Contacts of the helix formed by residues 420 - 433 (chain G) 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 MET 420 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200G GLU* 3.5 16.4 - - + +
204G LEU* 3.8 38.4 - - + -
409G ALA 4.0 6.3 - - - +
410G VAL* 3.3 42.8 - - + +
413G GLY* 4.0 3.4 - - - -
414G VAL* 3.9 19.1 - - + +
418G ILE* 3.2 13.4 + - + +
419G PRO* 1.3 76.9 - - - +
421G PRO* 1.3 57.2 - - - +
422G CYS 3.3 2.7 - - - -
423G PHE* 3.7 19.1 - - + -
424G THR* 2.6 37.4 + - + +
428H SER* 3.6 8.7 + - - +
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Residues in contact with PRO 421 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G GLN* 4.3 10.8 - - - +
200G GLU* 3.0 15.0 - - - +
283G GLU* 3.4 36.9 - - + +
287G ALA* 5.1 7.9 - - + -
290G LEU* 6.5 1.1 - - + -
419G PRO* 3.4 11.2 - - + +
420G MET* 1.3 86.9 - - - +
422G CYS* 1.3 56.4 + - - +
424G THR* 3.0 16.1 + - - +
425G THR* 3.1 22.5 + - - +
425H THR* 5.8 0.7 - - - +
428H SER* 3.9 23.5 - - - +
429H PHE* 6.0 0.4 - - - -
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Residues in contact with CYS 422 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G GLN* 3.4 31.9 - - + -
197G LEU* 3.6 22.0 - - + -
200G GLU* 2.6 17.4 + - - +
280G LEU* 3.2 44.3 - - + +
283G GLU* 4.2 2.7 - - - -
284G ALA* 4.2 8.3 - - - -
421G PRO* 1.3 71.8 - - - +
423G PHE* 1.3 60.5 + - - +
425G THR* 3.8 1.3 - - - -
426G ALA* 2.9 33.4 + - - +
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Residues in contact with PHE 423 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G LEU* 3.5 37.5 - - + -
200G GLU* 2.9 29.0 + - + +
201G ALA* 3.9 10.5 - - + -
204G LEU* 3.9 18.2 - - + -
323G ILE* 4.6 2.7 - - + -
326G ALA* 3.9 15.5 - - + -
327G LEU* 3.8 33.2 - - + -
330G SER* 3.3 16.8 - - - +
406G TRP* 3.8 6.6 + - - -
409G ALA* 5.9 0.4 - - + -
410G VAL* 4.2 16.2 - - + +
420G MET* 3.5 28.2 + - + -
422G CYS* 1.3 76.2 - - - +
424G THR* 1.3 62.5 + - - +
426G ALA* 3.6 0.3 + - - +
427G LEU* 3.2 23.6 + - - +
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Residues in contact with THR 424 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410G VAL* 4.0 24.5 - - + -
414G VAL* 4.8 6.7 - - + -
420G MET* 2.6 35.5 + - + +
421G PRO* 3.0 13.2 + - - +
423G PHE* 1.3 76.5 - - - +
425G THR* 1.3 54.9 + - - +
427G LEU* 3.4 4.9 + - - +
428G SER* 2.9 34.3 + - - -
410H VAL* 5.9 0.2 - - + -
424H THR* 3.6 32.4 + - + +
425H THR* 4.8 1.6 + - - -
428H SER* 3.5 17.7 + - - +
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Residues in contact with THR 425 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G THR* 3.0 17.3 + - - +
280G LEU* 3.6 17.5 - - + -
283G GLU* 3.7 20.6 - - + -
421G PRO 3.1 22.2 + - - +
422G CYS* 3.5 7.4 - - - +
424G THR* 1.3 75.1 + - - +
426G ALA* 1.3 64.0 + - - +
428G SER* 4.1 6.4 - - - -
429G PHE* 3.0 28.1 + - - +
283H GLU* 2.9 32.6 + - - -
421H PRO* 5.1 1.6 - - - +
424H THR* 5.2 1.8 - - - -
425H THR* 6.1 1.6 - - - -
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Residues in contact with ALA 426 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G THR* 5.4 0.4 - - - -
280G LEU* 3.8 9.4 - - + -
330G SER* 3.8 17.3 - - - +
333G ILE* 3.6 26.8 - - + +
406G TRP* 3.3 26.6 - - + -
422G CYS 2.9 19.8 + - - +
423G PHE 4.0 0.2 - - - +
425G THR* 1.3 77.7 - - - +
427G LEU* 1.3 58.1 + - - +
429G PHE 3.7 0.2 + - - -
430G TYR* 3.2 19.9 + - - +
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Residues in contact with LEU 427 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403G GLN* 6.1 0.7 - - + -
