Contacts of the helix formed by residues 373 - 395 (chain D) in PDB entry 3GEB
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 GLY 373 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D GLY* 1.3 73.5 - - - +
374D VAL* 1.3 61.7 + - - +
375D ASP 3.2 0.9 - - - -
376D TRP* 3.3 9.4 + - - +
377D MET* 3.0 32.8 + - - +
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Residues in contact with VAL 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D ASP* 5.9 1.1 - - - +
372D GLY 4.4 9.9 - - - +
373D GLY* 1.3 78.1 - - - +
375D ASP* 1.3 60.6 + - - +
376D TRP 3.1 0.4 - - - -
377D MET* 4.2 6.7 - - + -
378D ARG* 2.7 69.3 + - - +
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Residues in contact with ASP 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D GLY* 3.0 33.3 + - - +
373D GLY 3.2 0.2 - - - -
374D VAL* 1.3 80.9 - - - +
376D TRP* 1.3 57.4 + - - +
378D ARG* 3.8 6.0 - - - +
379D LYS* 2.8 52.1 + - - +
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Residues in contact with TRP 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D ASP* 5.1 13.5 - - - -
328D CYS* 5.8 4.3 - - + -
355D PHE* 3.4 36.6 - + - -
356D HIS* 4.1 34.2 + + - -
372D GLY 3.7 7.4 + - - +
373D GLY* 3.3 15.6 - - - +
374D VAL 3.1 0.2 - - - -
375D ASP* 1.3 76.8 - - - +
377D MET* 1.3 94.6 + - - +
379D LYS* 3.0 16.4 + - + +
380D LEU* 2.9 42.5 + - + +
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Residues in contact with MET 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D VAL* 4.3 17.4 - - + +
339D ASP* 3.4 49.8 - - + +
373D GLY 3.0 21.9 + - - +
374D VAL* 3.7 9.2 - - + +
376D TRP* 1.3 104.5 - - + +
378D ARG* 1.3 56.0 + - - +
380D LEU* 3.4 11.3 + - + +
381D ALA* 2.9 22.5 + - - +
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Residues in contact with ARG 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D SER 3.8 13.7 + - - -
339D ASP* 3.1 28.0 + - - +
340D ASP* 3.4 19.8 + - - -
341D ASN* 3.6 29.4 - - - +
374D VAL* 2.7 51.9 + - - +
375D ASP* 3.8 7.4 - - - +
377D MET* 1.3 75.0 - - - +
379D LYS* 1.3 64.3 + - + +
380D LEU 3.0 1.6 - - - -
381D ALA* 3.3 0.5 + - - +
382D PHE* 2.9 40.4 + - + -
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Residues in contact with LYS 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D TYR* 4.1 9.2 - - - +
353D ASP* 3.2 37.2 + - + +
354D GLY 4.1 10.3 + - - -
355D PHE* 3.3 34.9 - - + +
372D GLY 5.5 1.6 + - - -
375D ASP* 2.8 43.6 + - - +
376D TRP* 3.0 8.6 + - - +
378D ARG* 1.3 76.1 - - + +
380D LEU* 1.3 57.3 + - - +
382D PHE* 3.5 10.2 - - + +
383D ARG* 3.0 40.1 + - - +
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Residues in contact with LEU 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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325D LEU* 3.7 22.2 - - + -
327D ASP* 5.8 0.9 - - - +
328D CYS* 4.8 10.8 - - + -
330D GLN* 4.8 2.7 - - - +
336D VAL* 3.9 29.8 - - + -
355D PHE* 3.7 23.5 - - + -
376D TRP* 2.9 33.6 + - + +
377D MET* 3.5 16.8 - - + +
379D LYS* 1.3 75.4 - - - +
381D ALA* 1.3 66.4 + - - +
382D PHE 3.0 1.3 - - - -
383D ARG* 2.8 18.0 + - - +
384D TYR* 3.0 28.1 + - + -
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Residues in contact with ALA 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D VAL* 3.3 33.1 - - - +
337D SER* 4.7 2.0 - - - +
339D ASP 3.1 29.2 - - - +
340D ASP* 3.6 16.4 - - + +
377D MET 2.9 8.9 + - - +
378D ARG 3.8 0.4 - - - +
380D LEU* 1.3 74.8 - - - +
382D PHE* 1.3 57.8 + - - +
384D TYR* 3.3 2.2 + - - +
385D ARG* 2.8 31.9 + - - +
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Residues in contact with PHE 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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340D ASP* 2.7 36.3 - - - -
341D ASN* 3.3 26.2 - - + -
343D GLN* 3.7 20.6 - - - -
345D LEU* 3.6 20.7 - - + +
348D TYR* 3.8 35.9 - + + -
