Contacts of the helix formed by residues 440 - 446 (chain N) 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 ALA 440 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1851L THR* 4.6 9.4 - - + +
1853L GLU* 4.5 8.7 - - + -
1854L HIS* 3.9 29.8 - - + +
439N HIS* 1.3 71.4 + - - +
441N ILE* 1.3 60.8 + - - +
443N ARG* 3.3 2.9 + - - +
444N ARG* 2.9 34.2 + - - +
69R GLY 2.7 22.2 + - - +
71R LEU* 3.4 18.4 - - + +
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Residues in contact with ILE 441 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1677L LYS* 3.9 4.3 - - + +
1678L SER* 3.2 36.6 - - - +
1854L HIS* 4.0 11.0 - - - +
432N TRP* 3.5 42.0 - - + +
439N HIS* 3.1 18.0 + - + +
440N ALA* 1.3 76.8 - - - +
442N GLU* 1.3 57.3 + - - +
444N ARG* 3.1 11.3 + - - +
445N ALA* 2.9 30.2 + - + +
503N PHE* 4.2 2.7 - - + -
507N TRP* 3.5 32.3 - - + +
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Residues in contact with GLU 442 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432N TRP* 3.3 31.7 - - + -
433N PHE* 3.6 10.9 - - - -
437N SER 4.6 1.1 - - - +
438N VAL* 3.4 8.7 - - + -
439N HIS 3.1 23.8 + - - +
441N ILE* 1.3 75.7 - - - +
443N ARG* 1.3 59.2 + - - +
445N ALA 4.1 0.7 - - - -
446N LEU* 3.4 20.0 + - - +
450N PHE* 3.4 14.5 - - - -
462N TYR* 2.9 43.6 + - + +
466N ARG* 3.2 21.0 + - - -
503N PHE* 3.7 17.5 - - + -
509N LEU* 5.3 0.2 - - - +
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Residues in contact with ARG 443 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1736L VAL* 3.2 44.9 + - - +
1737L GLY* 3.4 19.6 + - - -
1834L VAL* 5.4 1.0 - - - +
1837L PHE* 3.5 28.4 - - - -
1850L ASP* 3.9 6.5 - - - +
1851L THR* 3.5 31.2 - - - +
177M HIS* 4.3 3.6 - - - -
439N HIS 3.2 8.5 + - - +
440N ALA* 3.6 9.4 - - - +
441N ILE 3.1 0.4 - - - -
442N GLU* 1.3 77.6 - - - +
444N ARG* 1.3 64.4 + - - +
445N ALA 3.3 0.2 - - - -
447N PRO* 3.5 22.2 - - - +
450N PHE* 3.6 29.1 - - + +
71R LEU* 3.6 31.9 - - + +
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Residues in contact with ARG 444 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1677L LYS* 4.9 10.3 + - - +
1715L LEU* 4.1 23.2 - - - +
1718L GLU* 3.3 18.9 + - - +
1850L ASP* 2.5 55.1 + - - +
1851L THR* 3.0 36.9 + - + +
1852L THR* 4.2 1.8 - - - +
1854L HIS* 3.2 39.2 + - - -
173M PRO* 5.9 3.2 - - - +
176M ILE* 5.0 3.5 - - - +
177M HIS* 4.1 6.2 + - - -
440N ALA 2.9 19.6 + - - +
441N ILE* 3.8 7.4 - - - +
443N ARG* 1.3 79.8 - - - +
445N ALA* 1.3 61.9 + - - +
447N PRO* 4.1 5.9 - - - +
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Residues in contact with ALA 445 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M ILE* 3.7 18.5 - - - +
441N ILE* 2.9 10.6 + - + +
442N GLU 4.7 0.2 - - - +
444N ARG* 1.3 79.5 - - - +
446N LEU* 1.3 66.9 + - + +
447N PRO* 3.3 8.1 - - - +
499N ARG* 5.9 0.7 - - - -
503N PHE* 3.4 40.4 - - + -
506N GLN* 5.9 1.1 - - - +
507N TRP* 5.3 2.0 - - - +
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Residues in contact with LEU 446 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442N GLU 3.4 9.2 + - - +
443N ARG 3.8 2.5 - - - -
445N ALA* 1.3 89.9 - - + +
447N PRO* 1.3 62.3 - - - +
448N GLU* 3.1 10.4 + - - +
449N PHE* 3.7 16.6 + - + -
450N PHE* 3.1 22.3 - - - -
462N TYR* 3.4 31.2 - - + -
499N ARG* 3.8 38.8 - - + +
500N VAL* 3.8 22.9 - - + -
503N PHE* 4.0 18.4 - - + -
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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