Contacts of the helix formed by residues 375 - 389 (chain A) in PDB entry 1F7U
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 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A TYR* 2.8 29.8 + - - -
371A ILE* 3.6 22.7 - - + +
372A ALA* 2.8 17.6 + - + +
374A GLN* 1.3 85.1 - - + +
376A ASP* 1.3 61.4 + - - -
377A LEU 3.3 2.7 - - - -
378A HIS* 3.4 15.2 + - + +
379A ALA* 3.1 24.1 + - - +
399A HIS* 4.2 1.3 - - - -
800A ARG* 2.8 32.4 + - - +
976B A 3.6 33.2 + - + +
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Residues in contact with ASP 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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373A SER* 2.9 38.3 + - - +
374A GLN 3.5 1.0 - - - -
375A GLN* 1.3 78.1 - - - +
377A LEU* 1.3 58.8 + - - +
379A ALA* 3.5 1.7 + - - +
380A ALA* 2.9 30.1 + - - +
399A HIS* 3.1 22.7 + - - -
401A ASN* 3.1 22.9 + - - -
468A ILE* 5.5 0.7 - - - +
904B C 4.7 12.6 + - - +
905B U 5.6 2.9 - - - +
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Residues in contact with LEU 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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332A LYS 4.1 20.2 - - - +
333A LEU* 4.1 10.8 - - + +
374A GLN 5.4 0.6 + - - -
375A GLN 3.3 0.4 - - - -
376A ASP* 1.3 75.1 - - - +
378A HIS* 1.3 68.9 + - - +
380A ALA* 3.0 5.1 + - + +
381A GLN* 2.8 59.9 + - + +
971B A 3.5 26.9 - - - +
972B A 3.7 26.2 - - - +
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Residues in contact with HIS 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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347A TYR* 3.2 39.4 - + - -
348A LEU* 3.4 43.2 - - + +
351A ASP* 2.8 26.2 + - - -
371A ILE* 5.6 2.2 - - + -
375A GLN* 3.4 25.2 + - + +
377A LEU* 1.3 81.4 - - - +
379A ALA* 1.3 65.5 - - + +
381A GLN* 3.1 19.2 + - - +
382A PHE* 3.1 23.2 + + - -
800A ARG* 4.5 2.5 - - - -
976B A 4.4 16.5 + - - +
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Residues in contact with ALA 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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369A TYR* 6.3 0.9 - - + -
371A ILE* 5.3 7.2 - - + -
375A GLN* 3.1 10.7 + - + +
376A ASP 3.8 0.7 - - - +
378A HIS* 1.3 81.8 - - + +
380A ALA* 1.3 62.8 + - - +
382A PHE* 3.6 17.6 + - + -
383A PHE* 3.1 36.6 + - + -
399A HIS* 3.4 40.6 - - + +
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Residues in contact with ALA 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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333A LEU* 3.7 22.2 - - + +
376A ASP 2.9 18.1 + - - +
377A LEU* 3.5 7.9 - - + +
379A ALA* 1.3 77.3 - - - +
381A GLN* 1.3 61.7 + - - +
383A PHE* 3.9 5.9 - - - +
384A GLU* 3.3 22.5 + - - +
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Residues in contact with GLN 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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326A LEU* 3.8 16.9 - - + +
333A LEU* 2.6 33.4 + - + +
335A LYS 3.9 8.5 + - - -
336A ALA* 3.8 27.0 - - + +
348A LEU* 4.3 10.9 - - + +
377A LEU* 2.8 44.9 + - + +
378A HIS* 3.1 10.7 + - - +
380A ALA* 1.3 74.7 - - - +
382A PHE* 1.3 61.5 + - - +
383A PHE 3.2 1.6 - - - -
384A GLU* 3.3 2.9 + - - +
385A ILE* 2.9 33.4 + - - +
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Residues in contact with PHE 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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348A LEU* 3.2 22.0 - - + +
351A ASP* 3.8 37.2 - - + -
352A VAL* 4.1 11.8 - - + +
369A TYR* 3.6 38.4 - + - -
371A ILE* 5.3 2.2 - - + -
378A HIS* 3.1 32.6 + + - -
379A ALA* 3.9 17.5 - - + -
381A GLN* 1.3 74.2 - - - +
