Contacts of the helix formed by residues 384 - 397 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382L LYS 3.3 8.8 + - - +
383L HIS* 1.3 69.3 - - - +
385L PRO* 1.3 61.3 - - + +
387L VAL* 4.2 14.2 - - + +
388L LYS* 2.7 76.3 + - - +
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Residues in contact with PRO 385 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297L TYR* 3.6 22.4 - - + +
383L HIS* 3.1 33.4 - - + +
384L GLU* 1.3 95.6 - - + +
386L THR* 1.3 54.2 + - - +
388L LYS* 3.5 15.9 + - - +
389L ALA* 3.1 28.1 + - - +
420L THR* 3.9 8.5 - - + +
423L GLN* 3.9 19.7 + - - +
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Residues in contact with THR 386 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298L THR* 5.7 0.9 - - - +
375L VAL* 3.8 23.4 - - + +
378L ALA* 3.5 11.5 - - + +
379L TYR* 3.7 31.4 - - + +
383L HIS* 2.7 33.3 + - - -
385L PRO* 1.3 75.1 - - - +
387L VAL* 1.3 60.8 + - - +
389L ALA* 3.1 4.2 + - - +
390L VAL* 2.8 30.6 + - + +
416L ILE* 4.7 3.5 - - + +
420L THR* 4.0 15.4 + - - +
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Residues in contact with VAL 387 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379L TYR* 3.8 33.2 - - + +
382L LYS* 3.8 29.2 - - + -
383L HIS 2.7 23.0 + - - +
384L GLU* 3.7 16.2 - - - +
386L THR* 1.3 71.2 - - - +
388L LYS* 1.3 68.6 + - + +
389L ALA 3.2 0.3 + - - -
391L ASP* 3.1 39.9 + - - +
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Residues in contact with LYS 388 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384L GLU* 2.7 60.5 + - - +
385L PRO* 3.8 16.7 - - - +
387L VAL* 1.3 76.4 - - + +
389L ALA* 1.3 55.3 + - - +
391L ASP* 3.7 6.6 + - - +
392L LEU* 3.4 22.7 + - - +
423L GLN* 5.6 3.0 - - - +
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Residues in contact with ALA 389 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385L PRO 3.1 18.2 + - - +
386L THR* 3.1 4.9 + - - +
388L LYS* 1.3 72.9 - - - +
390L VAL* 1.3 64.1 + - - +
391L ASP 3.2 1.6 - - - -
392L LEU* 3.4 15.3 - - + +
393L VAL* 3.3 22.0 - - - +
416L ILE* 3.8 24.7 - - + -
419L LEU* 4.7 16.4 - - + -
420L THR* 4.5 6.1 - - + -
423L GLN* 6.0 0.4 - - - +
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Residues in contact with VAL 390 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375L VAL* 3.9 27.8 - - + -
379L TYR* 3.4 42.4 - - + -
386L THR* 2.8 21.4 + - + +
389L ALA* 1.3 72.2 - - - +
391L ASP* 1.3 67.7 + - - +
393L VAL* 3.3 4.4 + - - +
394L LEU* 3.0 48.7 + - + +
404L LEU* 4.4 14.1 - - + -
416L ILE* 3.9 14.4 - - + -
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Residues in contact with ASP 391 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379L TYR* 4.0 12.4 + - - -
387L VAL* 3.1 30.1 + - - +
388L LYS* 3.8 7.1 - - - +
389L ALA 3.2 0.4 - - - -
390L VAL* 1.3 86.8 - - - +
392L LEU* 1.3 63.1 + - - +
394L LEU* 4.1 7.5 - - - +
395L LYS* 2.9 28.6 + - - +
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Residues in contact with LEU 392 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258L ILE* 4.8 11.7 - - + -
262L LEU* 4.7 9.9 - - + -
388L LYS 3.4 12.1 + - - +
389L ALA* 3.4 16.6 - - + +
391L ASP* 1.3 78.7 - - - +
393L VAL* 1.3 59.7 + - + +
395L LYS* 3.6 20.8 - - + +
396L THR* 2.5 50.8 + - - +
419L LEU* 5.6 8.5 - - + -
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Residues in contact with VAL 393 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258L ILE* 5.5 5.4 - - + -
261L LEU* 6.4 1.6 - - + -
262L LEU* 3.7 30.7 - - + -
389L ALA 3.3 13.7 - - - +
390L VAL* 3.4 8.7 - - - +
392L LEU* 1.3 84.1 - - + +
394L LEU* 1.3 58.9 + - + +
395L LYS 3.0 3.8 - - - -
396L THR* 2.8 5.4 + - - -
397L LEU* 2.7 44.2 + - + +
404L LEU* 5.5 3.1 - - + -
412L ALA* 4.1 22.2 - - + +
416L ILE* 4.1 21.5 - - + -
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Residues in contact with LEU 394 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C LYS* 4.8 1.1 - - - -
379L TYR* 4.7 1.6 - - - +
390L VAL* 3.0 38.2 + - + +
391L ASP* 4.1 9.6 - - - +
393L VAL* 1.3 78.1 - - + +
395L LYS* 1.3 56.5 - - - +
398L GLY* 2.7 28.2 + - - -
399L VAL* 2.8 35.9 + - + +
400L GLY* 3.5 20.9 - - - +
401L PRO* 3.9 27.8 - - + -
403L ALA* 5.2 0.7 - - + -
404L LEU* 4.1 25.8 - - + -
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Residues in contact with LYS 395 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C LYS* 4.7 20.5 - - - +
391L ASP* 2.9 17.9 + - + +
392L LEU* 3.7 21.6 - - + +
394L LEU* 1.3 81.6 - - - +
396L THR* 1.3 82.7 + - - +
398L GLY* 3.5 9.4 + - - -
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Residues in contact with THR 396 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262L LEU* 3.5 36.7 - - + +
392L LEU* 2.5 32.0 + - - +
393L VAL 2.8 5.7 + - - -
395L LYS* 1.3 99.3 + - - +
397L LEU* 1.3 59.8 + - + +
398L GLY 3.3 0.6 + - - -
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Residues in contact with LEU 397 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262L LEU* 3.4 37.7 - - + +
265L ALA* 3.9 16.4 - - + +
266L GLY* 3.9 18.6 - - - +
269L LYS* 2.8 42.7 + - + +
393L VAL* 2.7 36.7 + - + +
394L LEU* 5.9 0.2 - - + -
396L THR* 1.3 75.4 - - + +
398L GLY* 1.3 59.6 + - - +
399L VAL* 3.4 24.3 + - + +
408L LEU* 4.9 11.4 - - + -
412L ALA* 5.2 7.0 - - + -
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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