Contacts of the helix formed by residues 384 - 407 (chain D) in PDB entry 2GPV
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 384 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292D LEU* 5.5 0.7 - - + -
293D SER* 6.1 2.9 - - - +
296D ASP* 2.9 13.5 + - - +
382D ILE* 3.2 13.7 - - - +
383D GLU* 1.3 74.9 - - + +
385D VAL* 1.3 61.9 + - - +
386D GLU* 3.2 11.4 + - - +
387D ALA* 3.0 36.9 + - + +
388D VAL* 3.3 15.2 + - - +
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Residues in contact with VAL 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LYS* 5.2 19.7 - - - +
382D ILE* 4.1 26.5 - - + +
383D GLU 3.6 3.9 + - - +
384D ASP* 1.3 70.8 + - - +
386D GLU* 1.3 56.3 + - - +
388D VAL* 3.2 5.2 + - + +
389D GLN* 2.7 63.5 + - + +
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Residues in contact with GLU 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D ASP* 3.2 7.3 + - - +
385D VAL* 1.3 78.7 - - - +
387D ALA* 1.3 57.0 + - - +
389D GLN* 3.1 9.5 + - - +
390D LYS* 2.8 30.9 + - - +
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Residues in contact with ALA 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D THR 6.0 0.7 - - - +
292D LEU* 3.6 22.7 - - + +
384D ASP* 3.0 30.9 + - + +
386D GLU* 1.3 74.8 - - - +
388D VAL* 1.3 58.3 + - - +
390D LYS* 3.5 7.4 + - - +
391D LEU* 3.0 26.9 + - - +
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Residues in contact with VAL 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D LEU* 3.8 27.4 - - + -
296D ASP* 4.2 5.2 - - + +
300D LEU* 4.3 18.8 - - + -
375D ALA* 3.8 21.3 - - + +
382D ILE* 3.6 22.2 - - + -
384D ASP 3.3 15.4 + - - +
385D VAL* 3.2 9.2 + - + +
387D ALA* 1.3 75.2 - - - +
389D GLN* 1.3 63.3 + - + +
391D LEU* 3.4 7.5 + - + +
392D GLN* 3.0 28.4 + - - +
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Residues in contact with GLN 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LYS* 4.9 15.0 - - - +
358A SER* 5.0 14.0 + - - -
385D VAL* 2.7 49.1 + - + +
386D GLU* 3.1 9.2 + - - +
388D VAL* 1.3 73.1 - - + +
390D LYS* 1.3 57.4 + - - +
392D GLN* 3.0 23.3 + - - +
393D ASP* 2.9 33.6 + - - +
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Residues in contact with LYS 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D GLU 2.8 19.5 + - - +
387D ALA* 3.7 8.5 - - - +
389D GLN* 1.3 69.4 - - - +
391D LEU* 1.3 66.9 + - - +
393D ASP* 3.2 9.7 + - + +
394D VAL* 3.0 37.9 + - + +
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Residues in contact with LEU 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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286D ILE* 4.5 4.0 - - + -
287D PRO 2.9 29.6 - - - +
288D GLY* 3.8 14.6 - - - -
289D PHE* 3.8 18.2 - - + +
292D LEU* 4.3 23.3 - - + -
300D LEU* 4.6 2.9 - - + -
374D LEU* 6.3 0.2 - - + -
375D ALA* 3.9 21.1 - - + -
387D ALA 3.0 13.3 + - - +
388D VAL* 3.5 10.3 - - + +
389D GLN 3.3 0.2 - - - -
390D LYS* 1.3 76.3 - - - +
392D GLN* 1.3 62.7 + - - +
394D VAL* 3.2 9.6 + - + +
395D LEU* 3.2 37.3 + - + +
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Residues in contact with GLN 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LYS* 6.0 4.7 - - - +
419A MET* 3.4 26.9 - - + +
372D ILE* 5.3 1.3 - - - +
375D ALA* 3.0 39.8 + - + +
376D ASN* 3.6 20.8 + - - +
378D ASP 5.9 0.4 - - - +
388D VAL* 3.0 25.7 + - - +
389D GLN* 3.0 24.2 + - - +
391D LEU* 1.3 76.1 - - - +
393D ASP* 1.3 55.4 + - - +
