Contacts of the helix formed by residues 408 - 426 (chain A) in PDB entry 5ULM
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 ASP 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A MET* 4.1 16.7 - - - +
401A PHE* 3.2 12.4 - - - -
404A SER* 2.9 25.3 + - - +
406A PHE 3.6 0.4 - - - -
407A THR* 1.3 73.3 + - - +
409A THR* 1.3 56.5 + - - +
410A GLU* 3.5 12.3 + - - +
411A SER* 2.6 41.0 + - - -
412A ARG 3.1 20.4 + - - -
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Residues in contact with THR 409 (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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401A PHE* 4.6 2.5 - - + -
406A PHE 4.5 8.1 - - - +
407A THR* 2.8 21.0 + - - +
408A ASP* 1.3 69.8 - - - +
410A GLU* 1.3 62.8 + - - +
412A ARG* 3.3 40.0 - - - +
413A ASP* 3.0 33.5 + - - -
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Residues in contact with GLU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ASP* 3.3 9.8 + - - +
409A THR* 1.3 77.6 + - - +
411A SER* 1.3 61.3 + - - +
413A ASP* 3.2 7.1 + - - +
414A HIS* 2.9 51.5 + - + -
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Residues in contact with SER 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A TYR* 3.3 38.5 - - - +
400A MET* 3.4 26.0 - - - +
401A PHE 4.2 2.0 - - - -
408A ASP* 2.6 34.8 + - - -
410A GLU* 1.3 78.6 - - - +
412A ARG* 1.3 57.9 + - - +
414A HIS* 3.4 2.4 + - - -
415A GLY* 2.8 25.8 + - - -
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Residues in contact with ARG 412 (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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397A TYR 5.2 0.4 - - - -
398A LYS 5.9 0.2 - - - +
401A PHE* 3.5 49.5 - - + +
408A ASP 3.1 6.0 + - - +
409A THR* 3.3 38.6 - - - +
411A SER* 1.3 74.6 - - - +
413A ASP* 1.3 89.8 + - - +
415A GLY* 3.3 2.5 + - - -
416A ALA* 2.9 27.4 + - + +
438A LEU* 3.9 23.3 - - + +
441A ALA 3.6 15.1 + - - -
442A ALA* 3.6 35.2 + - - +
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Residues in contact with ASP 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A THR 3.0 14.9 + - - +
410A GLU* 3.2 6.6 + - - +
412A ARG* 1.3 109.2 + - - +
414A HIS* 1.3 67.6 + - + +
416A ALA* 3.4 9.4 + - - +
417A SER* 3.0 22.9 + - - -
442A ALA* 4.2 7.3 - - - +
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Residues in contact with HIS 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A TYR* 3.8 35.1 - + + -
410A GLU* 2.9 44.8 + - + +
411A SER* 3.8 6.6 + - - +
413A ASP* 1.3 75.8 - - + +
415A GLY* 1.3 64.2 + - - +
417A SER* 2.7 25.0 + - - -
418A TRP* 3.1 16.9 + - + -
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Residues in contact with GLY 415 (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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394A GLY* 4.0 8.3 - - - -
397A TYR* 3.5 21.7 - - - +
398A LYS 4.6 0.2 - - - -
411A SER 2.8 12.4 + - - -
412A ARG 3.7 3.6 - - - -
414A HIS* 1.3 76.1 - - - +
416A ALA* 1.3 62.6 + - - +
418A TRP* 3.3 2.9 + - - +
419A PHE* 3.1 27.9 + - - -
438A LEU* 3.6 13.9 - - - -
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Residues in contact with ALA 416 (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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412A ARG* 2.9 14.8 + - + +
413A ASP* 3.5 13.5 - - - +
414A HIS 3.3 0.2 - - - -
415A GLY* 1.3 75.9 - - - +
417A SER* 1.3 57.3 + - - +
419A PHE* 3.8 1.5 - - - -
420A LYS* 2.8 31.6 + - - +
435A TYR* 3.5 22.2 - - + +
438A LEU* 3.4 25.6 - - + +
439A LEU* 4.9 5.8 - - + -
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Residues in contact with SER 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ASP 3.0 13.3 + - - -
414A HIS* 2.7 26.2 + - - +
416A ALA* 1.3 75.8 - - - +
418A TRP* 1.3 64.8 + - - +
420A LYS* 3.4 12.6 + - - +
421A LYS* 3.0 28.9 + - - +
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Residues in contact with TRP 418 (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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376A ILE* 4.1 24.6 - - + +