383A PHE* 1.3 88.3 + + - +
385A ILE* 3.9 8.5 - - - +
386A LEU* 3.1 40.2 + - + +
800A ARG* 5.2 1.8 - - - -
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Residues in contact with PHE 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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369A TYR* 4.0 14.6 - + - -
379A ALA* 3.1 27.5 + - + +
380A ALA* 3.9 7.0 - - - +
381A GLN 3.2 0.2 - - - -
382A PHE* 1.3 107.8 - + - +
384A GLU* 1.3 67.3 + - - +
386A LEU* 3.3 7.8 + - - +
387A LYS* 3.1 20.6 + - - +
394A ALA* 4.6 5.8 - - - +
397A LEU* 3.8 30.0 - - + +
398A GLN* 3.7 26.0 - - - -
399A HIS* 3.6 30.7 - - + -
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Residues in contact with GLU 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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326A LEU* 4.2 12.8 - - + -
329A PHE* 3.9 15.2 - - + +
330A ASN* 5.1 2.9 + - - +
333A LEU* 3.3 28.0 - - + +
380A ALA 3.3 16.4 + - - +
381A GLN 3.3 4.0 + - - +
383A PHE* 1.3 78.3 - - - +
385A ILE* 1.3 65.4 + - - +
387A LYS* 3.0 22.2 + - - +
388A GLN* 2.7 55.0 + - + +
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Residues in contact with ILE 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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309A PHE* 3.7 29.6 - - + -
314A LEU* 4.5 3.1 - - + +
324A ILE* 3.9 24.5 - - + -
326A LEU* 3.8 27.1 - - + -
336A ALA* 5.0 0.7 - - + -
338A VAL* 4.9 3.1 - - + -
348A LEU* 4.0 28.5 - - + -
352A VAL* 4.2 11.9 - - + -
381A GLN 2.9 23.7 + - - +
382A PHE* 4.0 8.5 - - - +
383A PHE 3.3 0.2 - - - -
384A GLU* 1.3 76.7 - - - +
386A LEU* 1.3 63.0 + - - +
388A GLN* 3.2 6.4 + - - +
389A MET* 2.9 32.8 + - + +
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Residues in contact with LEU 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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352A VAL* 3.7 37.0 - - + +
355A ALA* 3.6 17.7 - - + -
382A PHE* 3.1 29.6 + - + +
383A PHE* 3.6 4.5 - - - +
384A GLU 3.3 0.2 - - - -
385A ILE* 1.3 79.2 - - - +
387A LYS* 1.3 63.5 + - - +
389A MET* 3.3 16.3 + - - +
391A PHE* 3.5 38.9 + - + +
393A TRP* 4.1 9.2 - - + -
394A ALA* 3.9 12.1 - - + -
397A LEU* 3.5 29.6 - - + -
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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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383A PHE 3.1 12.0 + - - +
384A GLU* 3.0 33.1 + - - +
386A LEU* 1.3 77.5 - - - +
388A GLN* 1.3 67.1 + - - +
389A MET 3.0 0.2 - - - -
390A GLY* 3.0 21.5 + - - -
391A PHE 4.1 3.8 + - - +
394A ALA* 3.7 16.4 - - + +
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Residues in contact with GLN 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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312A LYS* 3.6 21.5 - - - +
314A LEU* 3.9 20.5 - - + +
326A LEU* 5.4 0.7 - - + -
329A PHE* 3.1 47.8 - - + +
384A GLU* 2.7 41.4 + - - +
385A ILE* 3.2 6.3 + - - +
387A LYS* 1.3 91.9 - - - +
389A MET* 1.3 60.8 + - - +
390A GLY 3.1 2.0 + - - -
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Residues in contact with MET 389 (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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305A ALA* 3.7 27.4 - - + -
308A LEU* 3.6 39.4 - - + +
309A PHE* 3.4 23.6 - - + -
312A LYS* 3.7 20.3 - - - -
314A LEU* 3.9 15.9 - - + -
352A VAL* 3.8 14.1 - - + -
356A MET* 4.0 4.7 - - - -
385A ILE* 2.9 25.9 + - - +
386A LEU* 3.5 12.1 - - - +
387A LYS 3.0 0.6 - - - -
388A GLN* 1.3 77.0 - - - +
390A GLY* 1.3 58.2 + - - +
391A PHE* 3.5 29.1 + - + -
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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