Contacts of the helix formed by residues 400 - 418 (chain F) in PDB entry 7C17
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 400 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D ARG* 3.3 39.3 - - - +
275D ARG* 2.8 31.4 + - - +
302D ALA* 6.0 1.0 - - - +
316D ILE* 3.4 25.7 - - + +
317D THR* 5.9 1.3 - - + +
399F LEU* 1.3 81.0 - - - +
401F PHE* 1.3 65.5 + - - +
402F LEU* 3.4 17.1 - - + +
403F ASP* 3.4 11.6 + - - +
404F LEU* 3.4 22.2 + - - +
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Residues in contact with PHE 401 (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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721 G 3.2 61.5 - + - +
731 G 4.8 5.6 - - - -
98F VAL* 4.6 7.4 - - + -
388F ILE* 4.1 17.5 - - + -
391F ALA* 3.3 41.5 - - + -
395F THR* 4.2 21.3 - - + -
400F GLN* 1.3 74.4 - - - +
402F LEU* 1.3 65.3 + - + +
404F LEU* 3.3 11.4 + - + +
405F ILE* 3.0 59.2 + - + +
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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
----------------------------------------------------------
275D ARG* 4.3 6.3 - - - +
294D ASN* 5.1 5.2 - - - +
298D MET* 3.4 45.9 - - + +
96F ASP* 6.0 0.9 - - - +
97F PRO* 4.3 13.0 - - + +
98F VAL* 3.8 48.7 - - + +
101F TYR* 5.5 2.2 - - + -
400F GLN* 3.4 20.1 - - + +
401F PHE* 1.3 82.6 - - + +
403F ASP* 1.3 56.7 + - - +
405F ILE* 3.6 7.9 - - - +
406F GLN* 2.9 24.3 + - - +
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Residues in contact with ASP 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D ARG* 4.3 6.2 + - - +
274D ASN* 6.2 0.4 - - - -
275D ARG* 2.6 33.2 + - - +
278D ARG* 3.4 31.6 + - - +
298D MET* 3.4 3.3 - - - +
399F LEU* 3.9 21.2 - - + +
400F GLN* 3.4 29.7 + - - +
401F PHE 3.3 0.6 - - - -
402F LEU* 1.3 77.2 - - - +
404F LEU* 1.3 58.9 + - - +
406F GLN 3.5 0.9 + - - -
407F GLU* 2.9 30.0 + - - +
442F SER* 5.2 0.8 - - - -
446F GLN* 4.2 8.7 - - - +
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Residues in contact with LEU 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387F VAL* 5.7 0.2 - - - +
391F ALA* 5.1 15.3 - - + +
394F TYR* 3.3 33.2 - - + +
395F THR* 5.2 2.7 - - - -
396F ASN* 5.3 2.0 - - - +
399F LEU* 3.7 35.0 - - + +
400F GLN 3.4 19.5 - - - +
401F PHE* 3.3 10.2 + - + +
403F ASP* 1.3 73.0 - - - +
405F ILE* 1.3 61.1 + - - +
407F GLU* 3.8 4.9 - - - +
408F GLY* 2.9 26.3 + - - -
439F ILE* 4.3 25.5 - - + +
442F SER* 3.8 15.5 - - - +
443F ILE* 5.2 7.6 - - + +
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Residues in contact with ILE 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D ASN* 5.7 1.3 - - - +
98F VAL* 6.0 1.3 - - + -
101F TYR* 3.3 39.7 - - + +
387F VAL* 3.4 42.5 - - + +
388F ILE* 3.7 15.7 - - + -
391F ALA* 3.8 6.3 - - + -
401F PHE* 3.0 44.5 + - + +
402F LEU* 3.6 8.5 - - - +
403F ASP 3.3 0.2 - - - -
404F LEU* 1.3 75.1 - - - +
406F GLN* 1.3 59.4 + - + +
408F GLY* 3.3 2.8 + - - -
409F ASN* 2.9 33.4 + - - +
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Residues in contact with GLN 406 (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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278D ARG* 3.7 15.5 - - - -
