Contacts of the helix formed by residues 379 - 395 (chain D) in PDB entry 3GV5
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 VAL 379 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329D LEU* 4.7 12.3 - - + -
368D VAL* 3.7 29.2 - - + +
371D LYS* 3.6 51.4 - - + +
372D LEU 4.6 0.7 - - - +
377D TYR* 3.1 15.4 + - + +
378D ASP* 1.3 73.7 - - - +
380D MSE 1.3 64.5 + - - +
381D THR 3.6 0.2 - - - -
382D PRO* 3.2 7.6 - - - +
383D MSE 3.1 29.5 + - + +
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Residues in contact with MSE 380 (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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322D GLU* 3.1 44.0 - - + +
325D LEU* 3.7 24.7 - - - -
326D ALA* 3.8 16.4 - - + -
329D LEU* 3.9 16.3 - - + +
378D ASP* 3.2 12.1 + - - +
379D VAL* 1.3 78.2 - - - +
381D THR* 1.3 62.4 + - + +
383D MSE 3.3 2.8 + - - +
384D VAL* 2.8 40.4 + - + +
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Residues in contact with THR 381 (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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378D ASP* 3.0 23.9 + - - +
380D MSE 1.3 74.9 - - + +
382D PRO* 1.4 72.7 - - - +
384D VAL* 3.9 6.4 - - - +
385D ASP* 3.0 40.2 + - - +
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Residues in contact with PRO 382 (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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368D VAL* 3.9 26.9 - - + -
378D ASP* 3.4 20.9 - - - +
379D VAL* 3.2 17.7 - - - +
381D THR* 1.4 97.7 - - - +
383D MSE 1.3 58.3 + - - +
385D ASP* 3.4 8.8 + - + +
386D ILE* 3.1 29.6 + - - +
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Residues in contact with MSE 383 (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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325D LEU* 3.6 22.2 - - + -
329D LEU* 4.8 3.4 - - + -
342D VAL* 3.7 38.4 - - + -
364D ILE* 4.2 17.9 - - - -
368D VAL* 3.9 24.2 - - + -
371D LYS* 4.8 1.8 - - - +
379D VAL* 3.1 29.6 + - + +
382D PRO* 1.3 74.9 - - - +
384D VAL* 1.3 64.2 + - - +
386D ILE* 3.4 13.9 + - + +
387D LEU* 3.0 37.9 + - + +
410D PHE* 3.7 21.1 - - + -
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Residues in contact with VAL 384 (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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318D LYS* 3.6 35.2 - - + +
321D ILE* 5.5 3.4 - - + -
322D GLU* 3.8 30.5 - - + +
325D LEU* 3.8 14.1 - - + +
380D MSE 2.8 33.0 + - + +
381D THR* 3.9 6.5 - - - +
383D MSE 1.3 71.3 - - - +
385D ASP* 1.3 61.7 + - - +
387D LEU* 3.0 9.8 + - + +
388D MSE 2.8 37.6 + - + +
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Residues in contact with ASP 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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318D LYS* 5.4 4.5 + - - -
381D THR* 3.0 28.1 + - - +
382D PRO* 3.4 9.3 - - + +
383D MSE 3.3 0.2 - - - -
384D VAL* 1.3 78.6 - - - +
386D ILE* 1.3 63.0 + - + +
388D MSE 3.4 5.8 + - - +
389D LYS* 3.1 38.0 + - - +
392D ARG* 5.2 0.5 + - - -
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Residues in contact with ILE 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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342D VAL* 3.9 16.2 - - + -
362D CYS* 3.5 30.7 - - - -
363D PRO 5.1 0.4 - - - +
364D ILE* 4.9 2.2 - - - -
365D PRO* 3.5 36.3 - - + -
368D VAL* 4.6 5.8 - - + -
382D PRO 3.1 15.8 + - - +
383D MSE 3.6 23.8 - - + +
385D ASP* 1.3 76.4 - - + +
387D LEU* 1.3 59.0 + - - +
389D LYS* 3.3 15.6 + - + +
390D LEU* 3.0 27.2 + - + +
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Residues in contact with LEU 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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321D ILE* 3.7 31.2 - - + -
325D LEU* 4.0 30.3 - - + -
342D VAL* 3.8 21.1 - - + -
343D ARG 4.5 0.9 - - - +
344D LEU* 3.6 28.2 - - + +
