Contacts of the helix formed by residues 409 - 416 (chain B) in PDB entry 1LV5
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 ASP 409 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371B PHE* 3.4 17.1 - - - -
407B VAL 3.7 0.6 - - - -
408B ASP* 1.3 92.3 - - - +
410B VAL* 1.3 64.3 + - - +
411B ALA* 3.8 5.4 - - - +
412B ALA* 2.9 33.6 + - - +
413B ALA 3.3 4.5 + - - -
424B PRO* 3.1 15.7 - - - +
425B ASP* 3.1 47.3 + - + +
426B GLU 4.6 1.0 + - - -
450B LYS* 6.0 0.2 - - + -
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Residues in contact with VAL 410 (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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371B PHE* 3.6 40.1 - - + -
394B LEU* 4.3 10.9 - - + +
409B ASP* 1.3 74.1 - - - +
411B ALA* 1.3 52.7 + - - +
413B ALA* 3.2 3.7 + - - +
414B ALA* 2.7 32.3 + - + +
422B VAL* 4.6 4.0 - - + -
425B ASP* 5.0 1.0 + - - -
450B LYS* 3.9 56.7 - - + +
453B ALA* 4.0 17.9 - - + -
454B ILE* 4.3 6.7 - - + -
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Residues in contact with ALA 411 (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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409B ASP* 3.2 2.8 - - - +
410B VAL* 1.3 78.4 - - - +
412B ALA* 1.3 62.5 + - - +
414B ALA* 3.5 8.8 - - - +
415B LYS* 3.0 32.2 + - + +
422B VAL* 3.9 14.7 - - + +
423B ARG 3.6 10.4 + - - +
424B PRO* 3.5 40.4 - - + -
450B LYS* 5.6 0.2 - - - +
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Residues in contact with ALA 412 (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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405B GLN* 5.3 2.8 - - - +
407B VAL* 3.8 28.6 - - + +
408B ASP* 4.0 8.3 - - - +
409B ASP* 2.9 24.9 + - - +
411B ALA* 1.3 77.3 - - - +
413B ALA* 1.3 61.5 + - - +
415B LYS* 3.7 11.7 + - - +
416B MET* 3.4 19.2 + - - +
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Residues in contact with ALA 413 (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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371B PHE* 4.1 4.7 - - + -
394B LEU* 3.8 24.9 - - + -
398B ALA* 3.8 23.3 - - + -
407B VAL* 4.0 7.6 - - + +
409B ASP 3.3 2.0 + - - -
410B VAL 3.2 7.4 + - - +
412B ALA* 1.3 76.5 - - - +
414B ALA* 1.3 66.5 + - - +
416B MET* 3.2 28.6 + - - +
457B LEU* 4.4 0.4 - - - -
461B PHE* 3.4 15.4 - - + -
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Residues in contact with ALA 414 (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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410B VAL 2.7 18.3 + - - +
411B ALA 3.5 5.8 - - - +
412B ALA 3.3 0.2 - - - -
413B ALA* 1.3 77.9 - - - +
415B LYS* 1.3 60.2 + - - +
417B LYS* 3.2 8.0 + - - -
419B TYR* 2.9 50.4 + - + +
422B VAL* 3.8 14.1 - - + -
453B ALA* 4.7 1.1 - - + -
457B LEU* 3.2 24.8 - - + +
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Residues in contact with LYS 415 (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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411B ALA* 3.0 22.7 + - + +
412B ALA* 3.9 9.6 - - - +
413B ALA 3.2 0.2 - - - -
414B ALA* 1.3 75.4 - - - +
416B MET* 1.3 63.0 + - + +
417B LYS 3.2 1.0 + - - -
418B GLN* 3.3 16.5 + - - +
419B TYR 3.5 6.7 - - - +
420B GLU* 3.5 41.1 + - + +
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Residues in contact with MET 416 (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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398B ALA* 3.9 26.5 - - - +
401B LEU* 4.0 22.7 - - + -
402B ASP* 4.3 16.8 - - + +
405B GLN* 4.4 18.8 - - + +
407B VAL* 3.4 31.9 - - + -
412B ALA 3.4 12.1 - - - +
413B ALA* 3.2 14.7 + - - +
415B LYS* 1.3 75.8 - - + +
417B LYS* 1.3 67.7 + - + +
418B GLN* 3.6 10.0 + - - -
461B PHE* 4.5 5.6 - - + -
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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