Contacts of the helix formed by residues 417 - 425 (chain N) in PDB entry 5GJQ
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 LYS 417 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415N HIS 3.2 0.2 - - - -
416N GLU* 1.3 88.5 - - + +
418N GLU* 1.3 78.9 + - + +
419N ALA 3.1 2.5 + - - -
420N LEU* 3.3 16.1 + - - +
421N GLN* 3.7 10.5 + - - +
938N GLU* 6.5 1.3 - - + -
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Residues in contact with GLU 418 (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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381N THR* 6.0 2.2 - - + -
412N HIS* 5.6 3.6 - - - +
415N HIS* 3.0 34.4 - - + +
416N GLU 3.7 0.5 + - - -
417N LYS* 1.3 87.4 + - + +
419N ALA* 1.3 50.7 + - - +
421N GLN* 2.6 17.0 + - + +
422N LEU* 2.3 37.9 + - + -
938N GLU* 4.5 18.5 - - - +
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Residues in contact with ALA 419 (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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412N HIS* 4.6 2.0 - - - -
415N HIS* 3.2 17.1 + - - +
416N GLU 5.4 0.4 - - - -
417N LYS 3.1 1.0 + - - -
418N GLU* 1.3 77.5 - - - +
420N LEU* 1.3 52.5 + - - +
422N LEU* 3.1 9.6 - - - +
423N MET* 2.6 39.3 + - - +
446N LEU* 4.3 4.9 - - + -
449N ILE* 2.5 45.5 - - + -
450N HIS* 5.0 7.2 - - + -
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Residues in contact with LEU 420 (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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417N LYS 3.3 10.2 + - - +
418N GLU 3.2 0.4 - - - -
419N ALA* 1.3 78.0 - - - +
421N GLN* 1.3 55.0 + - + +
423N MET* 3.0 3.8 + - - +
424N ALA* 2.5 35.5 + - + +
427N LEU* 3.6 17.1 - - + +
446N LEU* 3.6 19.8 - - + +
450N HIS* 5.8 2.8 - - + -
457N ILE* 5.1 14.6 - - + -
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Residues in contact with GLN 421 (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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417N LYS 4.2 8.5 - - - +
418N GLU* 2.6 20.0 + - + +
420N LEU* 1.3 73.2 - - + +
422N LEU* 1.3 63.3 + - - +
424N ALA* 3.0 24.3 + - + +
425N THR* 4.1 5.0 + - - -
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Residues in contact with LEU 422 (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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408N LEU* 4.6 15.4 - - + +
412N HIS* 3.3 47.1 - - + +
418N GLU* 2.3 28.5 + - + +
419N ALA* 3.1 15.9 - - - +
421N GLN* 1.3 69.7 - - - +
423N MET* 1.3 64.1 + - + +
424N ALA 3.3 0.2 + - - -
425N THR* 4.0 9.4 + - - -
426N TYR* 4.5 10.9 - - - -
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Residues in contact with MET 423 (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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405N THR* 4.7 1.3 - - - -
408N LEU* 3.5 24.7 - - + -
409N GLY* 3.3 26.0 - - - +
419N ALA* 2.6 23.0 + - + +
420N LEU 3.5 4.3 - - - +
422N LEU* 1.3 74.5 - - + +
424N ALA* 1.3 51.7 + - - +
425N THR 3.3 0.2 - - - -
426N TYR* 2.7 11.6 + - - +
427N LEU* 2.3 53.9 + - + -
442N GLY* 3.6 20.6 - - - +
445N ALA* 2.7 38.6 - - + +
446N LEU* 3.7 20.2 - - + -
449N ILE* 5.5 1.6 - - + -
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Residues in contact with ALA 424 (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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420N LEU* 2.5 17.9 + - + +
421N GLN* 3.0 26.5 + - + +
423N MET* 1.3 71.3 - - - +
425N THR* 1.3 58.3 + - - +
427N LEU* 2.9 17.5 + - + +
430N ASP* 2.7 30.2 - - - +
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Residues in contact with THR 425 (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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421N GLN 4.2 4.9 + - - -
422N LEU 4.0 8.5 + - - -
424N ALA* 1.3 75.8 - - - +
426N TYR* 1.3 82.7 + - - +
430N ASP* 3.4 19.1 - - - +
431N THR 4.4 4.3 - - - +
432N SER* 5.2 2.8 - - - -
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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