Contacts of the helix formed by residues 393 - 416 (chain P) in PDB entry 5D4E
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 THR 393 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387P GLY* 4.8 0.4 - - - -
392P VAL* 1.3 79.8 - - - +
394P ARG* 1.3 69.5 + - + +
395P GLU* 3.8 18.4 - - + +
396P ARG* 2.9 31.4 + - - +
397P ILE* 2.9 11.8 + - - +
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Residues in contact with ARG 394 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383P LEU* 3.4 46.8 - - - +
384P GLU* 3.3 34.1 + - + -
387P GLY* 4.8 2.4 - - - -
392P VAL 3.9 1.8 + - - -
393P THR* 1.3 78.0 - - + +
395P GLU* 1.3 66.9 + - + +
397P ILE* 3.3 12.8 - - - +
398P ARG* 2.9 36.7 + - - +
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Residues in contact with GLU 395 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393P THR* 3.1 12.7 - - + +
394P ARG* 1.3 91.3 + - + +
396P ARG* 1.3 59.0 + - + +
398P ARG* 2.6 39.4 + - - +
399P GLN* 2.9 41.8 + - + +
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Residues in contact with ARG 396 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364P ARG* 3.8 25.0 - - - +
392P VAL* 4.0 20.1 - - + +
393P THR* 2.9 22.4 + - - +
395P GLU* 1.3 81.5 - - + +
397P ILE* 1.3 56.3 + - - +
399P GLN* 3.2 10.5 + - - +
400P ILE* 2.9 59.6 + - - +
403P LYS* 4.8 6.9 - - - +
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Residues in contact with ILE 397 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364P ARG* 5.4 0.2 - - + -
368P VAL* 3.6 27.4 - - + +
383P LEU* 3.4 36.0 - - + +
386P VAL* 3.6 22.2 - - + +
387P GLY* 3.8 5.4 - - - +
390P PHE* 3.8 19.5 - - + -
392P VAL* 3.6 24.8 - - + +
393P THR 2.9 5.8 + - - +
394P ARG* 3.3 16.6 - - - +
396P ARG* 1.3 74.6 - - - +
398P ARG* 1.3 65.9 + - - +
400P ILE* 3.4 14.4 + - + +
401P GLU* 2.9 27.0 + - - +
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Residues in contact with ARG 398 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383P LEU* 3.7 26.9 - - + -
394P ARG* 2.9 23.5 + - - +
395P GLU* 2.6 41.3 + - - +
397P ILE* 1.3 76.7 - - - +
399P GLN* 1.3 65.5 + - - +
401P GLU* 3.3 16.9 + - - +
402P ASN* 2.9 67.9 + - - +
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Residues in contact with GLN 399 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395P GLU* 2.9 35.7 + - + +
396P ARG* 3.5 12.1 - - - +
398P ARG* 1.3 86.2 + - - +
400P ILE* 1.3 59.8 - - + +
402P ASN* 3.3 12.2 + - - +
403P LYS* 2.9 31.8 + - + +
406P ARG* 5.2 10.2 + - - +
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Residues in contact with ILE 400 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364P ARG* 3.6 35.9 - - + +
365P GLU* 3.7 31.9 - - + +
368P VAL* 3.9 11.7 - - + -
392P VAL* 5.0 3.4 - - + -
396P ARG* 2.9 41.0 + - - +
397P ILE* 3.6 24.0 - - + +
398P ARG 3.3 0.2 - - - -
399P GLN* 1.3 74.5 - - - +
401P GLU* 1.3 60.5 + - - +
403P LYS* 3.1 20.2 - - - +
404P ALA* 2.9 28.8 + - - +
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Residues in contact with GLU 401 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368P VAL* 4.0 9.4 - - + +
369P LEU* 3.7 24.1 - - + +
372P ARG* 3.2 38.9 + - + +
373P LYS* 4.4 14.0 + - - +
383P LEU* 3.5 20.2 - - + +
397P ILE 2.9 14.5 + - - +
398P ARG* 3.4 14.7 - - - +
400P ILE* 1.3 77.3 - - - +
402P ASN* 1.3 61.8 + - - +
404P ALA* 3.6 1.4 - - - +
405P LEU* 2.9 33.8 + - + +
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Residues in contact with ASN 402 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398P ARG* 2.9 57.9 + - - +
399P GLN* 3.5 18.4 + - - +
400P ILE 3.2 0.2 - - - -
401P GLU* 1.3 82.9 - - - +
403P LYS* 1.3 57.2 + - - +
405P LEU* 3.4 8.4 + - - +
406P ARG* 2.9 48.2 + - - +
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Residues in contact with LYS 403 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362P SER* 5.5 2.0 + - - -
364P ARG* 4.7 11.3 - - - +
365P GLU* 3.4 21.4 + - - +
396P ARG* 4.8 5.5 - - - +
399P GLN* 2.9 19.2 + - + +
400P ILE* 3.1 41.0 - - - +
402P ASN* 1.3 73.5 - - - +
404P ALA* 1.3 55.7 + - - +
406P ARG* 3.7 20.7 - - - +
407P LYS* 2.9 52.5 + - - +
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Residues in contact with ALA 404 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361P LEU* 4.0 10.7 - - + +
365P GLU* 3.6 29.8 - - + +
369P LEU* 3.7 23.1 - - + -
400P ILE 2.9 18.8 + - - +
401P GLU 3.6 3.8 - - - +
403P LYS* 1.3 74.6 - - - +
405P LEU* 1.3 61.2 + - - +
407P LYS* 3.2 5.6 + - - +
408P LEU* 2.9 31.5 + - - +
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Residues in contact with LEU 405 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773M LEU* 5.0 1.1 - - + -
