Contacts of the helix formed by residues 443 - 453 (chain A) in PDB entry 3Q36
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 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A THR* 5.7 0.8 - - - +
364A PRO* 2.7 32.0 + - + -
365A PHE 3.0 14.9 + - - -
366A SER* 3.3 25.4 - - - -
367A CYS* 3.4 4.2 - - - -
441A LEU* 4.0 3.9 - - - +
442A ASN* 1.3 89.1 - - - +
444A PRO* 1.3 60.6 - - + +
445A ASN* 3.0 47.0 + - + +
446A GLN* 2.6 42.4 + - + +
447A PHE 3.1 5.2 + - - -
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Residues in contact with PRO 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A PRO* 3.9 13.8 - - + +
288A MET* 3.8 20.9 - - + -
312A PHE* 3.5 16.5 - - + -
365A PHE 3.3 20.6 - - - +
367A CYS* 3.8 15.6 - - - +
370A ILE* 3.6 27.6 - - + -
443A HIS* 1.3 83.4 - - - +
445A ASN* 1.3 59.8 + - - +
447A PHE* 3.4 6.3 + - + +
448A PHE* 3.2 16.1 + - - +
458A SF4 4.0 22.2 - - - -
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Residues in contact with ASN 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A MET* 5.6 0.2 - - - +
312A PHE* 3.2 45.2 + - - -
315A GLY* 3.4 22.6 - - - +
316A ILE* 3.5 6.3 - - - +
364A PRO* 3.4 14.5 - - - +
365A PHE 4.6 0.7 + - - +
443A HIS* 2.9 32.5 + - + +
444A PRO* 1.3 76.4 - - - +
446A GLN* 1.3 60.7 + - - +
448A PHE* 3.3 4.3 + - - +
449A CYS* 3.0 35.5 + - - -
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Residues in contact with GLN 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A PHE* 3.3 27.5 - - + +
440A SER 3.2 18.3 + - - +
441A LEU* 3.3 1.6 - - - +
442A ASN* 2.8 39.3 + - - +
443A HIS* 2.6 27.4 + - + +
445A ASN* 1.3 70.4 - - - +
447A PHE* 1.3 51.1 + - - +
449A CYS* 3.3 7.8 + - - +
450A GLU* 2.8 57.1 + - + +
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Residues in contact with PHE 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A LYS 4.9 1.6 - - - -
283A SER* 3.4 22.4 - - - -
284A PHE 3.8 3.4 - - - -
285A PRO* 3.6 28.0 - - + -
424A CYS* 3.5 36.3 - - - -
425A GLN* 5.9 0.2 - - - -
427A TYR* 3.9 20.6 - + - -
428A PHE* 3.5 41.8 - + + -
431A ILE* 4.7 1.8 - - + -
432A HIS* 4.6 5.8 - + - -
439A PHE* 4.4 7.0 - + - -
441A LEU* 3.7 22.4 - - + -
443A HIS 3.1 5.1 + - - +
444A PRO* 3.4 11.7 - - + +
446A GLN* 1.3 75.1 - - - +
448A PHE* 1.3 60.4 + - - +
451A SER* 2.9 24.6 + - - -
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Residues in contact with PHE 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ILE 6.2 0.4 - - - -
279A LEU* 4.0 19.3 - - + -
283A SER* 3.3 44.9 - - - +
284A PHE* 4.0 24.2 - + - -
312A PHE* 4.1 11.2 - + + -
316A ILE* 3.9 35.7 - - + -
444A PRO 3.2 10.6 + - - +
445A ASN* 3.6 8.7 - - - +
446A GLN 3.3 0.2 - - - -
447A PHE* 1.3 81.2 - - - +
449A CYS* 1.3 61.9 + - - +
451A SER* 3.4 2.1 + - - -
452A GLN* 2.9 51.2 + - + +
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Residues in contact with CYS 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A ASN* 3.0 22.2 + - - -
446A GLN* 3.5 11.0 - - - +
448A PHE* 1.3 78.8 - - - +
450A GLU* 1.3 71.5 + - + +
451A SER 3.0 1.3 - - - -
452A GLN* 3.0 7.5 + - - +
453A ARG* 3.0 30.1 + - + +
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Residues in contact with GLU 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A PHE* 3.8 5.2 - - + -
437A CYS 4.1 3.8 - - - +
438A GLY 4.2 2.4 - - - +
439A PHE* 3.1 61.3 - - + +
446A GLN* 2.8 39.6 + - + +
447A PHE 3.8 3.4 - - - +
449A CYS* 1.3 77.5 - - - +
451A SER* 1.3 62.7 + - - +
453A ARG* 3.5 38.8 + - - +
454A ILE* 3.6 16.8 - - - +
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Residues in contact with SER 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A LYS 3.4 0.2 + - - -
283A SER* 3.0 32.1 + - - -
428A PHE* 3.6 10.3 - - - -
432A HIS* 2.8 32.3 + - - -
447A PHE* 2.9 18.7 + - - -
448A PHE 3.4 5.2 - - - -
449A CYS 3.0 0.2 - - - -
450A GLU* 1.3 77.0 - - - +
452A GLN* 1.3 63.9 + - - +
454A ILE* 3.0 15.1 + - - +
455A LEU* 3.4 14.6 + - - +
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Residues in contact with GLN 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A LEU* 3.3 22.9 - - - +
283A SER* 3.0 19.2 + - - +
448A PHE* 2.9 45.6 + - + +
449A CYS* 3.0 6.7 + - - +
451A SER* 1.3 76.8 - - - +
453A ARG* 1.3 61.4 + - - +
454A ILE 3.0 2.0 + - - -
455A LEU* 3.9 22.0 + - - +
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Residues in contact with ARG 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A GLY 5.7 1.2 + - - -
449A CYS* 3.0 20.6 + - + +
450A GLU* 3.6 39.4 + - - +
451A SER 3.2 0.4 - - - -
452A GLN* 1.3 76.4 - - - +
454A ILE* 1.3 60.5 + - + +
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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