Contacts of the helix formed by residues 1832 - 1852 (chain A) in PDB entry 6AH0
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 ARG1832 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1830A GLN 3.1 7.6 + - - +
1831A LYS* 1.3 71.7 - - - +
1833A LEU* 1.3 63.3 + - - +
1834A GLY 3.5 2.4 + - - -
1835A GLN* 3.6 3.8 + - - +
1836A LEU* 3.2 18.2 + - - -
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Residues in contact with LEU1833 (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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1830A GLN* 4.3 3.5 + - - +
1831A LYS 3.7 4.8 + - - -
1832A ARG* 1.3 67.9 - - - +
1834A GLY* 1.3 54.8 + - - +
1836A LEU 4.8 0.2 - - - -
1837A ALA* 1.9 50.4 + - - +
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Residues in contact with GLY1834 (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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1832A ARG 3.5 0.8 - - - -
1833A LEU* 1.3 74.2 - - - +
1835A GLN* 1.3 59.5 + - - +
1838A LYS* 3.0 25.5 + - - -
1839A TRP 4.5 0.2 + - - -
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Residues in contact with GLN1835 (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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1832A ARG* 3.6 5.8 + - - +
1833A LEU 3.3 0.4 - - - -
1834A GLY* 1.3 77.1 - - - +
1836A LEU* 1.3 58.3 + - - +
1839A TRP* 4.1 9.0 + - - -
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Residues in contact with LEU1836 (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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1830A GLN 5.7 1.6 - - - -
1832A ARG 3.2 13.3 + - - -
1833A LEU 3.6 0.2 - - - -
1835A GLN* 1.3 77.4 - - - +
1837A ALA* 1.3 57.7 + - - +
1838A LYS 3.3 1.6 - - - -
1839A TRP* 3.2 2.9 + - - -
1840A LYS* 2.9 26.2 + - - -
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Residues in contact with ALA1837 (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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1833A LEU* 1.9 35.5 + - - +
1834A GLY* 4.6 0.2 - - - -
1836A LEU* 1.3 67.7 - - - +
1838A LYS* 1.3 61.1 + - - +
1840A LYS* 3.2 2.1 + - - +
1841A THR* 2.9 20.8 + - - -
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Residues in contact with LYS1838 (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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1833A LEU 3.3 0.6 + - - -
1834A GLY* 3.0 21.1 + - - -
1837A ALA* 1.3 76.6 - - - +
1839A TRP* 1.3 62.5 + - - +
1841A THR* 3.2 2.5 + - - +
1842A ALA* 3.0 19.6 + - - -
1871A PRO* 5.7 6.8 - - - +
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Residues in contact with TRP1839 (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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1834A GLY 4.5 0.2 + - - -
1835A GLN 4.1 8.3 + - - -
1836A LEU 3.2 7.6 + - - -
1838A LYS* 1.3 77.0 - - - +
1840A LYS* 1.3 62.5 + - - +
1842A ALA* 3.2 2.5 + - - +
1843A GLU* 2.9 20.4 + - - -
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Residues in contact with LYS1840 (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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1836A LEU 2.9 13.9 + - - -
1837A ALA* 3.2 4.0 + - - +
1839A TRP* 1.3 74.9 - - - +
1841A THR* 1.3 63.6 + - - +
1843A GLU* 3.2 2.5 + - - +
1844A GLU* 2.9 20.8 + - - -
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Residues in contact with THR1841 (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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1837A ALA 2.9 14.4 + - - -
1838A LYS 3.7 2.0 - - - -
1840A LYS* 1.3 76.2 - - - +
1842A ALA* 1.3 64.7 + - - +
1844A GLU* 3.2 2.7 + - - +
1845A VAL* 3.0 19.8 + - - -
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Residues in contact with ALA1842 (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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1838A LYS 3.0 14.0 + - - -
1839A TRP* 3.7 2.9 - - - +
1841A THR* 1.3 77.2 - - - +
1843A GLU* 1.3 61.6 + - - +
1845A VAL* 3.2 2.8 + - - +
1846A ALA* 2.9 20.8 + - - -
