Contacts of the helix formed by residues 379 - 394 (chain B) in PDB entry 2FQ6
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 379 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265B GLN* 5.9 0.9 - - - +
378B GLU* 1.3 74.8 - - - +
380B VAL* 1.3 65.2 + - - +
381B ASP* 2.9 37.0 + - - +
382B ASP* 3.1 31.0 + - - +
383B LEU* 3.0 19.6 + - - +
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Residues in contact with VAL 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B GLN* 5.7 1.0 - - - +
269B SER* 3.6 46.9 + - - +
272B LYS* 3.8 33.4 - - + +
273B VAL* 3.7 15.7 - - + -
378B GLU 3.3 5.0 + - - -
379B ASP* 1.3 73.9 + - - +
381B ASP* 1.3 66.9 + - - +
383B LEU* 3.2 7.9 + - + +
384B ILE* 2.8 31.0 + - + +
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Residues in contact with ASP 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LYS* 2.9 29.7 + - - -
379B ASP* 2.9 13.5 + - - +
380B VAL* 1.3 79.3 - - - +
382B ASP* 1.3 60.7 + - - +
384B ILE* 3.7 10.6 - - - +
385B ALA* 2.8 30.5 + - - +
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Residues in contact with ASP 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B LEU* 3.4 27.7 - - + +
378B GLU* 5.5 1.3 - - + +
379B ASP* 3.1 33.6 + - + +
381B ASP* 1.3 76.5 - - - +
383B LEU* 1.3 61.8 + - - +
385B ALA* 3.4 7.4 + - - +
386B ASP* 3.1 17.0 + - - +
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B SER* 5.5 0.4 - - - -
273B VAL* 4.9 6.1 - - + -
333B LEU* 4.1 17.5 - - + -
334B PHE* 3.6 23.2 - - + -
345B SER* 3.3 31.6 - - - +
375B ILE* 3.8 27.4 - - + -
376B GLY 4.6 1.3 - - - +
378B GLU* 3.8 31.6 - - + +
379B ASP 3.0 16.2 + - - +
380B VAL* 3.5 12.8 - - - +
381B ASP 3.1 0.2 - - - -
382B ASP* 1.3 75.9 - - - +
384B ILE* 1.3 65.5 + - - +
386B ASP* 3.1 5.6 + - - +
387B LEU* 3.1 27.1 + - - +
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Residues in contact with ILE 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LYS* 4.4 15.7 - - + -
273B VAL* 3.9 19.1 - - + -
276B TRP* 3.5 57.6 - - + +
380B VAL* 2.8 31.3 + - + +
381B ASP* 3.3 15.5 + - - +
383B LEU* 1.3 76.1 - - - +
385B ALA* 1.3 56.8 + - - +
387B LEU* 3.4 6.9 + - - +
388B ASP* 2.8 29.2 + - + +
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Residues in contact with ALA 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B ASP 2.8 21.1 + - - +
382B ASP* 3.6 9.2 - - - +
383B LEU 3.3 0.2 - - - -
384B ILE* 1.3 74.3 - - - +
386B ASP* 1.3 57.0 + - - +
388B ASP* 3.3 7.7 + - - +
389B ALA* 2.9 29.1 + - - +
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Residues in contact with ASP 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B ASN 4.9 0.9 - - - +
331B PHE* 3.4 21.8 - - - -
332B SER* 3.0 30.8 + - - -
333B LEU* 2.8 33.4 + - + -
334B PHE* 3.2 18.9 + - + -
382B ASP 3.1 12.7 + - - +
383B LEU 3.1 7.8 + - - +
385B ALA* 1.3 73.9 - - - +
387B LEU* 1.3 64.8 + - - +
389B ALA* 3.3 9.3 + - - +
390B GLY 3.1 17.0 + - - -
393B ARG* 4.8 1.4 + - - -
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B VAL* 3.5 32.3 - - + -
276B TRP* 3.8 18.2 - - + -
277B LEU* 4.5 3.4 - - + -
313B PHE* 5.0 4.5 - - + -
327B TYR* 4.5 13.9 + - - +