776M SER* 4.0 42.2 - - - +
777M ILE* 4.1 17.5 - - + +
369P LEU* 4.0 17.9 - - + +
373P LYS* 5.0 6.1 - - - +
401P GLU* 2.9 21.3 + - + +
402P ASN* 3.8 8.1 - - - +
404P ALA* 1.3 76.4 - - - +
406P ARG* 1.3 57.1 + - - +
408P LEU* 3.4 4.7 + - + +
409P LYS* 2.9 49.8 + - - +
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Residues in contact with ARG 406 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399P GLN* 5.2 8.7 + - - +
402P ASN* 2.9 31.0 + - - +
403P LYS* 3.7 28.1 - - - +
405P LEU* 1.3 74.5 - - - +
407P LYS* 1.3 59.9 + - - +
409P LYS* 3.1 13.9 + - + +
410P TYR* 2.9 27.6 + - + +
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Residues in contact with LYS 407 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360P LYS 5.9 0.4 - - - +
361P LEU* 3.7 14.6 - - + -
362P SER* 6.1 0.2 - - - -
365P GLU* 3.5 32.4 + - - +
403P LYS* 2.9 38.0 + - - +
404P ALA 3.6 4.5 - - - +
406P ARG* 1.3 75.9 - - + +
408P LEU* 1.3 57.7 + - - +
410P TYR* 3.2 6.3 + - - +
411P HIS* 2.9 47.5 + - + +
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Residues in contact with LEU 408 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773M LEU* 4.8 1.8 - - + -
777M ILE* 4.2 33.6 - - + +
357P ALA* 3.3 39.3 - - + +
358P LEU* 3.7 15.0 - - + -
361P LEU* 3.9 17.5 - - + -
369P LEU* 3.6 28.9 - - + -
404P ALA 2.9 13.8 + - - +
405P LEU* 3.5 10.1 - - - +
407P LYS* 1.3 78.3 - - - +
409P LYS* 1.3 56.5 + - - +
411P HIS* 3.8 8.1 - - + +
412P GLU* 2.9 29.8 + - - +
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Residues in contact with LYS 409 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776M SER 3.9 12.7 + - - -
777M ILE* 3.3 31.6 - - - +
778M PHE 5.4 0.6 - - - -
779M GLY* 5.3 6.6 - - - +
405P LEU* 2.9 35.9 + - + +
406P ARG* 3.1 14.3 + - + +
408P LEU* 1.3 73.4 - - - +
410P TYR* 1.3 59.8 + - - +
412P GLU* 3.4 6.7 + - - +
413P SER* 2.9 28.9 + - - -
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Residues in contact with TYR 410 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406P ARG* 2.9 12.7 + - + +
407P LYS* 3.2 10.1 + - - +
409P LYS* 1.3 75.1 - - - +
411P HIS* 1.3 81.5 + + - +
413P SER* 2.6 24.5 + - - -
414P ARG* 2.9 36.0 + - + +
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Residues in contact with HIS 411 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357P ALA* 5.0 3.1 - - + +
360P LYS* 3.8 38.0 + - + +
361P LEU* 4.5 7.8 - - + +
407P LYS* 2.9 37.2 + - + +
408P LEU* 3.9 12.1 - - + +
410P TYR* 1.3 95.7 - + - +
412P GLU* 1.3 57.1 + - - +
414P ARG* 3.6 16.2 + - - +
415P THR* 2.8 38.8 + - + +
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Residues in contact with GLU 412 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777M ILE* 4.5 10.1 - - + -
778M PHE* 3.2 42.8 - - + -
408P LEU 2.9 18.9 + - - +
409P LYS* 3.7 7.9 - - - +
411P HIS* 1.3 74.7 - - - +
413P SER* 1.3 61.9 + - - +
414P ARG 3.1 1.3 - - - -
415P THR* 4.3 1.9 + - - -
416P ARG* 2.8 46.9 + - - +
417P LYS 3.8 1.7 + - - -
418P LEU* 3.1 35.8 + - + +
419P ARG* 3.5 9.4 + - - +
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Residues in contact with SER 413 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409P LYS 2.9 15.6 + - - -
410P TYR* 2.6 30.1 + - - -
412P GLU* 1.3 76.5 - - - +
414P ARG* 1.3 60.6 + - - +
416P ARG* 3.8 12.6 - - - +
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Residues in contact with ARG 414 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410P TYR* 2.9 38.3 + - + +
411P HIS* 3.6 14.4 + - - +
412P GLU 3.1 0.4 - - - -
413P SER* 1.3 81.4 + - - +
415P THR* 1.3 77.6 + - + +
416P ARG* 3.8 5.7 - - - +
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Residues in contact with THR 415 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360P LYS* 5.9 4.5 - - - +
411P HIS* 2.8 29.6 + - + +
412P GLU* 4.3 2.4 + - - -
414P ARG* 1.3 90.3 - - + +
416P ARG* 1.3 71.0 + - - +
417P LYS* 3.3 31.5 + - - +
418P LEU* 5.4 2.1 - - - +
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Residues in contact with ARG 416 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668N PRO* 6.1 1.0 - - - +
412P GLU* 2.8 33.7 + - - +
413P SER* 3.8 16.6 - - - +
414P ARG 3.8 4.5 - - - +
415P THR* 1.3 82.0 + - - +
417P LYS* 1.3 62.2 + - - +
418P LEU 3.5 2.0 - - - -
419P ARG* 4.1 26.5 + - + +
420P ASP* 4.2 6.1 - - - +
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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
------------------------------------------------------------
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