Contacts of the helix formed by residues 420 - 434 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428E SER* 3.7 8.3 + - - -
200F GLU* 3.6 17.3 - - + +
204F LEU* 3.9 34.5 - - + -
409F ALA 4.0 11.2 - - - +
410F VAL* 3.2 43.1 - - + +
413F GLY* 4.0 12.1 - - - -
414F VAL* 4.0 7.0 - - + +
418F ILE* 3.3 10.6 + - + +
419F PRO* 1.3 77.2 - - - +
421F PRO* 1.3 64.9 - - - +
422F CYS 3.3 2.7 - - - -
423F PHE* 3.7 17.9 - - + -
424F THR* 2.7 33.7 + - + +
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Residues in contact with PRO 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425E THR* 6.0 1.0 - - - -
428E SER* 3.8 19.7 - - - +
196F GLN* 3.8 15.5 - - + +
200F GLU* 3.1 17.5 - - + +
283F GLU* 3.6 30.6 - - + +
287F ALA* 4.6 11.0 - - + -
419F PRO* 3.5 12.6 - - + +
420F MET* 1.3 88.5 - - - +
422F CYS* 1.3 55.2 + - - +
424F THR* 3.1 15.2 + - - +
425F THR* 3.2 20.1 + - - +
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Residues in contact with CYS 422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F GLN* 3.5 30.1 - - + -
197F LEU* 3.6 21.3 - - + -
200F GLU* 2.6 18.8 + - - +
280F LEU* 3.5 39.9 - - + +
283F GLU* 4.0 4.7 - - - -
284F ALA* 3.9 8.3 - - - -
330F SER* 4.4 0.5 + - - -
421F PRO* 1.3 71.1 - - - +
423F PHE* 1.3 64.8 + - - +
424F THR 3.2 2.0 - - - -
425F THR* 3.5 5.8 - - - +
426F ALA* 3.1 26.9 + - - +
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Residues in contact with PHE 423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197F LEU* 3.8 35.9 - - + -
200F GLU* 2.8 33.9 + - + +
201F ALA* 3.9 11.0 - - + -
204F LEU* 3.7 23.1 - - + -
323F ILE* 4.8 2.2 - - + -
326F ALA* 4.0 14.8 - - + -
327F LEU* 3.9 28.9 - - + -
330F SER* 3.4 15.9 - - - +
406F TRP* 3.6 7.4 + - - +
409F ALA* 5.9 1.1 - - + -
410F VAL* 4.1 16.1 - - + +
420F MET* 3.4 28.5 + - + -
422F CYS* 1.3 73.0 - - - +
424F THR* 1.3 61.3 + - - +
427F LEU* 3.3 24.3 + - - +
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Residues in contact with THR 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424E THR* 3.5 30.0 + - + +
425E THR* 4.9 1.2 + - - -
428E SER* 3.4 16.9 + - - +
410F VAL* 3.8 25.4 - - + -
414F VAL* 5.0 6.5 - - + -
420F MET* 2.7 33.3 + - + +
421F PRO* 3.1 10.0 + - - +
423F PHE* 1.3 75.4 - - - +
425F THR* 1.3 57.8 + - - +
427F LEU* 3.4 4.3 + - - +
428F SER* 2.7 35.1 + - - -
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Residues in contact with THR 425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E GLU* 2.3 34.3 + - - -
421E PRO* 6.0 0.7 - - - -
424E THR* 5.0 2.7 - - - -
425E THR* 6.1 2.0 - - - -
279F THR* 3.1 10.8 + - - +
280F LEU* 3.8 19.3 - - - -
283F GLU* 3.7 14.6 - - + -
421F PRO 3.2 18.6 + - - +
422F CYS* 3.5 13.2 - - - +
424F THR* 1.3 79.7 + - - +
426F ALA* 1.3 64.2 + - - +
428F SER* 4.0 5.9 - - - -
429F PHE* 3.0 28.8 + - - +
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Residues in contact with ALA 426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F THR* 5.2 0.7 - - - -
280F LEU* 3.6 21.8 - - + -
330F SER* 3.9 6.1 - - - +
333F ILE* 3.8 22.3 - - + +
337F GLN* 5.4 0.2 - - - +
406F TRP* 3.3 25.9 - - + -
422F CYS 3.1 18.8 + - - +
425F THR* 1.3 76.8 - - - +
427F LEU* 1.3 61.3 + - - +
429F PHE* 3.5 2.0 + - - +
430F TYR* 3.1 22.3 + - - +
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Residues in contact with LEU 427 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414E VAL* 3.6 35.0 - - + -
403F GLN* 5.3 0.7 - - + -
406F TRP* 3.3 37.0 - - + -
407F ARG* 3.8 42.0 - - + +
410F VAL* 3.8 22.7 - - + -
423F PHE 3.3 14.9 + - - +
424F THR* 3.9 3.4 - - - +
426F ALA* 1.3 78.3 - - - +
428F SER* 1.3 63.5 + - - +