331B PHE* 4.0 14.6 - - + -
334B PHE* 3.5 30.7 - - + -
347B ILE* 4.6 0.2 - - + -
373B LEU* 3.9 26.7 - - + -
383B LEU 3.1 11.7 + - - +
384B ILE* 3.7 8.7 - - - +
386B ASP* 1.3 74.3 - - - +
388B ASP* 1.3 63.5 + - - +
390B GLY* 3.1 3.1 + - - -
391B PHE* 3.1 31.0 + - + -
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Residues in contact with ASP 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B TRP* 3.7 23.9 - - + -
280B HIS* 4.0 13.7 - - - -
384B ILE* 2.8 22.6 + - + +
385B ALA* 3.5 9.0 - - - +
386B ASP 3.2 0.2 - - - -
387B LEU* 1.3 74.9 - - - +
389B ALA* 1.3 62.8 + - - +
391B PHE* 3.2 12.1 + - - +
392B ALA* 3.3 12.6 + - - +
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B ALA 2.9 19.6 + - - +
386B ASP* 3.3 10.0 + - - +
388B ASP* 1.3 73.7 + - - +
390B GLY* 1.3 63.3 + - - +
392B ALA* 3.2 17.1 + - - +
393B ARG* 3.2 29.5 + - - +
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Residues in contact with GLY 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B TYR* 3.4 27.2 - - - -
331B PHE* 4.2 1.6 - - - -
386B ASP 3.1 13.0 + - - -
387B LEU 3.1 4.9 + - - -
389B ALA* 1.3 74.3 - - - +
391B PHE* 1.3 64.5 + - - +
393B ARG* 3.0 40.6 + - - +
394B ILE* 3.4 2.9 + - - +
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Residues in contact with PHE 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B TRP* 3.5 31.0 - + - -
277B LEU* 3.5 21.3 - - + -
280B HIS* 3.3 28.7 - + + +
282B GLN* 2.8 50.4 + - + +
283B VAL* 3.5 17.5 - - + -
313B PHE* 4.1 8.7 - + - -
315B LEU* 3.7 28.0 - - + -
327B TYR* 4.7 6.1 - + - -
387B LEU* 3.1 24.7 + - + -
388B ASP* 3.2 7.2 + - - +
390B GLY* 1.3 75.4 - - - +
392B ALA* 1.3 62.1 + - - +
394B ILE* 3.1 14.5 + - + -
395B VAL* 3.2 3.1 + - - +
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Residues in contact with ALA 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B ASP 3.3 8.1 + - - +
389B ALA* 3.2 13.8 + - - +
390B GLY 3.2 0.6 - - - -
391B PHE* 1.3 78.6 - - - +
393B ARG* 1.3 60.8 + - + +
394B ILE 3.3 0.4 + - - -
395B VAL* 3.6 27.8 - - + +
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Residues in contact with ARG 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B GLU* 5.9 0.7 - - - +
326B ASN* 2.7 58.6 + - - +
327B TYR* 2.8 22.7 + - - +
330B ASN* 3.3 42.4 + - - +
331B PHE* 3.6 13.5 - - - +
386B ASP* 4.9 1.2 + - - -
389B ALA* 3.2 28.6 + - - +
390B GLY* 3.0 27.8 + - - +
392B ALA* 1.3 79.5 - - + +
394B ILE* 1.3 57.6 + - - +
395B VAL 3.7 0.4 - - - -
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Residues in contact with ILE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B GLN* 3.9 10.5 + - + +
315B LEU* 3.8 39.3 - - + -
317B LYS* 3.1 26.3 + - + -
319B LEU* 3.9 16.4 - - + -
323B GLU* 3.5 38.8 - - + +
326B ASN* 4.9 0.2 - - - +
327B TYR* 3.7 30.1 - - + +
390B GLY 3.7 6.1 - - - +
391B PHE* 3.1 12.5 + - + +
393B ARG* 1.3 82.0 - - - +
395B VAL* 1.3 59.4 + - - +
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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
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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