Contacts of the helix formed by residues 393 - 416 (chain F) in PDB entry 4OIP
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387F GLY* 4.9 0.7 - - - -
392F VAL* 1.3 78.6 - - - +
394F ARG* 1.3 68.7 + - + +
395F GLU* 3.9 14.6 - - + +
396F ARG* 3.0 14.9 + - - +
397F ILE* 2.9 28.0 + - - +
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Residues in contact with ARG 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383F LEU* 3.4 47.3 - - + +
384F GLU* 2.7 37.4 + - + +
387F GLY* 5.2 0.6 - - - -
392F VAL 4.0 1.0 + - - -
393F THR* 1.3 79.6 - - + +
395F GLU* 1.3 69.8 + - + +
397F ILE* 3.2 11.5 - - - +
398F ARG* 2.9 32.0 + - - +
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Residues in contact with GLU 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393F THR* 3.2 13.1 - - + +
394F ARG* 1.3 88.9 + - + +
396F ARG* 1.3 58.9 + - - +
398F ARG* 2.7 35.0 + - - +
399F GLN* 2.9 46.4 + - + +
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Residues in contact with ARG 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364F ARG* 3.2 35.5 - - - +
392F VAL* 3.9 25.8 - - + +
393F THR* 3.0 25.3 + - - +
395F GLU* 1.3 78.6 - - - +
397F ILE* 1.3 60.3 + - - +
399F GLN* 3.1 10.6 + - - +
400F ILE* 2.9 46.8 + - + +
403F LYS* 5.4 1.4 - - - +
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Residues in contact with ILE 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368F VAL* 3.6 28.5 - - + +
383F LEU* 3.3 40.6 - - + +
386F VAL* 3.6 34.1 - - + +
387F GLY* 3.9 4.9 - - - +
390F PHE* 3.9 6.7 - - + -
392F VAL* 3.7 17.5 - - + +
393F THR 2.9 11.7 + - - +
394F ARG* 3.2 15.7 - - - +
396F ARG* 1.3 76.0 - - - +
398F ARG* 1.3 62.1 + - - +
400F ILE* 3.3 16.0 - - + +
401F GLU* 2.9 28.4 + - - +
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Residues in contact with ARG 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372F ARG* 6.2 0.2 - - - +
383F LEU* 3.7 25.3 - - + +
394F ARG* 2.9 20.3 + - - +
395F GLU* 2.7 34.8 + - - +
397F ILE* 1.3 75.3 - - - +
399F GLN* 1.3 74.0 + - - +
401F GLU* 3.4 17.1 + - - +
402F ASN* 2.9 61.9 + - - +
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Residues in contact with GLN 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395F GLU* 2.9 42.0 + - + +
396F ARG* 3.3 13.5 - - - +
398F ARG* 1.3 89.6 + - - +
400F ILE* 1.3 59.6 + - + +
402F ASN* 3.1 11.3 + - - +
403F LYS* 2.9 27.5 + - - +
406F ARG* 4.9 8.1 + - - +
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Residues in contact with ILE 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364F ARG* 4.2 30.3 - - + +
365F GLU* 4.1 7.5 - - + +
368F VAL* 3.9 15.3 - - + -
392F VAL* 5.2 1.6 - - + -
396F ARG* 2.9 39.1 + - + +
397F ILE* 3.3 42.8 - - + +
399F GLN* 1.3 73.4 - - + +
401F GLU* 1.3 59.7 + - - +
403F LYS* 3.2 35.3 - - + +
404F ALA* 2.9 28.9 + - - +
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Residues in contact with GLU 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368F VAL* 4.1 9.4 - - + -
369F LEU* 3.6 23.0 - - + +
372F ARG* 3.0 49.9 + - + +
373F LYS* 4.2 13.8 + - - +
383F LEU* 3.9 12.5 - - + +
397F ILE 2.9 19.6 + - - +
398F ARG* 3.5 14.4 - - - +
400F ILE* 1.3 77.9 - - - +
402F ASN* 1.3 60.4 + - - +
404F ALA* 3.2 3.3 + - - +
405F LEU* 2.9 32.4 + - + +
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Residues in contact with ASN 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398F ARG* 2.9 48.8 + - - +
399F GLN* 3.4 11.8 - - + +
401F GLU* 1.3 84.5 + - - +
403F LYS* 1.3 57.1 + - - +
405F LEU* 3.5 13.6 + - - +
406F ARG* 2.9 42.6 + - - +
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Residues in contact with LYS 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362F SER* 5.7 1.4 + - - -
364F ARG* 4.3 13.4 - - - +
365F GLU* 3.4 22.6 - - - +
396F ARG* 5.4 1.6 - - - +
399F GLN 2.9 10.8 + - - +
400F ILE* 3.2 43.1 - - + +
402F ASN* 1.3 73.2 - - - +
404F ALA* 1.3 62.8 + - - +
406F ARG* 3.5 23.7 - - - +
407F LYS* 2.9 53.5 + - - +
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Residues in contact with ALA 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361F LEU* 3.9 8.2 - - + +
365F GLU* 3.7 31.0 - - + +
369F LEU* 3.7 25.1 - - + -
400F ILE 2.9 18.6 + - - +
401F GLU 3.2 5.1 + - - +
403F LYS* 1.3 75.6 - - - +
405F LEU* 1.3 59.7 + - - +
407F LYS* 3.4 3.1 + - - +
408F LEU* 2.9 32.4 + - - +
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Residues in contact with LEU 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773C LEU* 4.8 0.9 - - + -
776C SER* 3.5 39.3 - - - +
777C ILE* 4.1 18.8 - - + -
369F LEU* 4.2 12.9 - - + +
373F LYS* 4.2 18.6 - - - +
