Contacts of the helix formed by residues 420 - 434 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200E GLU* 3.8 7.9 - - + -
204E LEU* 4.1 18.2 - - + -
409E ALA 4.1 9.6 - - - +
410E VAL* 3.3 38.6 - - + +
413E GLY* 3.8 17.3 - - - -
414E VAL* 3.7 22.4 - - + +
418E ILE* 3.2 20.0 + - + +
419E PRO* 1.3 73.9 - - - +
421E PRO* 1.3 64.8 - - - +
422E CYS 3.3 2.7 - - - -
423E PHE* 3.8 27.1 - - + -
424E THR* 2.8 30.9 + - + +
428F SER* 3.7 9.5 + - - +
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Residues in contact with PRO 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E GLN* 4.2 9.9 - - - +
200E GLU* 3.0 17.3 - - + +
283E GLU* 3.6 37.0 - - + +
287E ALA* 4.8 9.2 - - + -
290E LEU* 6.3 2.9 - - + -
419E PRO* 3.4 12.6 - - + +
420E MET* 1.3 86.3 - - - +
422E CYS* 1.3 57.3 + - - +
424E THR* 3.3 5.3 + - - +
425E THR* 3.1 30.0 + - - +
425F THR* 5.9 0.8 - - - +
428F SER* 3.9 20.6 - - - +
429F PHE* 6.1 0.7 - - - -
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Residues in contact with CYS 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E GLY 4.7 0.9 - - - -
196E GLN* 3.5 32.3 - - - -
197E LEU* 3.6 18.6 - - + -
200E GLU* 2.6 21.1 + - - +
280E LEU* 3.7 38.8 - - + +
283E GLU* 4.4 1.8 - - - -
284E ALA* 4.1 8.7 - - - -
330E SER* 4.2 0.2 + - - -
421E PRO* 1.3 73.4 - - - +
423E PHE* 1.3 63.3 + - - +
425E THR* 3.4 6.5 - - - +
426E ALA* 3.0 27.2 + - - +
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Residues in contact with PHE 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E LEU* 3.8 24.7 - - + -
200E GLU* 3.0 40.2 + - + +
201E ALA* 4.4 5.4 - - + -
204E LEU* 4.0 20.2 - - + -
323E ILE* 4.7 3.1 - - + -
326E ALA* 3.7 14.8 - - + -
327E LEU* 3.7 37.0 - - + -
330E SER* 3.2 15.9 - - - -
406E TRP* 3.7 9.7 + - - +
409E ALA* 6.2 1.8 - - + -
410E VAL* 4.2 17.0 - - + +
420E MET* 3.5 28.0 + - + -
422E CYS* 1.3 77.9 - - - +
424E THR* 1.3 62.3 + - - +
426E ALA* 4.0 0.5 - - - +
427E LEU* 3.1 24.3 + - - +
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Residues in contact with THR 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410E VAL* 4.0 24.0 - - + -
414E VAL* 4.9 6.5 - - + -
420E MET* 2.8 36.2 + - + +
421E PRO* 3.3 6.1 + - - +
423E PHE* 1.3 75.3 - - - +
425E THR* 1.3 60.0 + - - +
427E LEU* 3.4 5.9 + - - +
428E SER* 2.8 34.7 + - - -
424F THR* 3.5 31.2 + - + +
425F THR* 4.7 1.7 + - - -
428F SER* 3.4 17.0 + - - +
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Residues in contact with THR 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E THR* 3.1 15.0 + - - +
280E LEU* 3.6 29.2 - - - +
283E GLU* 3.9 7.4 - - + -
421E PRO 3.1 18.4 - - - +
422E CYS* 3.4 10.5 - - - +
424E THR* 1.3 80.0 + - - +
426E ALA* 1.3 63.7 + - - +
428E SER* 4.1 5.6 - - - -
429E PHE* 3.1 27.7 + - - +
283F GLU* 2.4 32.0 + - - -
421F PRO* 6.0 0.9 - - - -
424F THR* 5.1 2.2 - - - -
425F THR* 6.1 2.2 - - - -
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Residues in contact with ALA 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E THR* 5.1 0.4 - - - -
280E LEU* 3.7 20.2 - - + -
330E SER* 3.7 8.3 - - - +
333E ILE* 3.6 25.7 - - + +
406E TRP* 3.3 24.5 - - + -
422E CYS 3.0 20.1 + - - +
425E THR* 1.3 78.9 - - - +
427E LEU* 1.3 63.4 + - - +
429E PHE 3.6 0.2 + - - -
430E TYR* 3.1 17.5 + - - +
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Residues in contact with LEU 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403E GLN* 5.8 0.2 - - + -
406E TRP* 3.3 35.6 - - + -
407E ARG* 3.8 37.5 - - + +
410E VAL* 4.1 18.6 - - + -
423E PHE 3.1 17.7 + - - +
424E THR* 3.8 4.7 - - - +
426E ALA* 1.3 76.1 - - - +
428E SER* 1.3 65.7 + - - +
