Contacts of the helix formed by residues 420 - 434 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428G SER* 3.8 5.9 + - - +
200H GLU* 3.5 24.5 - - + +
204H LEU* 4.0 17.0 - - + -
409H ALA 3.3 16.8 - - - +
410H VAL* 3.2 34.1 - - + +
413H GLY* 3.5 21.3 - - - -
414H VAL* 3.7 8.5 - - + +
418H ILE* 3.2 10.5 + - + +
419H PRO* 1.3 73.6 - - - +
421H PRO* 1.3 67.6 - - - +
422H CYS 3.2 3.0 + - - -
423H PHE* 3.3 30.7 + - + -
424H THR* 3.0 25.6 + - + +
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Residues in contact with PRO 421 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425G THR* 5.1 2.1 - - - +
428G SER* 3.5 22.0 - - - +
196H GLN* 5.1 1.3 - - - +
200H GLU* 3.0 14.6 - - + +
283H GLU* 3.5 36.9 - - + +
287H ALA* 4.6 12.8 - - + -
419H PRO* 3.6 11.0 - - + +
420H MET* 1.3 89.3 - - - +
422H CYS* 1.3 55.5 + - - +
424H THR* 3.1 9.0 + - - +
425H THR* 3.0 30.3 + - - +
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Residues in contact with CYS 422 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196H GLN* 3.6 26.9 - - + -
197H LEU* 3.6 18.3 - - + +
200H GLU* 2.8 23.8 + - - +
280H LEU* 3.6 39.4 - - + +
283H GLU* 4.2 4.3 - - - -
284H ALA* 3.9 11.9 - - - -
421H PRO* 1.3 71.6 - - - +
423H PHE* 1.3 64.4 + - - +
425H THR* 3.4 7.2 - - - +
426H ALA* 3.1 25.5 + - - +
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Residues in contact with PHE 423 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197H LEU* 3.6 31.6 - - + -
200H GLU* 3.0 15.4 + - + -
201H ALA* 4.1 15.7 - - + -
204H LEU* 3.9 20.2 - - + -
323H ILE* 4.0 9.0 - - - -
326H ALA* 4.2 7.6 - - + -
327H LEU* 3.5 41.3 - - + -
330H SER* 3.2 16.6 - - - +
406H TRP* 3.5 14.3 + - - +
409H ALA* 5.8 1.6 - - + -
410H VAL* 4.2 11.8 - - + +
420H MET* 3.3 35.4 + - + +
422H CYS* 1.3 77.7 - - - +
424H THR* 1.3 61.5 + - - +
427H LEU* 3.3 18.0 + - - +
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Residues in contact with THR 424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424G THR* 3.6 30.1 + - + +
425G THR* 5.2 0.7 - - - -
428G SER* 3.4 12.9 + - - +
410H VAL* 3.8 28.3 - - + -
414H VAL* 4.7 11.0 - - + -
420H MET* 3.0 28.1 + - + +
421H PRO* 3.1 14.9 + - - +
423H PHE* 1.3 73.7 - - - +
425H THR* 1.3 60.0 + - - +
427H LEU* 3.5 2.7 + - - +
428H SER* 2.9 33.1 + - - -
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Residues in contact with THR 425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G GLU* 2.6 33.1 + - - -
421G PRO* 5.6 0.8 - - - +
424G THR* 5.0 3.1 - - - -
425G THR* 6.1 1.8 - - - -
279H THR* 3.1 13.2 + - - +
280H LEU* 3.7 25.8 - - + -
283H GLU* 4.1 8.1 - - + -
421H PRO 3.0 22.8 + - - +
422H CYS* 3.4 13.9 - - - +
424H THR* 1.3 77.3 + - - +
426H ALA* 1.3 62.0 + - - +
428H SER* 3.9 5.3 - - - -
429H PHE* 3.0 27.2 + - - +
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Residues in contact with ALA 426 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279H THR* 5.3 0.7 - - - -
280H LEU* 3.7 19.7 - - + -
330H SER* 4.0 5.8 - - - +
333H ILE* 3.8 26.0 - - + +
406H TRP* 3.4 25.7 - - + -
422H CYS 3.1 18.4 + - - +
425H THR* 1.3 78.7 - - - +
427H LEU* 1.3 59.9 + - - +
429H PHE* 3.5 1.2 + - - +
430H TYR* 3.1 22.9 + - - +
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Residues in contact with LEU 427 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414G VAL* 3.6 35.0 - - + -
403H GLN* 6.1 0.7 - - + -
406H TRP* 3.2 38.6 - - + -
407H ARG* 3.4 44.0 - - + +
410H VAL* 3.8 22.4 - - + -
423H PHE 3.3 14.1 + - - +
424H THR* 4.0 4.7 - - - +
426H ALA* 1.3 75.3 - - - +
428H SER* 1.3 61.4 + - - +
430H TYR* 3.5 3.3 + - + +
431H ASP* 3.0 33.1 + - - +
