Contacts of the helix formed by residues 399 - 414 (chain F) in PDB entry 6CP3
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 GLN 399 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397F SER* 3.4 4.7 + - - +
398F GLU* 1.3 78.0 - - - +
400F ASP* 1.3 66.0 + - - +
401F LYS 3.3 0.4 - - - -
402F LEU* 3.2 25.1 + - - +
403F THR* 2.9 37.9 + - - +
120G ARG* 5.7 1.2 - - - +
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Residues in contact with ASP 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380F THR* 5.1 6.2 - - - +
384F LEU* 4.2 21.8 - - + +
396F LEU* 4.6 4.3 - - + -
397F SER* 3.0 28.1 + - - +
399F GLN* 1.3 81.4 - - - +
401F LYS* 1.3 61.1 + - - +
403F THR* 3.4 12.3 + - - -
404F VAL* 2.8 33.1 + - - +
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Residues in contact with LYS 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393F MET* 3.9 31.5 + - + +
394F ASP* 3.6 26.9 + - - +
396F LEU* 4.0 16.4 - - + +
397F SER 3.3 20.1 + - - +
398F GLU* 4.4 20.9 - - - +
399F GLN 3.3 0.6 - - - -
400F ASP* 1.3 77.6 - - - +
402F LEU* 1.3 58.2 + - - +
404F VAL* 3.4 1.8 + - - +
405F GLU* 3.0 49.8 + - + +
89G SER* 4.7 16.6 + - - -
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Residues in contact with LEU 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398F GLU 4.1 11.9 + - - +
399F GLN* 3.2 27.1 + - - +
401F LYS* 1.3 77.7 - - - +
403F THR* 1.3 57.6 + - - +
405F GLU* 3.4 16.6 + - + +
406F ARG* 2.9 50.9 + - + +
409F LYS* 5.9 2.0 - - - +
450F ASP* 4.7 24.2 - - + +
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Residues in contact with THR 403 (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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377F THR* 3.7 21.1 - - + +
380F THR* 3.9 29.8 - - + +
381F TYR 5.8 0.2 - - - +
399F GLN* 2.9 28.1 + - - +
400F ASP* 3.2 17.5 + - - +
402F LEU* 1.3 76.3 - - - +
404F VAL* 1.3 57.8 + - - +
406F ARG* 3.4 4.0 + - - -
407F ALA* 2.9 29.9 + - - +
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Residues in contact with VAL 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380F THR 5.8 0.4 - - - -
381F TYR* 3.9 30.3 - - + +
384F LEU* 3.8 28.9 - - + -
388F ILE* 4.8 8.5 - - + -
393F MET* 3.8 23.1 - - + -
396F LEU* 3.9 16.4 - - + -
400F ASP 2.8 20.1 + - - +
401F LYS 3.8 4.3 - - - +
402F LEU 3.4 0.2 - - - -
403F THR* 1.3 76.3 - - + +
405F GLU* 1.3 58.3 + - - +
407F ALA* 3.2 7.6 + - - +
408F ARG* 2.9 30.9 + - - +
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Residues in contact with GLU 405 (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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393F MET* 4.0 19.6 - - + +
401F LYS* 3.0 41.5 + - - +
402F LEU* 3.8 18.0 - - + +
404F VAL* 1.3 76.0 - - - +
406F ARG* 1.3 58.3 + - - +
408F ARG* 3.3 5.5 + - - +
409F LYS* 2.9 46.3 + - - +
450F ASP 5.5 1.2 - - - +
454F GLU* 5.6 0.7 - - - -
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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
----------------------------------------------------------
377F THR* 4.5 5.8 - - + -
402F LEU* 2.9 37.6 + - + +
403F THR* 4.0 5.2 - - - +
405F GLU* 1.3 76.3 - - - +
407F ALA* 1.3 57.5 + - - +
409F LYS* 3.2 14.5 + - + +
410F ILE* 2.9 47.9 + - + +
444F VAL* 3.4 24.5 + - + +
445F LEU* 2.4 40.2 + - - +
446F GLU 4.5 1.0 - - - -
447F GLY* 3.4 8.9 - - - -
450F ASP* 3.1 34.7 + - - +
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Residues in contact with ALA 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377F THR* 3.7 21.7 - - + +
378F LEU* 4.0 7.9 - - + +
381F TYR* 3.8 30.3 - - + -
403F THR 2.9 18.1 + - - +
404F VAL* 3.2 6.3 + - - +
406F ARG* 1.3 77.0 - - - +
408F ARG* 1.3 58.1 + - - +
410F ILE* 3.1 5.6 + - - +
411F GLN* 2.9 32.5 + - - +
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Residues in contact with ARG 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381F TYR* 3.6 36.9 + - + +
