Contacts of the helix formed by residues 439 - 451 (chain A) in PDB entry 5UQ9
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 PRO 439 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438A LEU* 1.3 87.8 - - + +
440A ALA* 1.3 56.7 + - - +
441A SER* 3.1 6.1 - - - +
442A LEU* 2.9 19.9 + - - +
196B GLN* 5.6 6.1 - - - +
199B CYS* 3.3 50.4 - - + +
200B GLU* 4.8 1.6 - - - +
202B TYR* 4.2 16.4 - - + -
203B HIS* 3.4 40.6 - - + +
419B PRO* 5.6 2.0 - - + +
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Residues in contact with ALA 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A LEU* 3.0 4.8 - - + -
439A PRO* 1.3 76.7 - - - +
441A SER* 1.3 63.3 + - - +
442A LEU 3.2 0.4 - - - -
443A ILE* 3.2 19.5 - - + +
444A GLN* 3.1 23.9 + - - +
196B GLN* 5.9 2.0 - - - +
255B ARG 4.8 0.3 - - - +
256B ASP* 3.2 20.4 - - - +
257B SER 4.8 1.2 - - - +
258B ALA* 4.3 4.7 - - + +
291B SER* 3.2 34.3 - - - +
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Residues in contact with SER 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A LEU 3.8 11.8 + - - -
439A PRO* 4.3 2.1 - - - +
440A ALA* 1.3 78.9 - - - +
442A LEU* 1.3 57.4 + - - +
444A GLN* 4.0 0.4 - - - -
445A ALA* 3.1 27.4 + - - +
202B TYR* 5.2 4.3 + - - -
251B LEU* 3.4 26.7 + - - +
254B ILE* 3.7 29.8 - - - +
255B ARG 3.7 13.7 - - - -
256B ASP* 3.5 8.1 + - - -
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Residues in contact with LEU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A PRO 2.9 11.5 + - - +
441A SER* 1.3 77.7 + - - +
443A ILE* 1.3 60.3 + - - +
444A GLN 3.1 2.2 - - - -
445A ALA* 3.1 0.8 + - - -
446A GLN* 2.9 56.1 + - + +
198B ILE* 4.3 3.4 - - + -
199B CYS* 3.9 16.4 - - - -
202B TYR* 3.9 37.0 - - + -
236B THR* 3.9 26.7 - - + +
239B ILE* 4.1 25.4 - - + -
240B LEU* 4.8 1.6 - - + -
251B LEU* 4.1 17.0 - - + -
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Residues in contact with ILE 443 (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 PRO 3.4 2.0 + - - -
440A ALA* 3.2 22.6 + - + +
442A LEU* 1.3 78.2 - - - +
444A GLN* 1.3 60.6 + - - +
446A GLN* 3.8 6.5 - - - -
447A ARG* 3.6 11.3 + - - +
192B TYR 4.8 1.3 - - - +
195B MET* 3.3 45.2 - - + +
196B GLN* 3.9 36.3 - - + +
199B CYS* 3.5 13.4 - - - -
258B ALA* 3.6 23.6 - - + -
284B ALA 5.6 0.2 - - - +
288B ARG* 3.4 32.3 - - + +
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Residues in contact with GLN 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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440A ALA 3.1 15.4 + - - +
441A SER* 4.3 4.3 - - - +
442A LEU 3.1 0.4 - - - -
443A ILE* 1.3 79.2 - - + +
445A ALA* 1.3 62.4 + - - +
446A GLN 3.1 2.0 - - - -
447A ARG* 3.3 12.7 + - + +
448A ASP* 3.2 20.4 + - - +
453A HIS* 6.6 0.2 - - + -
454A THR 4.2 11.9 + - - +
455A TYR* 3.9 30.6 - - + +
456A GLU* 4.0 12.7 - - - +
254B ILE* 5.0 1.7 - - + +
255B ARG* 4.5 9.5 + - - +
257B SER* 2.9 27.6 + - - +
258B ALA* 3.6 16.3 - - - -
259B GLY* 4.2 1.6 + - - -
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Residues in contact with ALA 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A SER 3.1 20.5 + - - +
442A LEU 3.1 4.5 + - - +
444A GLN* 1.3 75.0 - - - +