1871A PRO 4.9 13.0 - - - -
1872A LEU* 4.9 10.9 - - - +
1875A HIS* 4.9 13.2 - - - +
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Residues in contact with GLU1843 (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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1839A TRP 2.9 14.2 + - - -
1840A LYS* 3.2 3.1 + - - +
1842A ALA* 1.3 76.4 - - - +
1844A GLU* 1.3 63.0 + - - +
1846A ALA* 3.2 1.6 + - - +
1847A ALA* 2.9 21.5 + - - -
1875A HIS* 6.1 0.7 - - - +
53F A 4.8 13.1 + - - +
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Residues in contact with GLU1844 (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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1840A LYS 2.9 13.8 + - - -
1841A THR* 3.2 3.1 + - - +
1843A GLU* 1.3 76.3 - - - +
1845A VAL* 1.3 61.5 + - - +
1847A ALA* 3.2 2.0 + - - +
1848A LEU* 2.9 21.5 + - - -
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Residues in contact with VAL1845 (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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1841A THR 3.0 13.4 + - - -
1842A ALA* 3.2 3.6 + - - +
1844A GLU* 1.3 76.7 - - - +
1846A ALA* 1.3 62.2 + - - +
1848A LEU* 3.2 10.2 + - - +
1849A ILE* 3.2 10.6 + - - -
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Residues in contact with ALA1846 (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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1842A ALA 2.9 14.5 + - - -
1843A GLU 3.7 2.2 - - - -
1845A VAL* 1.3 76.4 - - - +
1847A ALA* 1.3 62.9 + - - +
1849A ILE* 3.2 4.3 + - - +
1850A ARG* 3.2 17.2 + - - -
1875A HIS 4.7 13.2 - - - -
1876A LEU* 5.7 3.4 - - - +
53F A 4.7 12.4 - - - +
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Residues in contact with ALA1847 (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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1843A GLU 2.9 14.1 + - - -
1844A GLU* 3.7 3.1 - - - +
1846A ALA* 1.3 76.4 - - - +
1848A LEU* 1.3 62.8 + - - +
1850A ARG* 3.1 11.8 + - - +
1851A SER* 3.3 8.5 + - - -
53F A 4.4 21.9 - - - +
54F G 4.6 7.6 + - - -
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Residues in contact with LEU1848 (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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1844A GLU 2.9 14.5 + - - -
1845A VAL* 3.2 4.4 + - - +
1847A ALA* 1.3 77.4 - - - +
1849A ILE* 1.3 61.0 + - - +
1851A SER* 3.3 10.8 + - - +
1852A LEU* 3.4 9.4 + - - -
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Residues in contact with ILE1849 (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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1845A VAL 3.2 8.6 + - - -
1846A ALA* 3.2 6.8 + - - +
1847A ALA 3.2 1.0 - - - -
1848A LEU* 1.3 72.9 - - - +
1850A ARG* 1.3 67.3 + - - +
1851A SER 3.2 0.5 + - - -
1852A LEU* 3.2 16.8 + - - +
1857A GLN* 5.3 9.5 - - - +
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Residues in contact with ARG1850 (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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1846A ALA 3.2 9.8 + - - -
1847A ALA* 3.1 9.0 + - - +
1849A ILE* 1.3 77.7 - - - +
1851A SER* 1.3 60.6 + - - +
1852A LEU 3.5 5.9 - - - +
53F A 5.2 11.4 - - - -
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Residues in contact with SER1851 (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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1847A ALA 3.3 7.3 + - - -
1848A LEU 3.3 8.0 + - - -
1849A ILE 3.2 0.8 - - - -
1850A ARG* 1.3 79.0 - - - +
1852A LEU* 1.3 60.3 + - - +
1853A PRO 3.9 0.3 - - - -
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Residues in contact with LEU1852 (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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1848A LEU 3.4 7.7 + - - -
1849A ILE* 3.2 15.0 + - - +
1850A ARG 3.5 8.3 - - - +
1851A SER* 1.3 79.8 - - - +
1853A PRO* 1.3 67.9 - - - +
1856A GLU* 5.3 2.9 - - - +
1857A GLN* 4.7 4.4 - - - +
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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