282D LEU* 5.0 0.6 - - - +
291D ILE* 2.7 40.4 + - - +
294D ASN* 3.4 28.6 - - - +
295D GLU* 2.9 40.5 - - - +
298D MET* 3.3 20.0 - - + +
402F LEU 2.9 13.4 + - - +
403F ASP 3.7 1.1 - - - +
405F ILE* 1.3 76.2 - - + +
407F GLU* 1.3 62.0 + - - +
409F ASN* 3.5 16.7 - - - +
410F ILE* 3.3 24.1 + - - +
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Residues in contact with GLU 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D ARG* 2.8 30.5 + - - -
281D ARG* 3.4 27.2 + - - -
403F ASP 2.9 16.5 + - - +
404F LEU 3.4 3.8 + - - +
406F GLN* 1.3 74.0 - - - +
408F GLY* 1.3 60.7 + - - +
409F ASN 3.1 1.1 - - - -
410F ILE* 3.3 22.9 + - + +
411F GLY 3.0 22.3 + - - -
438F ALA* 3.3 35.8 - - + +
439F ILE* 5.2 0.4 - - - +
441F ARG* 4.7 10.9 - - - +
442F SER* 3.7 20.7 - - - +
446F GLN* 4.2 5.3 + - - -
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Residues in contact with GLY 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387F VAL* 3.7 10.5 - - - +
404F LEU 2.9 15.7 + - - -
405F ILE 3.6 4.0 - - - -
407F GLU* 1.3 72.8 - - - +
409F ASN* 1.3 58.2 + - - +
411F GLY 4.3 0.9 - - - -
412F LEU* 2.9 30.1 + - - +
435F ILE* 3.5 30.7 - - - +
438F ALA* 4.4 4.7 - - - +
439F ILE* 5.0 1.4 - - - +
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Residues in contact with ASN 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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291D ILE* 4.0 29.0 - - + +
294D ASN* 5.3 0.6 - - - +
101F TYR* 4.0 16.0 + - - -
380F VAL* 5.2 3.7 - - - +
384F LEU* 3.4 26.9 - - - +
387F VAL* 3.7 10.8 - - - +
405F ILE* 2.9 22.9 + - - +
406F GLN* 3.5 29.4 - - - +
407F GLU 3.1 0.2 - - - -
408F GLY* 1.3 76.8 - - - +
410F ILE* 1.3 57.9 + - - +
412F LEU* 3.3 7.0 + - - +
413F MET* 2.9 30.8 + - - +
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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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278D ARG* 4.6 6.5 - - + -
281D ARG* 4.3 26.5 - - + +
282D LEU* 3.8 33.0 - - + -
406F GLN 3.3 14.1 + - - +
407F GLU* 3.3 37.4 + - + +
409F ASN* 1.3 74.9 - - + +
411F GLY* 1.3 63.2 + - - +
413F MET* 3.4 10.8 + - + +
414F LYS* 2.9 43.9 + - - +
438F ALA* 5.2 2.2 - - + -
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Residues in contact with GLY 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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407F GLU 3.0 14.4 + - - -
408F GLY* 3.4 3.6 + - - -
409F ASN 3.3 0.4 - - - -
410F ILE* 1.3 78.6 - - - +
412F LEU* 1.3 55.8 + - - +
414F LYS* 3.3 10.3 + - - +
415F ALA* 2.9 26.7 + - - +
434F TRP* 3.7 17.0 - - - +
435F ILE* 4.4 5.6 - - - -
437F GLN* 5.4 0.4 - - - -
438F ALA* 4.1 15.5 - - - -
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Residues in contact with LEU 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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379F MET 4.3 2.0 - - - +
380F VAL* 3.7 34.1 - - + +
383F ASN* 3.4 34.3 - - + +
384F LEU* 6.0 0.7 - - + -
386F LEU* 4.7 2.5 - - + -
387F VAL* 4.3 6.5 - - + -
408F GLY 2.9 15.6 + - - +
409F ASN* 3.7 7.2 - - - +
411F GLY* 1.3 72.2 - - - +
413F MET* 1.3 60.2 + - - +
415F ALA* 3.2 7.7 + - - +
416F VAL* 2.9 32.9 + - + +
