Contacts of the helix formed by residues 384 - 397 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382D LYS 3.3 8.4 + - - +
383D HIS* 1.3 70.3 - - - +
385D PRO* 1.3 60.9 - - + +
387D VAL* 3.6 15.0 - - + +
388D LYS* 2.7 77.1 + - - +
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Residues in contact with PRO 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D TYR* 3.6 22.2 - - + +
383D HIS* 3.1 33.2 - - + +
384D GLU* 1.3 96.7 - - + +
386D THR* 1.3 53.8 + - - +
388D LYS* 3.5 16.2 + - - +
389D ALA* 3.1 29.1 + - - +
420D THR* 3.9 8.1 - - + +
423D GLN* 3.9 20.3 + - - +
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Residues in contact with THR 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D THR* 5.7 0.9 - - - +
375D VAL* 3.8 23.5 - - + +
378D ALA* 3.5 10.7 - - + +
379D TYR* 3.7 32.1 - - + +
383D HIS* 2.7 33.2 + - - -
385D PRO* 1.3 75.1 - - - +
387D VAL* 1.3 61.4 + - - +
389D ALA* 3.1 4.5 + - - +
390D VAL* 2.8 30.0 + - + +
416D ILE* 4.7 4.6 - - + +
420D THR* 4.0 14.7 + - - +
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Residues in contact with VAL 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D TYR* 3.8 33.9 - - + +
382D LYS* 3.8 29.6 - - + -
383D HIS 2.7 23.8 + - - +
384D GLU* 3.7 16.2 - - - +
386D THR* 1.3 72.5 - - - +
388D LYS* 1.3 66.7 + - + +
389D ALA 3.2 0.3 + - - -
391D ASP* 3.0 40.1 + - - +
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Residues in contact with LYS 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D GLU* 2.7 59.9 + - - +
385D PRO* 3.8 17.1 - - - +
387D VAL* 1.3 75.8 - - + +
389D ALA* 1.3 56.4 + - - +
391D ASP* 3.7 6.1 + - - +
392D LEU* 3.4 22.7 + - - +
423D GLN* 5.6 3.0 - - - +
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Residues in contact with ALA 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D PRO 3.1 18.8 + - - +
386D THR* 3.1 5.1 + - - +
388D LYS* 1.3 72.6 - - - +
390D VAL* 1.3 63.2 + - - +
391D ASP 3.2 1.1 - - - -
392D LEU* 3.4 15.7 - - + +
393D VAL* 3.3 22.7 - - + +
416D ILE* 3.8 25.6 - - + -
419D LEU* 4.7 15.3 - - + -
420D THR* 4.5 6.3 - - + -
423D GLN* 6.0 0.4 - - - +
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Residues in contact with VAL 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375D VAL* 3.9 28.0 - - + -
379D TYR* 3.4 42.8 - - + -
386D THR* 2.8 21.0 + - + +
389D ALA* 1.3 71.7 - - - +
391D ASP* 1.3 67.1 + - - +
393D VAL* 3.3 4.5 + - - +
394D LEU* 3.0 48.9 + - + +
404D LEU* 4.4 14.6 - - + -
416D ILE* 3.9 15.0 - - + -
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Residues in contact with ASP 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D TYR* 4.0 12.3 + - - -
387D VAL* 3.0 31.5 + - - +
388D LYS* 3.7 6.3 - - - +
389D ALA 3.2 0.4 - - - -
390D VAL* 1.3 88.3 - - - +
392D LEU* 1.3 63.0 + - - +
394D LEU* 4.1 8.2 - - - +
395D LYS* 2.9 28.5 + - + +
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Residues in contact with LEU 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D ILE* 4.8 11.7 - - + -
262D LEU* 4.7 10.3 - - + -
388D LYS 3.4 12.0 + - - +
389D ALA* 3.4 15.5 - - + +
391D ASP* 1.3 78.0 - - - +
393D VAL* 1.3 59.3 + - + +
395D LYS* 3.6 21.1 - - + +
396D THR* 2.5 51.3 + - - +
419D LEU* 5.6 8.5 - - + -
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Residues in contact with VAL 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D ILE* 5.5 5.4 - - + -
261D LEU* 6.4 1.6 - - + -
262D LEU* 3.7 30.3 - - + -
389D ALA 3.3 13.9 - - - +
390D VAL* 3.4 9.2 - - - +
392D LEU* 1.3 85.0 - - + +
394D LEU* 1.3 58.0 + - + +
395D LYS 3.0 3.8 - - - -
396D THR* 2.8 5.1 + - - -
397D LEU* 2.7 44.4 + - + +
404D LEU* 5.5 2.7 - - + -
412D ALA* 4.1 23.3 - - + +
416D ILE* 4.1 21.3 - - + -
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Residues in contact with LEU 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D TYR* 4.7 1.8 - - - +
390D VAL* 3.0 38.2 + - + +
391D ASP* 4.1 10.1 - - - +
393D VAL* 1.3 77.0 - - + +
395D LYS* 1.3 56.2 + - - +
397D LEU* 5.9 0.2 - - + -
398D GLY* 2.7 27.3 + - - -
399D VAL* 2.8 36.6 + - + +
400D GLY* 3.5 20.2 - - - +
401D PRO* 3.9 27.4 - - + -
403D ALA* 5.2 0.4 - - + -
404D LEU* 4.1 26.9 - - + -
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Residues in contact with LYS 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D ASP* 2.9 18.6 + - + +
392D LEU* 3.7 21.4 - - + +
394D LEU* 1.3 81.0 - - - +
396D THR* 1.3 81.6 + - - +
398D GLY* 3.5 9.6 + - - -
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Residues in contact with THR 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D LEU* 3.5 38.4 - - + +
392D LEU* 2.5 32.0 + - - +
393D VAL 2.8 5.3 + - - -
395D LYS* 1.3 99.8 + - - +
397D LEU* 1.3 59.1 + - + +
398D GLY 3.3 0.6 + - - -
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Residues in contact with LEU 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D LEU* 3.4 36.3 - - + +
265D ALA* 3.9 16.6 - - + +
266D GLY* 3.9 18.4 - - - +
269D LYS* 2.8 41.1 + - + +
393D VAL* 2.7 36.8 + - + +
394D LEU* 5.9 0.4 - - + -
396D THR* 1.3 76.0 - - + +
398D GLY* 1.3 59.4 + - - +
399D VAL* 3.4 24.1 - - + +
408D LEU* 4.9 12.1 - - + -
412D ALA* 5.2 6.7 - - + -
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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