Contacts of the helix formed by residues 414 - 424 (chain B) in PDB entry 5JHQ
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 HIS 414 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B ALA 3.4 13.7 - - - -
378B GLY 2.9 28.3 + - - -
379B TYR* 4.3 1.4 - - - -
380B ASN* 3.4 38.1 + - + +
409B ALA* 3.1 11.9 + - - +
412B TYR* 3.6 28.9 - - + +
413B GLY* 1.3 75.4 + - - +
415B TYR* 1.3 57.1 + - - +
416B GLU 3.4 2.0 - - - -
417B VAL* 3.3 18.2 - - + -
418B THR* 2.5 36.6 + - - -
450B VAL* 4.2 1.5 - - - +
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Residues in contact with TYR 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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413B GLY 3.7 5.0 + - - +
414B HIS* 1.3 69.8 - - - +
416B GLU* 1.3 72.4 + - + +
418B THR* 3.8 5.1 - - - -
419B GLU* 3.0 51.3 + - - +
449B GLU* 3.4 49.6 - - + -
450B VAL* 4.3 8.0 - - + +
453B LEU* 3.6 28.2 - - + +
520B GLN* 4.1 12.8 + - - -
390C GLN* 5.7 6.9 - - + +
424C HIS* 6.4 3.4 - + - -
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Residues in contact with GLU 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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380B ASN* 4.4 6.3 - - - +
382B VAL* 3.5 39.0 - - + +
415B TYR* 1.3 83.6 - - + +
417B VAL* 1.3 60.7 + - - +
419B GLU* 3.6 4.5 + - - +
420B LEU* 3.3 19.5 + - - +
383C ARG* 5.8 1.0 + - - -
386C GLN* 4.5 23.6 - - - +
390C GLN* 3.5 34.4 + - + +
420C LEU* 5.9 2.3 - - - +
423C LYS* 5.6 5.5 + - - +
424C HIS* 5.2 11.9 + - - -
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Residues in contact with VAL 417 (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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376B ALA 4.9 1.3 - - - +
377B ALA* 3.6 24.0 - - - +
380B ASN* 4.3 4.0 - - - +
382B VAL* 4.4 16.2 - - + +
385B VAL* 3.5 40.6 - - + -
409B ALA* 3.6 9.4 - - + -
414B HIS* 3.3 28.3 - - + +
416B GLU* 1.3 76.8 - - - +
418B THR* 1.3 62.9 + - - +
420B LEU* 3.6 5.7 - - + +
421B LEU* 3.0 34.5 + - + +
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Residues in contact with THR 418 (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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406B LEU* 3.8 9.8 - - + +
409B ALA* 3.7 23.5 + - - +
410B CYS* 3.8 23.6 - - - -
414B HIS 2.5 26.3 + - - -
415B TYR* 3.8 4.7 - - - -
417B VAL* 1.3 77.3 - - - +
419B GLU* 1.3 62.8 + - - +
421B LEU* 3.4 3.4 + - - +
422B LEU* 3.1 31.5 + - + +
450B VAL* 4.0 10.9 - - + +
453B LEU* 3.8 18.4 - - + -
454B LEU* 4.5 3.1 - - + -
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Residues in contact with GLU 419 (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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415B TYR* 3.0 46.7 + - - +
416B GLU* 3.8 4.3 - - - +
418B THR* 1.3 76.8 - - - +
420B LEU* 1.3 58.8 + - - +
422B LEU* 3.4 6.9 + - - +
423B LYS* 3.0 29.2 + - + +
453B LEU* 3.9 22.2 - - + +
457B HIS* 5.2 7.5 + - + +
520B GLN* 4.8 7.6 + - - +
423C LYS* 5.4 6.4 + - - +
424C HIS* 5.9 3.5 - - - -
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Residues in contact with LEU 420 (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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382B VAL* 3.9 12.8 - - + +
385B VAL* 3.7 21.3 - - + -
386B GLN* 3.6 36.1 - - + +
389B LEU* 3.9 10.1 - - + -
416B GLU 3.3 11.8 + - - +
417B VAL* 3.6 11.2 - - - +
418B THR 3.3 0.4 - - - -
419B GLU* 1.3 76.9 - - - +
421B LEU* 1.3 62.1 + - - +
423B LYS* 3.5 13.7 - - + +
424B HIS* 3.1 51.3 + - + -
423C LYS* 5.5 9.9 - - - +
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Residues in contact with LEU 421 (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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373B LEU* 4.1 19.3 - - + -
377B ALA* 3.9 25.1 - - + -
385B VAL* 4.7 3.4 - - + -
389B LEU* 4.5 5.8 - - + -
395B VAL* 3.5 25.7 - - + +
405B PRO* 4.0 24.7 - - + +
406B LEU* 4.2 7.0 - - + +
409B ALA* 4.0 15.5 - - + -
417B VAL* 3.0 27.4 + - + +
418B THR* 3.4 5.6 + - - +
420B LEU* 1.3 72.8 - - - +
422B LEU* 1.3 65.5 + - - +
424B HIS* 3.2 12.9 + - - +
425B GLY 3.5 0.7 + - - -
426B ALA* 3.2 29.2 + - + +
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Residues in contact with LEU 422 (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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406B LEU* 4.0 22.2 - - + -
418B THR* 3.1 35.2 + - + +
419B GLU* 3.7 5.6 - - - +
421B LEU* 1.3 73.3 - - - +
423B LYS* 1.3 66.6 + - - +
425B GLY* 3.0 14.9 + - - -
426B ALA* 3.8 20.5 + - - +
428B VAL* 4.0 20.6 - - + -
453B LEU* 4.1 13.7 - - + +
454B LEU* 4.5 6.3 - - + -
457B HIS* 3.7 44.7 + - + +
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Residues in contact with LYS 423 (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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419B GLU* 3.0 19.2 + - + +
420B LEU* 3.5 16.4 - - + +
422B LEU* 1.3 75.4 - - - +
424B HIS* 1.3 74.5 + - + +
425B GLY 3.3 2.8 + - - -
457B HIS* 5.1 2.8 - - - -
423C LYS* 5.4 10.5 - - - +
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Residues in contact with HIS 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B LEU* 3.7 44.6 - - + +
395B VAL* 3.9 12.5 - - + +
420B LEU* 3.1 39.9 + - + +
421B LEU 3.2 9.4 + - - +
422B LEU 3.1 1.0 - - - -
423B LYS* 1.3 88.8 - - + +
425B GLY* 1.3 57.7 + - - +
426B ALA 3.5 2.6 + - - -
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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