446A GLN* 1.3 59.2 + - - +
448A ASP* 3.6 8.2 + - - +
449A TYR* 3.0 20.8 + - - +
455A TYR* 5.4 1.8 - - - -
469A TRP* 4.4 8.2 - - + -
239B ILE* 3.3 33.4 - - + +
251B LEU* 4.0 2.2 - - + -
254B ILE* 3.8 23.3 - - + +
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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
----------------------------------------------------------
442A LEU* 2.9 32.9 + - + +
443A ILE* 3.8 10.2 - - - +
444A GLN 3.1 0.2 - - - -
445A ALA* 1.3 74.5 - - - +
447A ARG* 1.3 59.7 + - - +
449A TYR* 2.9 16.5 + - - +
450A PHE* 2.9 23.8 + - + -
195B MET* 3.3 40.6 + - + +
198B ILE* 4.1 17.4 - - - +
232B LEU* 4.1 10.1 + - + +
235B ILE* 3.9 18.8 - - + -
236B THR* 3.0 24.0 + - - +
239B ILE* 3.7 14.8 - - + -
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Residues in contact with ARG 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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443A ILE 3.6 16.8 - - - +
444A GLN* 3.3 13.8 + - + +
446A GLN* 1.3 75.4 - - - +
448A ASP* 1.3 57.9 + - - +
450A PHE* 3.5 22.3 - - + -
451A GLY 2.9 24.8 + - - +
453A HIS* 3.1 52.9 + - + -
191B GLU* 4.1 14.6 + - - -
192B TYR* 4.3 11.8 + - - -
195B MET* 3.8 4.7 - - + -
263B THR* 5.7 5.5 - - - +
288B ARG* 3.2 37.2 - - - +
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Residues in contact with ASP 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLN 3.2 10.1 + - - +
445A ALA* 3.9 7.6 - - - +
447A ARG* 1.3 77.6 - - - +
449A TYR* 1.3 59.2 + - - +
451A GLY 2.8 13.4 - - - +
453A HIS* 2.6 31.2 - - - +
454A THR* 3.6 1.7 - - - +
455A TYR* 3.3 23.0 - - + -
465A ILE 3.0 21.7 - - - +
466A HIS* 3.2 16.4 + - - -
467A THR 3.4 7.1 + - - +
469A TRP* 2.5 32.5 + - - +
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Residues in contact with TYR 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 ALA 3.0 12.9 + - - +
446A GLN* 2.9 10.9 + - - +
448A ASP* 1.3 81.0 - - - +
450A PHE* 1.3 64.6 + - - +
451A GLY 3.4 1.4 + - - +
466A HIS* 5.5 0.7 + - - -
469A TRP* 3.5 53.9 + + + +
470A THR* 5.1 10.5 + - - -
231B PHE* 4.6 7.6 - + - -
235B ILE* 3.5 35.3 - - + +
238B ASN* 3.8 32.9 + - + +
239B ILE* 3.5 24.7 - - + -
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Residues in contact with PHE 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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446A GLN* 2.9 38.5 + - + -
447A ARG* 3.5 33.2 - - + -
449A TYR* 1.3 77.3 - - - +
451A GLY* 1.3 59.3 + - - +
453A HIS* 4.2 15.9 - + - -
133B GLU* 5.8 0.9 - - - +
191B GLU* 3.6 23.3 - - - -
195B MET* 4.3 6.3 - - + -
231B PHE* 3.8 26.5 - - + -
232B LEU* 4.5 0.9 - - + -
235B ILE* 4.0 13.2 - - + -
367B ILE* 3.7 38.7 - - + +
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Residues in contact with GLY 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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447A ARG 2.9 12.1 + - - +
448A ASP 2.8 23.0 - - - +
449A TYR 4.0 1.3 - - - +
450A PHE* 1.3 81.1 - - - +
452A ALA* 1.3 57.3 + - - -
453A HIS* 3.0 23.7 + - - -
466A HIS* 4.0 4.3 + - - -
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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