388F ILE* 6.1 1.4 - - - +
393F MET* 3.5 28.7 - - - +
404F VAL* 2.9 25.7 + - - +
405F GLU* 4.0 4.7 - - - +
407F ALA* 1.3 73.4 - - - +
409F LYS* 1.3 67.3 + - - +
411F GLN* 4.0 8.5 - - - +
412F ARG* 3.5 50.1 + - - +
454F GLU* 2.9 41.5 + - - +
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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
----------------------------------------------------------
402F LEU* 5.9 2.2 - - - +
405F GLU* 2.9 38.9 + - - +
406F ARG* 3.3 19.4 - - + +
407F ALA 3.2 0.2 - - - -
408F ARG* 1.3 76.4 - - - +
410F ILE* 1.3 59.9 + - + +
412F ARG 3.3 2.9 + - - -
413F PHE* 2.9 29.0 + - - +
444F VAL* 4.9 5.4 - - + -
449F TYR 4.0 2.5 - - - +
450F ASP* 3.2 40.8 + - - +
452F ILE 3.6 19.3 + - - -
454F GLU* 4.5 11.3 - - + +
457F PHE* 3.5 41.5 - - + +
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Residues in contact with ILE 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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374F VAL* 4.2 21.3 - - + -
377F THR* 4.8 11.7 - - + -
378F LEU* 4.6 10.3 - - + -
406F ARG* 2.9 36.0 + - + +
407F ALA* 3.1 5.3 + - - +
409F LYS* 1.3 76.5 - - - +
411F GLN* 1.3 56.8 + - - +
413F PHE* 3.2 8.2 + - + +
414F LEU* 2.9 30.6 + - + +
441F PHE* 3.6 27.8 - - + -
444F VAL* 4.1 21.3 - - + -
445F LEU* 4.3 24.0 - - + -
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Residues in contact with GLN 411 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339F ILE* 6.2 3.2 - - - +
342F LEU* 5.3 7.6 - - - +
344F ILE* 3.9 22.5 - - + +
350F PRO* 5.6 6.5 - - + +
378F LEU* 3.8 24.9 - - + +
381F TYR* 4.0 31.6 + - - -
407F ALA 2.9 12.9 + - - +
408F ARG* 4.2 8.4 - - - +
410F ILE* 1.3 76.7 - - - +
412F ARG* 1.3 74.3 + - - +
414F LEU* 2.9 32.3 + - + +
415F SER 3.8 2.8 + - - -
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Residues in contact with ARG 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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401B GLU* 4.0 19.6 + - - -
342F LEU* 5.5 19.9 + - - +
344F ILE* 4.0 23.2 - - + +
381F TYR* 5.8 0.4 + - - -
408F ARG* 3.5 39.1 + - - +
409F LYS 3.3 4.4 + - - +
411F GLN* 1.3 93.9 + - - +
413F PHE* 1.3 55.1 + - - +
415F SER* 2.6 27.2 + - - -
454F GLU* 3.0 38.1 + - + +
455F HIS* 5.7 1.1 - - - -
457F PHE* 3.0 13.7 - - + +
458F TYR* 3.3 29.9 - - + +
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Residues in contact with PHE 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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139F LYS* 2.3 58.9 + - - -
409F LYS 2.9 17.8 + - - +
410F ILE* 3.5 9.0 - - + +
411F GLN 3.1 0.4 - - - -
412F ARG* 1.3 74.8 - - - +
414F LEU* 1.3 58.1 + - - +
415F SER 3.1 4.7 + - - +
437F THR* 5.9 0.2 - - + -
440F SER* 4.0 24.2 - - - -
441F PHE* 3.5 48.5 - + - -
444F VAL* 5.2 6.1 - - + -
457F PHE* 3.5 23.1 - + + +
460F VAL* 3.8 12.6 - - + +
461F GLY 4.1 5.6 - - - -
462F GLY* 4.4 2.7 - - - -
463F ILE* 4.5 8.1 - - + -
466F VAL* 3.5 28.5 - - + -
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Residues in contact with LEU 414 (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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139F LYS* 4.5 6.1 - - + +
140F VAL* 3.3 42.8 - - + +
143F LEU* 5.0 1.1 - - + -
144F LEU* 4.7 12.1 - - + -
344F ILE* 4.9 8.7 - - + -
346F PRO* 4.5 5.3 - - - +
348F VAL 5.1 2.2 - - - +
350F PRO* 3.6 35.2 - - + -
374F VAL* 5.6 0.7 - - + -
378F LEU* 4.5 7.6 - - + -
410F ILE* 2.9 20.3 + - + +
411F GLN* 2.9 16.7 + - + +
413F PHE* 1.3 74.2 - - - +
415F SER* 1.3 64.7 + - - +
416F GLN* 3.8 4.5 + - - +
441F PHE* 3.6 30.1 - - + -
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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
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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