427F PHE* 3.6 27.6 - - + -
431F ALA* 4.7 4.0 - - + -
435F ILE* 3.7 26.8 - - + +
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Residues in contact with MET 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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282D LEU* 3.9 24.9 - - + -
285D LEU* 4.1 33.2 - - + +
286D ALA 4.7 0.9 - - - +
287D ALA* 4.1 10.3 - - + -
288D PRO* 3.9 25.6 - - + -
291D ILE* 4.5 12.6 - - + -
376F LYS* 5.7 11.5 - - + -
380F VAL* 4.5 11.4 - - + +
409F ASN 2.9 17.6 + - - +
410F ILE* 3.6 10.5 - - - +
411F GLY 3.3 0.2 - - - -
412F LEU* 1.3 77.4 - - - +
414F LYS* 1.3 59.4 + - - +
416F VAL* 3.5 17.7 + - + +
417F ASP* 2.9 14.0 - - - +
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Residues in contact with LYS 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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631 T 5.4 7.3 + - - -
285D LEU* 4.8 21.7 - - + +
410F ILE* 2.9 34.6 + - + +
411F GLY* 3.6 6.3 - - - +
413F MET* 1.3 75.1 - - + +
415F ALA* 1.3 59.8 + - - +
417F ASP* 2.9 21.8 - - - +
418F LYS* 3.0 23.2 + - + +
434F TRP* 3.9 32.1 - - + -
437F GLN* 5.6 2.0 - - - +
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Residues in contact with ALA 415 (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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411F GLY 2.9 17.4 + - - +
412F LEU* 3.2 9.4 + - - +
414F LYS* 1.3 73.3 - - - +
416F VAL* 1.3 60.1 + - - +
418F LYS* 3.5 9.1 - - - -
419F PHE* 2.9 31.0 + - - +
427F PHE* 3.3 15.9 - - + -
430F TYR* 4.8 3.1 - - + -
431F ALA* 4.2 11.9 - - - -
434F TRP* 4.0 24.2 - - + -
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Residues in contact with VAL 416 (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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123F ILE* 4.1 25.8 - - + +
376F LYS* 3.7 36.6 - - + +
379F MET* 3.8 22.1 - - + +
380F VAL* 4.2 16.8 - - + -
412F LEU 2.9 19.6 + - - +
413F MET* 3.5 10.8 - - + +
414F LYS 3.2 0.4 - - - -
415F ALA* 1.3 79.7 - - - +
417F ASP* 1.3 60.5 + - - +
419F PHE* 3.5 13.7 - - - +
420F GLU 5.0 0.3 + - - -
427F PHE* 3.6 18.6 - - + -
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Residues in contact with ASP 417 (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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127F ILE* 6.0 7.6 - - + -
263F PRO* 6.0 2.1 - - - +
376F LYS* 5.3 10.0 - - - +
413F MET 2.9 26.2 - - - +
414F LYS* 2.9 17.1 - - - +
416F VAL* 1.3 81.0 - - + +
418F LYS* 1.3 72.1 + - - +
419F PHE 3.3 1.6 + - - -
420F GLU* 5.0 2.8 + - - +
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Residues in contact with LYS 418 (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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641 T 3.2 49.5 + - - +
651 T 5.4 1.5 + - - -
661 A 4.7 4.0 + - - -
263F PRO* 5.2 16.4 - - + +
414F LYS* 3.0 20.5 + - + +
415F ALA* 3.4 4.2 + - - -
416F VAL 3.3 0.2 - - - -
417F ASP* 1.3 88.4 - - - +
419F PHE* 1.3 63.3 + - - +
420F GLU* 3.7 4.0 - - - +
430F TYR* 3.2 23.5 + - - -
434F TRP* 3.8 31.4 - - + +
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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