395D LEU* 3.5 3.6 + - - +
396D HIS* 2.9 30.0 + - - +
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Residues in contact with ASP 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ARG* 3.5 27.7 + - - +
416A LYS* 3.3 35.0 + - - +
389D GLN* 2.9 21.9 + - - +
390D LYS* 3.7 13.5 - - + +
391D LEU 3.2 0.2 - - - -
392D GLN* 1.3 75.2 - - - +
394D VAL* 1.3 59.6 + - + +
396D HIS* 2.9 9.5 + - - -
397D GLU* 2.6 37.7 + - - +
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Residues in contact with VAL 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D ILE* 3.3 31.6 - - + +
287D PRO* 5.0 15.3 - - + +
390D LYS* 3.0 38.0 + - + +
391D LEU* 3.2 8.9 + - + +
393D ASP* 1.3 75.0 - - + +
395D LEU* 1.3 60.1 + - + +
397D GLU* 3.6 13.3 + - - +
398D ALA* 3.1 24.8 + - - +
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Residues in contact with LEU 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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237D ILE* 4.4 11.2 - - + -
241D LEU* 4.3 14.4 - - + -
286D ILE* 4.3 16.6 - - + -
287D PRO* 5.4 2.5 - - + +
368D THR* 3.9 10.8 - - + +
371D ALA* 3.4 48.7 - - + +
372D ILE* 3.8 14.6 - - + +
375D ALA* 3.9 16.8 - - + -
391D LEU* 3.2 24.2 + - + +
392D GLN* 3.8 6.3 - - - +
393D ASP 3.1 0.6 - - - -
394D VAL* 1.3 76.8 - - + +
396D HIS* 1.3 66.1 + - - +
398D ALA* 3.0 7.3 + - - +
399D LEU* 3.0 18.9 + - - +
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Residues in contact with HIS 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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412A ARG* 3.4 39.9 + - + +
415A GLY* 3.5 25.4 - - - -
416A LYS* 3.6 8.0 + - - +
419A MET* 3.8 19.5 - - - -
372D ILE* 4.2 11.0 - - + +
392D GLN 2.9 18.7 + - - +
393D ASP* 3.4 12.3 + - - +
395D LEU* 1.3 75.4 - - - +
397D GLU* 1.3 57.7 + - - +
399D LEU* 3.1 6.5 + - + +
400D GLN* 2.8 51.9 + - + +
418D LEU* 3.9 16.4 - - + +
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Residues in contact with GLU 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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412A ARG* 3.7 46.1 + - - +
237D ILE* 5.7 2.8 - - - +
393D ASP 2.6 20.2 + - - +
394D VAL* 3.7 13.1 - - - +
396D HIS* 1.3 73.1 - - - +
398D ALA* 1.3 56.6 + - - +
400D GLN* 3.7 2.9 - - + +
401D ASP* 3.0 46.7 + - - +
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Residues in contact with ALA 398 (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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235D ASN* 3.4 22.5 - - - +
237D ILE* 3.8 28.3 - - + -
238D VAL* 4.5 2.9 - - + -
368D THR* 4.5 8.1 - - + -
394D VAL 3.1 13.5 + - - +
395D LEU* 3.0 11.7 + - - +
397D GLU* 1.3 74.5 - - - +
399D LEU* 1.3 65.0 + - - +
401D ASP* 3.4 2.3 + - - -
402D TYR* 2.9 25.9 + - - +
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Residues in contact with LEU 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D GLU 5.7 0.2 - - - +
365D GLU* 4.9 13.7 - - + +
368D THR* 4.0 24.3 - - + +
369D LEU* 4.4 6.1 - - + -
372D ILE* 4.0 8.3 - - + -
395D LEU 3.0 10.7 + - - +
396D HIS* 3.4 9.4 - - + +
398D ALA* 1.3 78.1 - - - +
400D GLN* 1.3 57.5 + - - +
402D TYR* 3.2 7.0 + - + +
403D GLU* 2.9 51.7 + - + +
414D ALA* 4.0 20.0 - - + +
417D MET* 4.1 15.9 - - + -
418D LEU* 3.8 35.7 - - + -
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Residues in contact with GLN 400 (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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400A GLN* 5.7 3.2 + - - -