406G TRP* 3.3 34.7 - - + +
407G ARG* 3.7 43.5 - - + +
410G VAL* 4.3 15.9 - - + -
423G PHE 3.2 19.0 + - - +
424G THR* 3.9 4.0 - - - +
425G THR 3.3 0.2 - - - -
426G ALA* 1.3 75.3 - - - +
428G SER* 1.3 60.3 + - - +
430G TYR* 3.3 3.7 + - + +
431G ASP* 3.0 32.3 + - - +
414H VAL* 3.7 38.1 - - + -
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Residues in contact with SER 428 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424G THR 2.9 20.1 + - - -
425G THR* 4.1 4.0 - - - -
426G ALA 3.4 0.2 - - - -
427G LEU* 1.3 76.5 - - - +
429G PHE* 1.3 58.0 + - - +
431G ASP* 4.7 0.4 - - - -
432G GLY* 3.1 22.2 + - - -
290H LEU* 5.1 1.2 - - - +
419H PRO* 3.3 17.2 - - - +
420H MET 3.8 6.8 + - - -
421H PRO* 3.5 38.5 - - - +
424H THR* 3.4 19.9 + - - +
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Residues in contact with PHE 429 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G PRO* 3.6 30.7 - - + -
279G THR* 4.2 7.2 - - + +
333G ILE* 3.8 17.3 - - + -
336G ALA* 5.3 1.6 - - + -
337G GLN* 3.1 38.6 - - + +
340G MET* 4.0 22.4 - - + -
388G ASN* 5.3 0.2 - - - -
390G LEU* 4.4 18.4 - - + -
425G THR 3.0 19.4 + - - +
426G ALA 4.0 3.1 - - - +
428G SER* 1.3 76.3 - - - +
430G TYR* 1.3 60.7 + - - +
432G GLY* 3.3 0.9 + - - +
433G TYR* 2.9 36.1 + + + +
290H LEU* 3.6 32.3 - - + +
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Residues in contact with TYR 430 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333G ILE* 4.1 10.1 - - + -
390G LEU* 4.6 14.1 - - + -
399G VAL* 4.2 19.8 - - + +
400G GLU* 5.7 4.2 + - - +
403G GLN* 4.3 19.8 - - + +
406G TRP* 4.1 21.1 - + + -
407G ARG* 4.4 4.9 - - - -
426G ALA 3.2 19.2 + - - +
427G LEU* 3.7 5.6 - - + +
429G PHE* 1.3 80.8 - - - +
431G ASP* 1.3 72.1 + - - +
432G GLY 3.3 0.7 + - - -
433G TYR* 3.3 9.9 + - - -
434G ARG* 3.1 25.9 + - - +
304H LEU* 4.0 36.1 - - + +
305H LYS 2.6 36.1 + - - -
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Residues in contact with ASP 431 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407G ARG* 2.6 44.5 + - - -
427G LEU* 3.0 20.5 + - - +
428G SER* 5.3 0.2 - - - -
430G TYR* 1.3 84.7 - - - +
432G GLY* 1.3 58.7 + - - +
434G ARG* 3.3 13.6 + - - +
435G HIS* 2.7 29.6 + - - -
414H VAL* 5.4 1.2 - - - -
417H GLY* 3.1 20.2 - - - +
418H ILE 3.5 4.9 + - - +
419H PRO* 3.6 26.4 - - + +
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Residues in contact with GLY 432 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428G SER 3.1 15.2 + - - -
429G PHE 3.7 3.4 - - - -
430G TYR 3.2 0.2 - - - -
431G ASP* 1.3 74.5 - - - +
433G TYR* 1.3 54.7 + - - +
434G ARG 3.1 10.6 + - - -
435G HIS 3.5 5.7 + - - -
438G LEU* 4.0 13.2 - - - +
290H LEU* 3.9 17.3 - - - -
297H ARG* 3.2 19.6 - - - -
419H PRO* 3.9 12.1 - - - -
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Residues in contact with TYR 433 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340G MET* 5.3 0.4 - - - -
387G GLN* 5.1 1.4 + - - +
388G ASN* 3.1 42.8 - - + +
390G LEU* 3.6 20.0 - - + -
391G LEU* 4.3 11.8 - - + +
429G PHE* 2.9 31.4 + + + +
430G TYR* 3.3 7.3 + - - +
432G GLY* 1.3 75.3 - - - +
434G ARG* 1.3 57.8 + - - +
290H LEU* 4.1 19.0 - - + +
293H LEU* 5.1 3.8 - - + -
296H GLU* 3.3 45.7 + - + +
297H ARG* 4.0 15.7 - - + +
300H ALA* 3.3 26.1 - - + +
304H LEU* 3.6 17.9 - - + -
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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
------------------------------------------------------------
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