Contacts of the helix formed by residues 384 - 397 (chain F) in PDB entry 2FRV
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 GLU 384 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382F LYS 3.3 8.6 + - - +
383F HIS* 1.3 70.1 - - - +
385F PRO* 1.3 63.4 - - + +
387F VAL* 4.2 14.5 - - + +
388F LYS* 2.7 75.1 + - - +
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Residues in contact with PRO 385 (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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297F TYR* 3.6 22.0 - - + +
383F HIS* 3.1 34.1 - - + +
384F GLU* 1.3 95.5 - - + +
386F THR* 1.3 53.8 + - - +
388F LYS* 3.5 16.7 + - - +
389F ALA* 3.1 28.1 + - - +
420F THR* 3.9 8.8 - - + +
423F GLN* 3.9 19.9 + - - +
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Residues in contact with THR 386 (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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298F THR* 5.7 0.7 - - - +
375F VAL* 3.8 23.1 - - + +
378F ALA* 3.5 12.5 - - + +
379F TYR* 3.7 31.4 - - + +
383F HIS* 2.7 33.6 + - - -
385F PRO* 1.3 75.4 - - - +
387F VAL* 1.3 62.1 + - - +
389F ALA* 3.1 4.1 + - - +
390F VAL* 2.8 30.1 + - + +
416F ILE* 4.7 5.1 - - + +
420F THR* 4.0 15.8 + - - +
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Residues in contact with VAL 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379F TYR* 3.8 33.2 - - + +
382F LYS* 3.8 28.0 - - + -
383F HIS 2.7 23.8 + - - +
384F GLU* 3.7 16.4 - - + +
386F THR* 1.3 72.0 - - - +
388F LYS* 1.3 67.1 + - + +
389F ALA 3.2 0.3 + - - -
390F VAL* 4.2 0.2 - - - +
391F ASP* 3.1 39.5 + - - +
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Residues in contact with LYS 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384F GLU* 2.7 59.4 + - - +
385F PRO* 3.8 16.5 - - - +
387F VAL* 1.3 75.2 - - + +
389F ALA* 1.3 56.1 + - - +
391F ASP* 3.8 6.0 - - - +
392F LEU* 3.4 22.9 + - - +
423F GLN* 5.6 3.6 - - - +
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Residues in contact with ALA 389 (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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385F PRO 3.1 17.1 + - - +
386F THR* 3.1 4.7 + - - +
388F LYS* 1.3 73.3 - - - +
390F VAL* 1.3 64.8 + - - +
391F ASP 3.2 1.1 - - - -
392F LEU* 3.4 15.1 - - + +
393F VAL* 3.3 22.0 - - - +
416F ILE* 3.8 26.0 - - + -
419F LEU* 4.7 15.9 - - + -
420F THR* 4.5 6.1 - - + -
423F GLN* 6.0 0.2 - - - +
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Residues in contact with VAL 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375F VAL* 3.9 28.3 - - + -
379F TYR* 3.4 42.8 - - + -
386F THR* 2.8 21.8 + - + +
387F VAL 4.2 0.2 - - - +
389F ALA* 1.3 72.8 - - - +
391F ASP* 1.3 66.1 + - - +
393F VAL* 3.3 4.6 + - - +
394F LEU* 3.0 49.2 + - + +
404F LEU* 4.4 14.1 - - + -
416F ILE* 3.9 15.0 - - + -
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Residues in contact with ASP 391 (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 TYR* 4.0 12.1 + - - -
387F VAL* 3.1 30.8 + - - +
388F LYS* 3.8 6.3 - - - +
389F ALA 3.2 0.4 - - - -
390F VAL* 1.3 87.4 - - - +
392F LEU* 1.3 63.5 + - - +
394F LEU* 4.1 8.1 - - - +
395F LYS* 2.9 28.8 + - - +
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Residues in contact with LEU 392 (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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258F ILE* 4.8 11.9 - - + -
262F LEU* 4.7 9.6 - - + -
388F LYS 3.4 12.1 + - - +
389F ALA* 3.4 16.6 - - + +
391F ASP* 1.3 78.0 - - - +
393F VAL* 1.3 60.1 + - + +
395F LYS* 3.6 20.7 - - + +
396F THR* 2.5 50.0 + - - +
419F LEU* 5.6 7.6 - - + -
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Residues in contact with VAL 393 (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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258F ILE* 5.5 5.4 - - + -
261F LEU* 6.4 1.3 - - + -
262F LEU* 3.7 30.5 - - + -
389F ALA 3.3 13.9 - - - +
390F VAL* 3.4 9.6 - - - +
392F LEU* 1.3 84.6 - - + +
394F LEU* 1.3 58.0 + - + +
395F LYS 3.0 3.6 - - - -
396F THR* 2.8 5.0 + - - -
397F LEU* 2.7 44.6 + - + +
404F LEU* 5.5 2.9 - - + -
412F ALA* 4.1 22.9 - - + +
416F ILE* 4.1 21.8 - - + -
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Residues in contact with LEU 394 (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 TYR* 4.7 1.3 - - - +
390F VAL* 3.0 38.6 + - + +
391F ASP* 4.1 9.4 - - - +
393F VAL* 1.3 77.2 - - + +
395F LYS* 1.3 56.6 + - - +
397F LEU* 5.9 0.4 - - + -
398F GLY* 2.7 28.0 + - - -
399F VAL* 2.8 36.3 + - + +
400F GLY* 3.5 20.4 - - - +
401F PRO* 3.9 27.4 - - + -
403F ALA* 5.2 0.7 - - + -
404F LEU* 4.1 26.0 - - + -
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Residues in contact with LYS 395 (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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391F ASP 2.9 19.1 + - - +
392F LEU* 3.7 22.0 - - + +
394F LEU* 1.3 80.5 - - - +
396F THR* 1.3 82.5 + - - +
398F GLY* 3.5 9.5 + - - -
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Residues in contact with THR 396 (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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262F LEU* 3.5 37.2 - - + +
392F LEU* 2.5 32.1 + - - +
393F VAL 2.8 4.8 + - - -
395F LYS* 1.3 98.4 + - - +
397F LEU* 1.3 59.4 + - + +
398F GLY 3.6 0.2 + - - -
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Residues in contact with LEU 397 (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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262F LEU* 3.4 38.8 - - + +
265F ALA* 3.9 16.2 - - + +
266F GLY* 3.9 18.4 - - - +
269F LYS* 2.8 42.1 + - + +
393F VAL* 2.7 36.5 + - + +
394F LEU* 5.9 0.4 - - + -
396F THR* 1.3 74.7 - - + +
398F GLY* 1.3 58.5 + - - +
399F VAL* 3.4 24.3 + - + +
408F LEU* 4.9 11.2 - - + -
412F ALA* 5.2 6.3 - - + -
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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