383D MSE 3.0 27.4 + - + +
384D VAL* 3.0 6.5 + - - +
386D ILE* 1.3 76.3 - - + +
388D MSE 1.3 55.5 + - - +
390D LEU* 3.3 12.1 + - + +
391D PHE* 2.8 33.1 + - - +
408D VAL* 4.1 16.6 - - + -
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Residues in contact with MSE 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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314D GLU* 3.5 27.8 - - - +
317D ALA* 3.9 13.9 - - + -
318D LYS* 3.8 30.7 - - + -
321D ILE* 3.6 28.5 - - - -
384D VAL* 2.8 29.1 + - + +
385D ASP* 4.0 4.9 - - - +
387D LEU* 1.3 70.5 - - - +
389D LYS* 1.3 61.1 + - - +
391D PHE* 3.4 31.4 - - + +
392D ARG* 3.0 52.0 + - - +
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Residues in contact with LYS 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 ASP* 3.1 27.9 + - - +
386D ILE* 3.4 15.0 - - + +
388D MSE 1.3 74.7 - - - +
390D LEU* 1.3 66.4 + - + +
392D ARG* 3.4 21.3 + - - +
393D ASN* 3.1 23.4 + - - +
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Residues in contact with LEU 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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342D VAL* 4.0 14.4 - - + +
344D LEU* 4.0 20.9 - - + +
360D ARG* 3.5 39.6 - - + +
361D GLN 4.1 9.4 - - - +
362D CYS* 3.9 31.6 - - + -
386D ILE 3.0 16.5 + - - +
387D LEU* 3.4 18.6 - - + +
389D LYS* 1.3 76.7 - - + +
391D PHE* 1.3 62.7 + - - +
393D ASN* 3.3 15.9 + - + +
394D MSE 3.3 16.8 + - - +
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Residues in contact with PHE 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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314D GLU* 3.8 22.2 - - + -
317D ALA* 3.7 20.2 - - + -
321D ILE* 4.3 9.9 - - + -
344D LEU* 3.5 19.7 - - + +
346D ILE* 4.7 1.8 - - + -
387D LEU 2.8 19.3 + - - +
388D MSE 3.4 28.7 - - + +
389D LYS 3.2 0.2 - - - -
390D LEU* 1.3 72.0 - - - +
392D ARG* 1.3 63.8 + - + +
393D ASN 3.2 0.2 - - - -
394D MSE 3.0 17.8 + - - -
395D VAL* 3.0 54.9 - - + +
397D VAL* 4.0 4.9 - - + -
401D PHE* 3.9 9.4 - + - -
403D LEU* 3.5 28.7 - - + -
406D LEU* 4.4 7.4 - - + -
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Residues in contact with ARG 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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314D GLU* 3.8 27.5 + - - +
385D ASP 5.2 0.2 + - - -
388D MSE 3.0 50.3 + - - +
389D LYS* 3.8 23.6 - - - +
391D PHE* 1.3 76.7 - - + +
393D ASN* 1.3 59.9 + - - +
395D VAL 3.2 21.2 + - - +
396D ASN* 5.2 1.7 - - - +
397D VAL* 4.3 20.4 - - + +
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Residues in contact with ASN 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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360D ARG* 3.0 38.1 + - + +
389D LYS 3.1 13.3 + - - +
390D LEU* 3.5 13.2 - - + +
391D PHE 3.2 0.2 - - - -
392D ARG* 1.3 77.1 - - - +
394D MSE 1.3 62.2 + - - +
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Residues in contact with MSE 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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344D LEU* 3.7 46.2 - - + +
346D ILE* 3.8 24.5 - - + -
348D ARG* 2.6 28.6 + - - +
358D GLU* 3.7 35.0 - - - +
359D SER* 3.8 5.4 - - - +
360D ARG* 3.5 39.3 - - + +
390D LEU 3.3 12.2 + - - +
391D PHE* 3.0 4.8 + - - +
393D ASN* 1.3 76.6 - - - +
395D VAL* 1.4 68.8 + - + +
396D ASN* 4.4 0.6 + - - +
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Residues in contact with VAL 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D ILE* 3.7 20.6 - - + -
348D ARG* 4.4 9.0 - - - +
391D PHE* 3.0 58.1 - - + +
392D ARG* 3.2 17.5 + - - +
393D ASN 3.4 2.0 - - - -
394D MSE 1.4 88.9 - - + +
396D ASN* 1.3 63.8 + - - +
397D VAL* 3.2 17.2 - - + +
401D PHE* 4.0 23.6 - - + -
403D LEU* 4.8 4.3 - - + -
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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