Contacts of the helix formed by residues 1840 - 1846 (chain L) in PDB entry 6LTJ
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 GLY1840 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1839L SER* 1.3 80.7 - - - +
1841L LEU* 1.3 66.6 + - - -
1842L LEU* 3.3 3.4 - - - -
1843L HIS* 3.4 8.1 + - - +
1844L TRP* 3.2 23.9 - - - -
174M ALA 4.0 6.7 - - - +
177M HIS* 4.0 1.8 - - - +
178M GLU* 3.2 25.8 - - - -
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Residues in contact with LEU1841 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1840L GLY* 1.3 73.2 - - - -
1842L LEU* 1.3 56.3 + - - +
1844L TRP* 3.0 5.4 + - - +
1845L ARG* 2.9 51.0 + - - +
174M ALA* 3.7 35.7 - - + +
175M VAL* 3.9 17.7 - - + +
178M GLU* 2.8 33.1 + - + +
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Residues in contact with LEU1842 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1745L LEU* 3.5 36.3 - - + -
1840L GLY* 3.3 1.2 - - - -
1841L LEU* 1.3 78.6 - - - +
1843L HIS* 1.3 60.5 + - - +
1845L ARG* 3.6 37.4 + - + +
1846L ILE* 3.7 21.9 + - + +
178M GLU* 4.7 0.4 + - - -
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Residues in contact with HIS1843 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1734L TYR* 3.4 28.0 + - - -
1736L VAL* 3.3 26.4 - - + +
1741L GLN* 3.1 44.6 + - + +
1744L LEU* 5.0 7.4 - - + +
1745L LEU* 4.7 14.7 - - + +
1838L ASP 5.0 0.4 - - - +
1839L SER* 4.5 4.7 - - - -
1840L GLY 3.4 21.2 + - - +
1841L LEU 3.1 0.6 - - - -
1842L LEU* 1.3 78.7 - - - +
1844L TRP* 1.3 67.6 + - + +
1846L ILE* 3.2 19.4 + - + +
1847L GLY 3.7 10.0 + - - +
1848L GLY* 3.6 6.2 - - - -
1849L GLY 3.5 12.5 + - - -
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Residues in contact with TRP1844 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1714L GLU* 3.6 28.8 + - - -
1736L VAL* 4.2 7.2 - - + -
1839L SER* 4.2 2.5 - - - -
1840L GLY 3.2 24.9 - - - -
1841L LEU 3.0 5.8 + - - +
1843L HIS* 1.3 91.1 - - - +
1845L ARG* 1.3 56.5 + - - +
1846L ILE 2.7 18.1 - - - +
1848L GLY* 3.6 13.3 + - - -
1849L GLY* 3.5 6.5 - - - -
1850L ASP* 3.4 32.5 - - + -
2004L HIS* 6.0 1.1 - + - -
2005L PRO* 3.6 16.8 - - - +
2006L GLY 5.3 0.5 + - - -
172M ASP* 5.3 2.5 - - - -
173M PRO* 3.6 24.4 - - + +
174M ALA* 3.6 29.6 - - + -
177M HIS* 3.4 38.8 - + + -
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Residues in contact with ARG1845 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1841L LEU* 2.9 34.7 + - - +
1842L LEU* 4.0 40.4 - - + +
1843L HIS 3.4 0.6 - - - -
1844L TRP* 1.3 75.4 - - - +
1846L ILE* 1.3 63.9 + - + +
2005L PRO* 3.4 19.5 - - + +
2075L PRO 6.0 1.8 - - - -
2076L TYR* 4.8 1.9 - - - -
2077L PRO* 4.0 11.8 - - + +
2080L ILE* 3.9 4.5 - - - +
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Residues in contact with ILE1846 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1734L TYR* 4.0 20.6 - - + -
1744L LEU* 5.6 9.0 - - + +
1745L LEU* 4.8 18.6 - - + -
1842L LEU* 3.7 28.6 + - + +
1843L HIS* 3.2 7.4 - - + +
1844L TRP 2.7 23.7 - - - +
1845L ARG* 1.3 76.7 - - + +
1847L GLY* 1.3 78.4 + - - +
1848L GLY 3.3 0.3 + - - -
2005L PRO* 3.9 1.5 - - - +
2077L PRO* 4.4 11.0 - - + -
2079L SER* 3.7 22.9 - - - +
2080L ILE* 3.8 9.4 - - + -
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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