Contacts of the helix formed by residues 418 - 428 (chain j) in PDB entry 6QX2
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 SER 418 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379j HIS* 2.6 35.8 + - - -
412j GLN* 3.9 2.2 - - - -
416j LYS 4.4 0.2 + - - -
417j LEU* 1.3 75.2 - - - +
419j GLU* 1.3 59.6 + - - +
420j LYS* 3.5 4.7 + - - -
421j GLN* 3.0 25.6 + - - +
422j ALA* 3.0 27.4 + - - +
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Residues in contact with GLU 419 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408j MET* 3.4 26.8 - - + +
412j GLN* 3.6 24.7 + - - +
418j SER* 1.3 72.1 - - - +
420j LYS* 1.3 59.5 + - + +
422j ALA 3.3 0.5 + - - -
423j GLN* 3.0 31.9 + - + +
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Residues in contact with LYS 420 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376j ASP* 5.6 11.7 - - - +
379j HIS* 4.5 10.8 - - + +
380j ILE* 3.4 23.8 - - + +
418j SER* 3.3 7.7 + - - +
419j GLU* 1.3 78.2 - - + +
421j GLN* 1.3 55.8 + - - +
423j GLN* 3.6 6.8 + - - +
424j ALA* 3.2 20.6 + - - +
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Residues in contact with GLN 421 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379j HIS* 2.8 57.3 + - + +
380j ILE* 4.2 7.6 - - - +
382j GLU* 3.9 9.9 + - - +
383j GLY* 3.5 22.5 - - - +
386j ILE* 5.4 2.4 - - - +
416j LYS 4.7 2.1 - - - +
417j LEU* 3.5 21.0 - - + +
418j SER* 3.0 36.2 + - - +
420j LYS* 1.3 73.5 - - - +
422j ALA* 1.3 59.5 + - - +
424j ALA* 3.3 4.5 + - - +
425j ILE* 3.1 33.3 + - - +
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Residues in contact with ALA 422 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408j MET* 3.7 36.3 - - + +
411j LEU* 4.4 14.5 - - + +
412j GLN* 4.1 5.6 - - + -
417j LEU* 4.6 4.9 - - + +
418j SER 3.0 17.4 + - - +
419j GLU 3.8 2.0 - - - +
421j GLN* 1.3 71.6 - - - +
423j GLN* 1.3 65.9 + - - +
425j ILE* 3.3 11.3 + - - +
426j LEU* 3.1 27.9 + - - +
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Residues in contact with GLN 423 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408j MET* 3.4 22.4 - - + +
419j GLU* 3.0 18.8 + - + +
420j LYS* 3.7 7.9 - - - +
422j ALA* 1.3 75.9 - - - +
424j ALA* 1.3 54.7 + - - +
426j LEU* 3.2 4.2 + - - +
427j ASP* 3.0 53.6 + - - +
431l ARG* 2.5 33.4 + - - +
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Residues in contact with ALA 424 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380j ILE* 3.7 33.4 - - + +
384j LEU* 4.1 11.0 - - + +
420j LYS 3.2 13.5 + - - +
421j GLN* 3.4 9.9 - - - +
423j GLN* 1.3 77.9 - - - +
425j ILE* 1.3 55.7 + - - +
427j ASP* 3.4 8.1 + - - +
428j MET* 3.0 25.5 + - - +
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Residues in contact with ILE 425 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383j GLY 3.5 25.4 - - - +
384j LEU* 4.2 9.4 - - + -
387j ALA* 3.6 23.1 - - + +
394j ILE* 3.9 28.3 - - + -
398j ILE* 4.9 0.9 - - + -
411j LEU* 4.5 11.7 - - + -
417j LEU* 3.5 30.3 - - + -
421j GLN 3.1 22.0 + - - +
422j ALA* 3.7 5.2 - - - +
423j GLN 3.3 0.2 - - - -
424j ALA* 1.3 73.0 - - - +
426j LEU* 1.3 65.3 + - - +
427j ASP 3.2 0.2 - - - -
428j MET* 3.3 22.8 - - + +
430l LEU* 3.5 16.6 - - + +
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Residues in contact with LEU 426 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398j ILE* 4.0 31.9 - - + -
404j ASP* 4.0 10.5 - - + +
407j ALA* 4.3 5.8 - - + -
408j MET* 3.5 44.6 - - + +
411j LEU* 4.1 6.7 - - + -
422j ALA 3.1 10.8 + - - +
423j GLN 3.6 4.0 - - - +
425j ILE* 1.3 75.7 - - - +
427j ASP* 1.3 58.4 + - - +
429l ARG* 3.5 2.9 - - - +
430l LEU* 3.4 7.7 + - - -
431l ARG* 2.9 79.1 + - + +
434l THR* 5.2 0.9 - - + -
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Residues in contact with ASP 427 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423j GLN* 3.0 37.1 + - - +
424j ALA* 3.4 9.4 + - - +
425j ILE 3.2 0.2 - - - -
426j LEU* 1.3 74.0 - - - +
428j MET* 1.3 64.7 + - - +
429j ARG* 3.5 3.3 + - - +
429l ARG* 2.8 42.8 + - - +
431l ARG* 3.5 18.9 + - - -
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Residues in contact with MET 428 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384j LEU* 3.8 27.4 - - + +
387j ALA* 3.9 25.1 - - + -
388j LEU* 4.0 16.8 - - + -
391j ILE* 5.1 1.8 - - + -
424j ALA 3.0 10.9 + - - +
425j ILE* 3.3 20.3 + - + +
427j ASP* 1.3 74.9 - - - +
429j ARG* 1.3 67.6 + - - +
432j ARG* 3.9 24.2 - - + +
433j LEU* 3.9 25.8 - - - -
429l ARG* 3.1 3.0 - - - -
430l LEU* 3.1 40.7 + - + +
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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