430F TYR* 3.3 4.6 + - + +
431F ASP* 3.1 26.5 + - - +
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Residues in contact with SER 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E LEU* 5.3 0.7 - - - +
419E PRO* 3.4 17.9 - - - +
420E MET* 3.5 11.1 + - - +
421E PRO* 3.9 32.3 - - - +
424E THR* 3.4 19.8 + - - +
424F THR 2.7 23.8 + - - -
425F THR* 4.0 6.1 - - - -
427F LEU* 1.3 75.8 - - - +
429F PHE* 1.3 61.3 + - - +
431F ASP* 4.8 1.3 - - - -
432F GLY* 3.1 17.0 + - - -
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Residues in contact with PHE 429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290E LEU* 3.6 39.5 - - + -
421E PRO* 6.1 0.7 - - - -
277F PRO* 3.6 26.0 - - + -
279F THR* 4.2 8.5 - - + +
333F ILE* 3.6 22.7 - - + -
336F ALA* 5.7 1.3 - - + -
337F GLN* 3.4 28.0 - - + +
340F MET* 4.1 24.5 - - + -
388F ASN* 6.0 0.2 - - - -
390F LEU* 4.5 9.6 - - + -
425F THR 3.0 19.9 + - - +
426F ALA 3.8 3.6 - - - +
427F LEU 3.2 0.2 - - - -
428F SER* 1.3 75.7 - - - +
430F TYR* 1.3 56.8 + - - +
433F TYR* 2.7 52.4 + + + +
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Residues in contact with TYR 430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304E LEU* 3.5 39.4 - - + +
305E LYS 3.3 17.6 + - - -
333F ILE* 4.1 19.7 - - + -
390F LEU* 4.3 12.6 - - + -
396F LYS 5.4 1.4 + - - -
399F VAL* 3.7 26.2 - - + +
400F GLU* 5.0 4.9 + - - +
403F GLN* 3.9 27.8 + - + -
406F TRP* 4.1 17.7 - + + -
407F ARG* 4.5 2.5 - - - -
426F ALA 3.1 17.9 + - - +
427F LEU* 3.3 6.2 + - + +
429F PHE* 1.3 80.9 - - - +
431F ASP* 1.3 69.6 + - - +
433F TYR* 3.9 2.8 - + - -
434F ARG* 3.1 35.2 + - - +
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Residues in contact with ASP 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413E GLY 5.0 0.2 - - - +
414E VAL* 5.3 1.6 - - - -
417E GLY 3.3 25.8 - - - +
418E ILE 3.9 4.9 + - - +
419E PRO* 3.7 17.6 - - + +
407F ARG* 2.4 46.9 + - - -
427F LEU* 3.1 18.9 + - - +
428F SER* 4.8 0.7 - - - -
430F TYR* 1.3 77.8 - - - +
432F GLY* 1.3 60.2 + - - +
434F ARG* 3.0 19.8 + - - +
435F HIS* 2.5 29.4 + - - -
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Residues in contact with GLY 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290E LEU* 3.8 16.2 - - - -
297E ARG* 3.2 18.5 - - - -
419E PRO* 3.5 18.3 - - - +
428F SER 3.1 12.9 + - - -
429F PHE 3.7 2.2 - - - -
431F ASP* 1.3 78.5 - - - +
433F TYR* 1.3 60.5 + - - +
434F ARG 3.4 0.5 + - - -
435F HIS 3.5 6.8 + - - +
438F LEU* 3.5 13.9 - - - +
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Residues in contact with TYR 433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290E LEU* 3.9 21.0 - - + +
293E LEU* 4.9 8.3 - - + -
296E GLU* 2.4 50.0 + - + +
297E ARG* 3.2 21.5 - - + +
300E ALA* 3.2 33.0 - - + +
304E LEU* 4.4 6.3 - - + -
340F MET* 5.1 0.7 - - - -
388F ASN* 3.3 22.5 - - - +
390F LEU* 3.6 33.4 - - + -
391F LEU* 4.1 8.2 - - + +
429F PHE* 2.7 40.3 + + + +
430F TYR* 4.1 4.5 - - - +
432F GLY* 1.3 72.8 - - - +
434F ARG* 1.3 56.8 + - - +
435F HIS 3.5 0.2 - - - -
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Residues in contact with ARG 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297E ARG 4.7 0.2 - - - -
300E ALA* 4.4 2.9 - - - -
301E SER* 3.2 26.8 - - - +
304E LEU* 3.6 29.1 - - + +
305E LYS* 4.3 6.0 - - - +
306E GLY* 3.6 33.4 - - - +
307E PRO* 3.6 10.3 + - - +
416E ALA 4.2 2.6 + - - -
417E GLY* 2.9 35.2 + - - -
407F ARG* 4.1 0.6 - - - +
430F TYR* 3.1 29.2 + - - +
431F ASP* 3.0 26.1 + - - +
433F TYR* 1.3 76.9 - - - +
435F HIS* 1.3 76.5 + - - +
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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