - - - +
1803D ILE* 3.3 32.9 - - + +
1804D PRO* 4.3 13.8 - - - +
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Residues in contact with ALA1692 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ASP* 3.4 33.2 - - + +
637D LEU* 4.8 8.9 - - + +
1690D ASP* 3.2 2.3 - - + +
1691D GLN* 1.3 81.6 - - - +
1693D GLN* 1.3 59.0 + - - +
1695D LEU* 3.3 9.3 + - - +
1696D HIS* 2.9 28.9 + - - +
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Residues in contact with GLN1693 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635D THR* 5.1 9.6 - - - +
636D ASN* 6.1 1.6 - - - -
637D LEU* 3.9 26.7 - - + +
1689D VAL* 4.3 13.9 - - + -
1690D ASP* 3.3 19.8 + - + +
1692D ALA* 1.3 79.2 - - - +
1694D LEU* 1.3 56.4 + - - +
1696D HIS* 3.3 2.8 + - - +
1697D ALA* 2.9 31.4 + - - +
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Residues in contact with LEU1694 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1689D VAL* 4.9 6.9 - - + +
1690D ASP 3.6 7.7 + - - +
1691D GLN* 3.8 10.8 - - - +
1692D ALA 3.2 0.6 - - - -
1693D GLN* 1.3 79.0 - - - +
1695D LEU* 1.3 58.6 + - + +
1697D ALA* 3.3 5.0 + - - +
1698D LEU* 2.9 40.1 + - + +
1711D TYR* 5.6 7.4 - - + +
1715D LEU* 4.0 31.2 - - + -
1719D HIS* 6.0 0.2 - - - +
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Residues in contact with LEU1695 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1691D GLN 3.4 15.7 + - - +
1692D ALA* 3.3 11.0 + - - +
1694D LEU* 1.3 82.4 - - + +
1696D HIS* 1.3 56.9 + - - +
1698D LEU* 3.3 9.5 + - + +
1699D GLU* 2.9 31.0 + - - +
1715D LEU* 5.3 2.7 - - + -
1803D ILE* 5.2 5.2 - - + -
1804D PRO* 6.3 1.3 - - + -
1807D ALA* 4.9 17.5 - - + +
1808D LEU* 3.8 38.8 - - + -
1811D LYS* 5.2 10.8 - - + -
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Residues in contact with HIS1696 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637D LEU* 4.0 26.8 - - + +
1635D THR* 3.5 22.3 + - - -
1636D MET* 3.8 5.2 - - + -
1637D MET* 3.5 39.1 - - + +
1651D LEU* 5.6 8.5 - - + -
1692D ALA 2.9 17.2 + - - +
1693D GLN* 3.7 6.4 + - - +
1694D LEU 3.3 0.4 - - - -
1695D LEU* 1.3 78.1 - - - +
1697D ALA* 1.3 63.4 + - - +
1699D GLU* 3.5 6.8 + - + +
1700D ASP* 3.3 23.0 + - + +
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Residues in contact with ALA1697 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1693D GLN 2.9 17.4 + - - +
1694D LEU* 3.8 4.5 - - - +
1696D HIS* 1.3 78.2 + - - +
1698D LEU* 1.3 66.9 + - - +
1700D ASP* 3.3 19.9 + - - +
1703D LEU* 3.5 16.4 - - + +
1708D ARG* 4.1 3.2 + - - +
1711D TYR* 3.6 41.5 - - + -
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Residues in contact with LEU1698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1694D LEU* 2.9 30.2 + - + +
1695D LEU* 3.3 8.9 + - + +
1697D ALA* 1.3 78.6 - - - +
1699D GLU* 1.3 59.8 + - - +
1700D ASP 3.7 0.9 - - - +
1708D ARG* 3.3 26.0 + - + +
1711D TYR* 4.9 13.2 - - + +
1712D TYR* 3.5 50.6 + - + +
1715D LEU* 4.0 26.7 - - + -
1808D LEU* 4.9 10.8 - - + -
1811D LYS* 5.6 11.9 - - + -
1812D ALA* 6.5 0.2 - - - -
1815D MET* 5.5 3.6 - - - +
1845D LEU* 6.2 0.4 - - + -
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Residues in contact with GLU1699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1695D LEU 2.9 17.2 + - - +
1696D HIS* 3.5 7.6 + - + +
1697D ALA 3.3 0.2 - - - -
1698D LEU* 1.3 74.3 - - - +
1700D ASP* 1.3 63.6 + - - +
1701D ALA* 3.7 3.1 + - - +
1814D ARG* 3.9 30.8 + - - +
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Residues in contact with ASP1700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1651D LEU* 5.0 15.3 - - + -
1696D HIS* 3.3 16.1 + - + +
1697D ALA* 3.5 15.2 - - - +
1698D LEU 3.2 2.5 - - - +
1699D GLU* 1.3 79.8 - - - +
1701D ALA* 1.3 60.3 + - - +
1702D HIS 3.7 1.3 - - - +
1703D LEU* 4.3 22.2 + - + +
1708D ARG* 3.6 20.6 + - - -
1831D 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