430E TYR* 3.2 3.9 + - + +
431E ASP* 3.0 28.7 + - - +
414F VAL* 3.6 38.6 - - + -
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Residues in contact with SER 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424E THR 2.8 23.7 + - - -
425E THR* 4.1 5.2 - - - -
427E LEU* 1.3 76.6 - - - +
429E PHE* 1.3 58.0 + - - +
431E ASP* 3.6 1.5 + - - -
432E GLY* 3.0 22.5 + - - -
290F LEU* 5.1 1.2 - - - +
419F PRO* 3.5 17.1 - - - +
420F MET 3.6 12.8 + - - -
421F PRO* 3.8 30.2 - - - +
424F THR* 3.4 19.1 + - - +
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Residues in contact with PHE 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277E PRO* 3.6 34.8 - - + -
279E THR* 4.1 7.6 - - + +
333E ILE* 3.6 19.3 - - + -
336E ALA* 5.3 2.0 - - + -
337E GLN* 3.2 30.7 - - + +
340E MET* 3.9 25.6 - - + -
388E ASN* 5.3 1.1 - - - -
390E LEU* 4.3 13.9 - - + -
425E THR 3.1 20.3 + - - +
426E ALA 3.9 3.4 - - - +
428E SER* 1.3 75.7 - - - +
430E TYR* 1.3 60.5 + - - +
432E GLY 3.7 0.2 - - - -
433E TYR* 2.8 46.9 + + + +
290F LEU* 3.8 25.7 - - + +
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Residues in contact with TYR 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333E ILE* 3.9 21.3 - - + -
390E LEU* 4.2 11.0 - - + -
396E LYS* 3.3 18.5 + - - -
399E VAL* 3.5 27.3 - - + +
403E GLN* 3.6 17.9 + - + -
406E TRP* 4.1 18.8 - + + -
407E ARG* 4.4 2.7 - - - -
426E ALA 3.1 17.7 + - - +
427E LEU* 3.2 4.7 + - + +
429E PHE* 1.3 82.0 - - - +
431E ASP* 1.3 67.9 + - - +
433E TYR* 4.1 2.0 - - - +
434E ARG* 3.0 38.5 + - - +
304F LEU* 3.9 27.0 - - + +
305F LYS 2.6 30.8 + - - -
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Residues in contact with ASP 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407E ARG* 2.4 48.7 + - - -
427E LEU* 3.0 22.9 + - - +
428E SER* 5.1 0.3 - - - -
430E TYR* 1.3 77.6 - - - +
432E GLY* 1.3 58.4 + - - +
434E ARG* 2.9 21.2 + - - +
435E HIS* 3.2 28.8 - - - -
413F GLY 5.0 0.5 - - - +
414F VAL* 5.5 0.7 - - - -
417F GLY* 3.4 24.9 - - - +
418F ILE 4.2 3.3 + - - +
419F PRO* 4.0 16.9 - - + +
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Residues in contact with GLY 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428E SER 3.0 16.3 + - - -
429E PHE 3.7 2.5 - - - -
431E ASP* 1.3 76.2 - - - +
433E TYR* 1.3 64.1 + - - +
434E ARG 3.2 0.2 - - - -
435E HIS* 3.3 11.1 + - - +
438E LEU* 3.7 10.5 - - - +
290F LEU* 3.9 16.8 - - - -
297F ARG* 3.4 16.8 - - - -
419F PRO* 3.8 13.9 - - - +
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Residues in contact with TYR 433 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340E MET* 5.4 0.4 - - + -
387E GLN* 3.5 11.9 + - - -
388E ASN* 3.3 43.0 - - + +
390E LEU* 3.7 15.0 - - + -
391E LEU* 4.0 11.3 - - + +
429E PHE* 2.8 36.0 + + + +
430E TYR 4.1 2.5 - - - +
432E GLY* 1.3 73.0 - - - +
434E ARG* 1.3 59.1 + - - +
435E HIS 3.4 0.2 - - - -
290F LEU* 4.0 22.9 - - + +
293F LEU* 4.6 11.2 - - + -
296F GLU* 3.9 23.8 + - + +
297F ARG* 3.7 17.6 - - + +
300F ALA* 3.4 31.1 - - + +
304F LEU* 3.5 22.7 - - + -
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Residues in contact with ARG 434 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430E TYR* 3.0 26.1 + - + +
431E ASP* 2.9 22.8 + - - +
433E TYR* 1.3 76.0 - - - +
435E HIS* 1.3 86.1 + - - +
300F ALA* 4.7 2.0 - - - -
301F SER* 3.2 25.5 - - - +
304F LEU* 3.8 32.7 + - + +
305F LYS* 3.5 21.2 - - - +
306F GLY* 3.4 21.0 - - - +
307F PRO* 3.5 10.3 + - - +
416F ALA 4.5 2.0 + - - -
417F GLY* 3.0 37.2 + - - -
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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