411A PRO 5.2 7.3 + - - +
412A ARG* 4.7 16.1 - - + +
415A GLY* 5.6 2.8 - - - +
396D HIS* 2.8 38.5 + - + +
397D GLU* 3.7 10.1 - - + +
399D LEU* 1.3 77.6 - - - +
401D ASP* 1.3 61.3 + - - +
403D GLU* 3.3 2.8 + - - +
404D ALA* 2.9 30.9 + - + +
411D PRO 5.3 4.3 - - - +
414D ALA* 4.0 23.5 - - - +
418D LEU* 5.5 1.0 - - - +
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Residues in contact with ASP 401 (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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233D PRO* 5.1 6.1 - - - +
235D ASN* 4.8 11.0 + - + +
397D GLU* 3.0 39.2 + - - +
398D ALA* 3.9 4.4 - - - +
400D GLN* 1.3 76.1 - - - +
402D TYR* 1.3 66.1 + - - +
404D ALA* 3.4 8.1 + - - +
405D GLY* 3.2 18.2 + - - -
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Residues in contact with TYR 402 (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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235D ASN* 4.5 15.0 + - + +
238D VAL* 4.6 12.8 - - + -
362D GLU* 2.6 24.6 + - - -
364D GLU* 3.4 42.5 + - + +
365D GLU* 3.4 30.5 - - + -
368D THR* 6.0 0.2 - - - +
398D ALA 2.9 18.5 + - - +
399D LEU* 3.4 8.5 - - + +
401D ASP* 1.3 76.0 - - - +
403D GLU* 1.3 74.5 + - + +
405D GLY* 3.1 2.4 + - - -
406D GLN* 2.9 54.2 + - + +
407D HIS* 4.4 0.7 - + - -
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Residues in contact with GLU 403 (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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365D GLU* 2.3 35.7 - - - +
399D LEU* 2.9 27.3 + - + +
400D GLN* 3.8 4.7 - - - +
402D TYR* 1.3 80.0 - - + +
404D ALA* 1.3 64.9 + - - +
407D HIS* 3.0 45.6 + - - +
410D ASP 5.7 0.7 - - - +
413D ARG* 3.1 33.0 + - + +
414D ALA* 3.7 33.9 - - + +
417D MET* 4.2 3.1 - - - +
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Residues in contact with ALA 404 (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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400D GLN* 2.9 18.4 + - + +
401D ASP* 3.6 11.2 - - - +
402D TYR 3.3 0.2 - - - -
403D GLU* 1.3 76.4 - - - +
405D GLY* 1.3 57.3 + - - +
407D HIS 5.1 0.9 - - - -
408D MET* 3.3 30.2 - - - +
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Residues in contact with GLY 405 (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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233D PRO* 3.9 30.0 - - - +
401D ASP 3.2 7.9 + - - -
402D TYR 3.1 6.2 + - - -
404D ALA* 1.3 79.9 - - - +
406D GLN* 1.3 61.0 + - - +
407D HIS 3.4 0.7 - - - -
408D MET* 4.6 11.5 + - - +
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Residues in contact with GLN 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362D GLU* 4.1 3.8 + - - +
402D TYR* 2.9 46.9 + - + +
405D GLY* 1.3 73.1 - - - -
407D HIS* 1.3 87.9 + - + +
408D MET 3.9 0.7 - - - -
409D GLU* 4.2 5.5 - - - +
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Residues in contact with HIS 407 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D LYS* 6.5 0.4 - - + -
362D GLU* 2.7 37.3 + - - -
365D GLU* 4.1 3.4 - - - -
402D TYR* 4.4 1.1 - + - -
403D GLU* 3.0 41.3 + - - +
406D GLN* 1.3 106.9 + - + +
408D MET* 1.3 63.2 + - - +
409D GLU* 2.8 30.2 + - - +
410D ASP 3.0 21.5 - - - +
411D PRO* 4.9 0.3 - - - +
413D ARG* 3.4 30.3 + - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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