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Residues in contact with SER 428 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G LEU* 5.3 0.9 - - - +
414G VAL* 6.0 1.0 - - - +
418G ILE 5.6 0.2 - - - -
419G PRO* 3.6 13.5 - - - +
420G MET* 3.6 13.5 + - - +
421G PRO* 3.9 33.2 - - - +
424G THR* 3.5 18.4 + - - +
424H THR 2.9 18.5 + - - -
425H THR* 4.0 4.9 - - - -
427H LEU* 1.3 75.3 - - - +
429H PHE* 1.3 64.9 + - - +
431H ASP* 4.5 4.5 - - - -
432H GLY* 3.1 17.5 + - - -
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Residues in contact with PHE 429 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G LEU* 3.9 29.3 - - + +
421G PRO* 6.0 0.2 - - - -
277H PRO* 3.6 20.0 - - + -
279H THR* 4.2 9.9 - - + +
333H ILE* 3.5 19.7 - - + -
336H ALA* 5.5 1.8 - - + -
337H GLN* 3.2 43.5 - - + +
340H MET* 4.2 20.4 - - - -
390H LEU* 4.6 11.7 - - + -
425H THR 3.0 18.8 + - - +
426H ALA 3.8 3.4 - - - +
427H LEU 3.3 0.4 - - - -
428H SER* 1.3 75.9 - - - +
430H TYR* 1.3 61.4 + - - +
432H GLY* 3.2 1.3 + - - +
433H TYR* 2.8 49.3 + + + +
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Residues in contact with TYR 430 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304G LEU* 3.5 34.7 - - + +
305G LYS 3.4 19.3 + - - -
333H ILE* 3.8 22.4 - - + -
390H LEU* 4.0 11.7 - - + -
396H LYS* 4.9 1.7 + - - +
399H VAL* 3.3 43.7 - - + +
400H GLU* 4.8 0.9 + - - +
403H GLN* 3.5 23.9 + - + -
406H TRP* 4.5 8.7 - + + -
407H ARG* 4.5 3.8 - - - -
426H ALA 3.1 17.4 + - - +
427H LEU* 3.9 5.2 - - + +
429H PHE* 1.3 81.4 - - - +
431H ASP* 1.3 71.1 + - - +
433H TYR* 3.9 3.3 - - - +
434H ARG* 3.1 39.5 + - - +
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Residues in contact with ASP 431 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413G GLY 5.2 0.2 - - - +
414G VAL* 4.9 1.6 - - - +
417G GLY 3.3 28.9 - - - +
418G ILE 4.2 5.2 + - - +
419G PRO* 4.0 12.1 - - + +
407H ARG* 2.6 45.0 + - - -
427H LEU* 3.0 21.7 + - - +
428H SER* 4.0 3.5 - - - +
430H TYR* 1.3 77.8 - - - +
432H GLY* 1.3 58.5 + - - +
434H ARG* 3.4 15.7 + - - +
435H HIS* 2.4 31.9 + - - -
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Residues in contact with GLY 432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290G LEU* 3.7 15.0 - - - -
297G ARG* 3.4 17.2 - - - -
419G PRO* 3.8 15.7 - - - +
428H SER 3.1 15.7 + - - -
429H PHE 3.7 1.8 - - - -
431H ASP* 1.3 77.0 - - - +
433H TYR* 1.3 62.8 + - - +
434H ARG 3.2 1.0 + - - -
435H HIS* 3.4 8.0 + - - +
438H LEU* 3.7 13.3 - - - +
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Residues in contact with TYR 433 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G LEU* 3.8 26.6 - - + +
293G LEU* 4.7 6.7 - - + -
296G GLU* 2.9 54.7 + - + +
297G ARG* 3.5 18.3 - - + +
300G ALA* 3.3 32.3 - - + +
304G LEU* 4.2 5.6 - - + -
340H MET* 4.8 1.3 - - + -
388H ASN* 3.1 24.6 + - + +
390H LEU* 3.6 36.3 - - + -
391H LEU* 4.2 6.6 - - + +
429H PHE* 2.8 35.8 + + + +
430H TYR* 4.0 3.6 - - - +
432H GLY* 1.3 74.1 - - - +
434H ARG* 1.3 58.4 + - - +
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Residues in contact with ARG 434 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300G ALA* 4.1 8.1 - - - -
301G SER* 3.2 27.1 - - - -
304G LEU* 4.0 26.1 + - + +
305G LYS* 3.7 10.9 - - - +
306G GLY* 3.5 20.8 - - - +
307G PRO* 3.4 23.0 - - - +
416G ALA 4.4 1.8 + - - -
417G GLY* 3.1 27.3 + - - -
407H ARG* 4.4 0.2 - - - +
430H TYR* 3.1 37.4 + - - +
431H ASP* 3.4 20.0 + - - +
433H TYR* 1.3 76.1 - - - +
435H HIS* 1.3 78.6 + - - +
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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
------------------------------------------------------------
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