Contacts of the helix formed by residues 374 - 388 (chain A) in PDB entry 2FQ3
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 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A LYS* 4.7 15.4 + - - +
346A TYR* 4.6 4.0 + - + -
373A GLY* 1.3 69.7 - - - -
375A ALA* 1.3 62.9 + - - +
376A ALA* 3.5 12.7 + - - +
377A ALA* 3.0 35.8 + - + +
378A LEU* 2.9 29.7 + - - +
380A ARG* 4.3 3.8 + - - -
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Residues in contact with ALA 375 (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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368A ARG* 3.5 32.6 - - - +
373A GLY 3.1 7.0 + - - +
374A ASP* 1.3 73.5 + - - +
376A ALA* 1.3 57.8 + - - +
378A LEU* 3.3 6.2 + - - +
379A PHE* 2.9 28.6 + - - +
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Residues in contact with ALA 376 (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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374A ASP* 3.3 11.9 + - - +
375A ALA* 1.3 78.9 - - - +
377A ALA* 1.3 57.6 + - - +
379A PHE* 3.3 9.6 + - + +
380A ARG* 3.0 51.8 + - - +
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Residues in contact with ALA 377 (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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329A GLU* 3.6 20.7 - - - +
330A PHE* 4.3 18.6 - - + -
338A LYS* 4.4 5.6 - - - -
346A TYR* 5.8 4.7 - - + -
374A ASP* 3.0 29.9 + - + +
376A ALA* 1.3 75.7 - - - +
378A LEU* 1.3 59.8 + - + +
380A ARG* 3.3 13.3 + - - +
381A LEU* 2.9 29.9 + - - +
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Residues in contact with LEU 378 (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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346A TYR* 3.9 38.1 - - + -
350A MET* 3.5 26.9 - - + +
364A VAL* 5.3 1.8 - - + -
367A ALA* 4.4 7.0 - - + +
368A ARG* 4.1 27.8 - - + +
371A VAL* 4.0 25.4 - - + +
373A GLY* 3.9 22.0 - - - +
374A ASP 2.9 16.7 + - - +
375A ALA* 3.7 4.9 - - - +
377A ALA* 1.3 76.3 - - + +
379A PHE* 1.3 57.9 + - - +
381A LEU* 3.3 1.7 + - + -
382A HIS* 2.9 31.3 + - - +
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Residues in contact with PHE 379 (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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364A VAL* 4.2 30.4 - - + +
375A ALA 2.9 17.8 + - - +
376A ALA* 3.5 10.8 - - - +
377A ALA 3.2 0.2 - - - -
378A LEU* 1.3 77.2 - - - +
380A ARG* 1.3 68.3 + - + +
382A HIS* 3.3 6.3 + - - +
383A LYS* 2.9 53.9 + - + +
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Residues in contact with ARG 380 (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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327A LEU* 3.9 14.7 - - + +
329A GLU* 2.8 44.2 + - - +
338A LYS* 5.1 1.6 - - - +
374A ASP* 4.3 3.2 + - - -
376A ALA* 3.0 36.7 + - - +
377A ALA* 3.7 17.4 - - - +
379A PHE* 1.3 89.7 - - + +
381A LEU* 1.3 62.5 + - - +
383A LYS* 3.3 9.7 + - + +
384A PHE* 3.0 23.0 + - - +
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Residues in contact with LEU 381 (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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327A LEU* 3.9 13.8 - - + +
330A PHE* 4.8 6.1 - - + -
343A TYR* 3.8 33.9 - - + +
346A TYR* 3.5 37.2 - - + -
347A ARG* 3.6 18.4 - - + +
350A MET* 4.1 10.3 - - + -
377A ALA 2.9 16.3 + - - +
378A LEU* 3.6 6.7 - - + +
380A ARG* 1.3 75.8 - - - +
382A HIS* 1.3 59.0 + - - +
384A PHE* 3.2 2.7 + - + +
385A LEU* 2.9 54.4 + - + +
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Residues in contact with HIS 382 (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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350A MET* 4.0 13.4 - - + -
361A TYR* 3.5 24.9 - + - -
362A PHE* 2.8 38.5 + + - -
363A SER 3.9 2.9 - - - -
364A VAL* 3.5 42.0 + - + +
367A ALA* 5.2 0.7 - - + -
378A LEU 2.9 17.5 + - - +
379A PHE* 3.5 5.3 - - - +
381A LEU* 1.3 77.6 - - - +
383A LYS* 1.3 57.0 + - - +
385A LEU* 3.4 5.1 + - - +
386A THR* 2.8 47.3 + - - -
391A ILE* 3.7 13.1 - - + +
392A ASN* 4.1 1.6 - - - -
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Residues in contact with LYS 383 (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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379A PHE* 2.9 43.7 + - + +
380A ARG* 3.5 10.1 - - + +
382A HIS* 1.3 77.1 + - - +
384A PHE* 1.3 58.3 + - - +
386A THR* 3.3 7.3 + - - -
387A LYS* 2.9 32.6 + - + +
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Residues in contact with PHE 384 (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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313A TRP* 4.2 6.7 - + - -
322A ILE* 3.9 11.9 - - + -
323A GLU* 3.8 24.7 - - + -
326A SER* 3.4 35.7 - - - -
327A LEU* 3.8 23.6 - - + -
343A TYR* 3.8 16.6 - - - -
380A ARG 3.0 14.0 + - - +
381A LEU* 3.4 6.5 - - + +
383A LYS* 1.3 74.4 - - - +
385A LEU* 1.3 88.2 + - + +
387A LYS* 3.2 6.3 + - + -
388A TRP* 3.0 54.9 + + - +
390A LEU* 4.3 8.1 - - + -
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Residues in contact with LEU 385 (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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347A ARG* 4.1 20.2 - - + +
350A MET* 3.7 40.8 - - + -
351A VAL* 4.2 13.7 - - + -
381A LEU* 2.9 27.3 + - + +
382A HIS 3.9 0.2 - - - +
384A PHE* 1.3 89.5 - - + +
386A THR* 1.3 60.8 + - - +
388A TRP 3.8 0.2 + - - -
389A GLY 3.3 2.1 + - - -
390A LEU* 2.8 61.3 + - + +
391A ILE* 3.4 25.8 + - + -
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Residues in contact with THR 386 (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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361A TYR* 5.0 8.3 - - + +
382A HIS* 2.8 40.2 + - - -
383A LYS* 3.5 7.2 - - - -
385A LEU* 1.3 75.4 - - - +
387A LYS* 1.3 68.1 + - - +
389A GLY* 3.1 13.7 + - - -
391A ILE* 3.9 18.4 - - - +
392A ASN* 4.3 7.9 + - + +
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Residues in contact with LYS 387 (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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326A SER* 5.5 2.4 + - - -
383A LYS* 2.9 21.5 + - + +
384A PHE* 3.2 7.6 + - + +
386A THR* 1.3 80.0 - - - +
388A TRP* 1.3 91.7 + - + +
389A GLY 3.3 2.0 + - - -
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Residues in contact with TRP 388 (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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311A SER* 4.3 7.8 + - - -
313A TRP* 4.2 25.4 + + + -
322A ILE* 3.8 44.2 - - + -
326A SER* 4.1 7.3 + - - -
384A PHE* 3.0 49.4 + + + +
387A LYS* 1.3 113.1 - - + +
389A GLY* 1.3 63.8 + - - +
390A LEU* 3.4 12.1 + - + +
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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