401F GLU* 2.9 18.7 + - + +
402F ASN* 3.8 14.6 - - - +
404F ALA* 1.3 76.4 - - - +
406F ARG* 1.3 57.7 + - - +
408F LEU* 3.4 5.6 + - + +
409F LYS* 2.9 49.2 + - - +
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Residues in contact with ARG 406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399F GLN* 4.9 8.7 + - - +
402F ASN* 2.9 26.1 + - - +
403F LYS* 3.5 31.3 - - - +
405F LEU* 1.3 75.0 - - - +
407F LYS* 1.3 59.9 + - + +
409F LYS* 3.0 13.9 + - + +
410F TYR* 2.9 27.6 + - - +
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Residues in contact with LYS 407 (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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360F LYS 5.9 0.4 - - - +
361F LEU* 3.7 17.0 - - + -
365F GLU* 3.3 36.2 + - - +
403F LYS* 2.9 42.1 + - + +
406F ARG* 1.3 76.1 - - + +
408F LEU* 1.3 56.9 + - - +
410F TYR* 3.4 7.5 + - - +
411F HIS* 2.9 43.3 + - + +
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Residues in contact with LEU 408 (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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773C LEU* 4.8 1.3 - - + -
777C ILE* 3.8 35.6 - - + +
357F ALA* 3.3 37.5 - - + +
358F LEU* 3.7 13.7 - - + -
361F LEU* 4.0 18.8 - - + -
369F LEU* 3.5 26.0 - - + -
404F ALA 2.9 19.5 + - - +
405F LEU* 3.5 7.4 - - - +
406F ARG 3.1 0.2 - - - -
407F LYS* 1.3 75.4 - - - +
409F LYS* 1.3 60.0 + - - +
411F HIS* 3.8 7.6 - - + +
412F GLU* 2.9 31.6 + - - +
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Residues in contact with LYS 409 (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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776C SER 4.2 11.7 + - - -
777C ILE* 3.4 30.5 - - + +
778C PHE 5.7 0.7 - - - -
779C GLY* 5.5 4.5 - - - +
405F LEU* 2.9 31.4 + - - +
406F ARG* 3.0 13.2 + - + +
408F LEU* 1.3 73.3 - - - +
410F TYR* 1.3 59.7 + - - +
412F GLU* 3.8 5.4 - - - +
413F SER* 2.9 30.2 + - - -
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Residues in contact with TYR 410 (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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406F ARG 2.9 11.7 + - - +
407F LYS* 3.6 10.8 - - - +
409F LYS* 1.3 74.9 - - - +
411F HIS* 1.3 80.3 + + - +
413F SER* 2.4 26.7 + - - -
414F ARG* 2.9 35.0 + - + +
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Residues in contact with HIS 411 (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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357F ALA* 4.8 5.4 - - + +
360F LYS* 3.6 45.3 + - + +
361F LEU* 4.8 2.0 - - + -
407F LYS* 2.9 31.4 + - + +
408F LEU* 3.9 14.4 - - + +
410F TYR* 1.3 94.4 - + - +
412F GLU* 1.3 57.3 + - - +
414F ARG* 3.3 15.2 + - - +
415F THR* 2.9 39.4 + - + +
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Residues in contact with GLU 412 (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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777C ILE* 4.8 9.0 - - + -
778C PHE* 3.3 34.0 - - + -
408F LEU 2.9 20.1 + - - +
409F LYS* 3.9 6.7 - - - +
411F HIS* 1.3 74.0 - - - +
413F SER* 1.3 62.2 + - - +
415F THR* 4.2 2.0 + - - -
416F ARG* 2.8 34.8 + - - +
417F LYS 3.5 3.4 + - - -
418F LEU* 2.8 40.5 + - + +
419F ARG* 3.2 23.2 + - - +
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Residues in contact with SER 413 (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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409F LYS 2.9 14.7 + - - -
410F TYR* 2.4 33.4 + - - -
412F GLU* 1.3 78.6 - - - +
414F ARG* 1.3 61.6 + - - +
416F ARG* 3.6 14.9 + - - +
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Residues in contact with ARG 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410F TYR* 2.9 36.8 + - + +
411F HIS* 3.6 15.4 + - - +
413F SER* 1.3 81.9 + - - +
415F THR* 1.3 76.2 + - + +
416F ARG* 4.0 4.7 - - - +
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Residues in contact with THR 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360F LYS* 5.7 7.9 - - - +
411F HIS* 2.9 27.5 + - + +
412F GLU* 4.2 2.8 + - - -
414F ARG* 1.3 89.2 - - + +
416F ARG* 1.3 71.1 + - - +
417F LYS* 3.1 33.0 + - - +
418F LEU* 5.3 1.6 - - - +
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Residues in contact with ARG 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668D PRO* 6.0 1.7 - - - +
412F GLU* 2.8 25.2 + - - +
413F SER* 3.6 19.5 + - - +
414F ARG 4.0 4.9 - - - +
415F THR* 1.3 79.9 + - - +
417F LYS* 1.3 62.1 + - - +
418F LEU 3.6 1.8 - - - -
419F ARG* 4.1 22.5 + - + +
420F ASP* 4.0 11.1 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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