379A VAL* 3.6 40.8 - - + -
380A GLN* 3.8 30.3 - - + -
390A TYR* 3.7 33.5 - + - +
393A VAL* 3.5 21.8 - - + -
394A GLY* 3.9 18.2 - - - +
397A TYR* 3.8 22.7 + + - -
414A HIS* 3.1 26.0 + - + +
415A GLY 3.3 3.3 + - - +
417A SER* 1.3 88.8 + - - +
419A PHE* 1.3 61.4 + - - +
421A LYS* 3.3 8.5 + - + +
422A ALA* 3.1 21.3 + - - +
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Residues in contact with PHE 419 (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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391A CYS* 3.5 44.6 - - + -
394A GLY* 3.4 18.8 - - - -
395A ARG* 3.5 23.3 - - + -
398A LYS* 4.5 5.8 - - + -
415A GLY 3.1 24.8 + - - +
416A ALA 3.9 2.7 - - - +
418A TRP* 1.3 71.5 - - - +
420A LYS* 1.3 61.0 + - - +
422A ALA* 3.4 5.2 + - - +
423A PHE* 2.8 30.7 + - - +
430A GLN* 5.5 0.7 - - - -
431A SER* 3.7 17.4 - - - +
434A ASN* 3.5 44.0 - - + -
435A TYR* 3.9 10.5 - - + +
438A LEU* 3.9 17.5 - - + -
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Residues in contact with LYS 420 (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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416A ALA 2.8 21.2 + - - +
417A SER* 3.4 11.7 - - - +
419A PHE* 1.3 72.5 - - - +
421A LYS* 1.3 57.7 + - - +
423A PHE* 3.1 5.3 + - + +
424A GLU* 2.9 64.6 + - + +
435A TYR* 2.9 40.9 + - + +
451A GLU* 2.8 33.2 + - - +
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Residues in contact with LYS 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A TYR* 3.7 38.3 + - + -
417A SER 3.0 13.7 + - - +
418A TRP* 3.3 11.2 + - + +
420A LYS* 1.3 74.6 - - - +
422A ALA* 1.3 57.4 + - - +
424A GLU* 3.8 10.2 - - + +
425A SER* 2.8 50.3 + - - +
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Residues in contact with ALA 422 (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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387A SER* 4.4 7.4 + - - +
390A TYR* 3.6 35.3 - - + -
391A CYS* 4.2 9.4 - - - -
418A TRP 3.1 6.5 + - - +
419A PHE* 3.4 9.9 - - - +
421A LYS* 1.3 78.7 - - - +
423A PHE* 1.3 54.6 + - - +
425A SER* 3.2 1.2 + - - -
426A GLU* 2.7 39.4 + - - +
431A SER* 3.6 17.7 - - - -
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Residues in contact with PHE 423 (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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419A PHE 2.8 20.2 + - - +
420A LYS* 3.5 7.6 - - - +
422A ALA* 1.3 73.8 - - - +
424A GLU* 1.3 65.0 + - + +
427A PRO* 3.2 39.1 - - + +
428A THR 3.5 17.3 - - - -
431A SER* 3.3 12.5 + - - +
432A GLY* 3.4 27.8 - - - -
435A TYR* 4.6 15.5 - + + -
455A VAL* 4.0 26.5 - - + -
458A LYS* 3.5 35.7 - - + -
459A LEU* 4.5 3.4 - - + -
462A LEU* 4.0 13.7 - - + -
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Residues in contact with GLU 424 (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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420A LYS* 2.9 57.0 + - + +
421A LYS* 4.0 9.9 - - + +
423A PHE* 1.3 82.8 - - + +
425A SER* 1.3 64.0 + - - +
427A PRO* 4.6 5.2 - - - +
435A TYR* 5.8 0.6 - - + -
451A GLU* 5.7 0.2 - - - +
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Residues in contact with SER 425 (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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385A VAL 4.4 5.5 + - - -
390A TYR* 4.1 19.6 + - - -
421A LYS* 2.8 36.7 + - - +
422A ALA* 3.7 2.7 - - - -
424A GLU* 1.3 80.3 - - - +
426A GLU* 1.3 62.5 + - - +
427A PRO* 4.1 1.7 - - - +
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Residues in contact with GLU 426 (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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386A ALA* 4.9 4.2 - - - +
387A SER* 4.2 31.7 + - - +
422A ALA 2.7 19.7 + - - +
425A SER* 1.3 79.3 - - - +
427A PRO* 1.3 72.2 - - + +
428A THR* 3.2 26.7 + - + +
431A SER* 4.2 0.3 + - - -
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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