350D PHE* 3.9 11.4 - - + -
378D ARG* 2.9 31.7 + - + +
379D LYS* 3.5 7.2 - - + +
381D ALA* 1.3 76.9 - - - +
383D ARG* 1.3 64.4 + - - +
385D ARG* 3.2 18.9 + - - -
386D ARG* 2.9 26.7 + - - +
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Residues in contact with ARG 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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321D PHE* 3.4 36.4 - - - +
324D ASP* 3.5 23.0 + - - +
325D LEU* 4.2 24.9 - - + -
348D TYR* 4.5 1.4 - - - -
350D PHE* 3.1 52.2 + - - +
353D ASP* 3.3 10.9 + - - -
355D PHE* 3.3 33.1 - - + +
379D LYS* 3.0 45.1 + - - +
380D LEU* 2.8 20.0 + - - +
382D PHE* 1.3 74.8 - - - +
384D TYR* 1.3 56.2 + - + +
386D ARG* 3.6 2.6 - - - +
387D VAL* 3.1 33.1 + - - +
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Residues in contact with TYR 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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325D LEU* 4.1 14.1 - - + +
328D CYS* 3.1 24.8 - - - -
330D GLN* 3.4 37.1 - - + +
333D VAL* 3.7 27.6 - - + +
336D VAL* 4.3 6.3 - - + -
380D LEU* 3.0 40.8 + - + -
381D ALA 4.0 5.4 - - - +
383D ARG* 1.3 76.4 - - + +
385D ARG* 1.3 61.0 + - - +
387D VAL* 3.4 5.7 + - + +
388D LYS* 2.9 29.7 + - - +
451D LEU* 4.0 23.1 - - + +
452D ILE* 3.8 34.0 - - + +
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Residues in contact with ARG 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D ASP* 2.8 38.3 + - - +
342D GLY* 4.5 4.4 - - - -
343D GLN 2.6 34.0 + - - +
344D ASP* 4.7 0.2 - - - +
345D LEU* 3.1 34.4 - - + +
381D ALA 2.8 20.4 + - - +
382D PHE* 3.5 11.9 - - - +
384D TYR* 1.3 72.9 - - - +
386D ARG* 1.3 57.4 + - - +
388D LYS* 3.5 12.0 + - + +
389D GLU* 2.8 58.9 + - + +
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Residues in contact with ARG 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D PHE* 3.9 13.8 - - + -
345D LEU* 4.1 20.9 + - + +
346D SER* 5.4 4.3 - - - +
350D PHE* 3.9 31.1 - - + -
382D PHE 2.9 16.9 + - - +
383D ARG 3.6 4.7 - - - +
385D ARG* 1.3 75.1 - - - +
387D VAL* 1.3 65.7 + - - +
389D GLU* 3.1 26.9 + - - +
390D MET* 3.0 63.6 + - + +
394D TYR* 6.1 1.0 - - - -
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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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320D LEU* 3.9 40.5 - - + +
321D PHE* 4.0 10.8 - - + -
325D LEU* 5.0 1.1 - - + -
333D VAL* 5.2 1.1 - - + -
383D ARG 3.1 18.3 + - - +
384D TYR* 3.6 10.3 - - + +
386D ARG* 1.3 78.0 - - - +
388D LYS* 1.3 58.8 + - - +
390D MET* 3.2 11.0 + - - +
391D TYR* 2.9 27.6 + - + +
452D ILE* 4.1 15.5 - - + -
455D LEU* 3.4 32.3 - - + -
469D ILE* 4.7 1.8 - - + -
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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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333D VAL* 4.4 8.0 - - + +
334D ASP* 2.6 40.5 + - - +
384D TYR 2.9 19.0 + - - +
385D ARG* 3.5 11.2 - - + +
387D VAL* 1.3 77.9 - - - +
389D GLU* 1.3 63.3 + - + +
391D TYR* 3.2 11.1 + - - +
392D ASN* 3.0 28.2 + - - +
469D ILE* 3.6 29.2 - - + -
470D GLU* 3.7 20.9 + - - -
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Residues in contact with GLU 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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345D LEU* 4.9 6.8 + - - +
346D SER* 5.6 0.7 + - - -
385D ARG* 2.8 54.6 + - + +
386D ARG* 3.4 28.2 + - - +
388D LYS* 1.3 76.7 - - + +
390D MET* 1.3 61.3 + - + +
392D ASN* 3.6 6.1 + - - +
393D THR* 2.9 33.7 + - + +
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Residues in contact with MET 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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319D HIS* 3.1 33.0 - - - +
320D LEU* 4.3 8.1 - - + -
321D PHE* 4.1 6.5 - - + -
386D ARG* 3.0 66.9 + - + +
387D VAL* 3.6 11.9 - - - +
389D GLU* 1.3 75.5 - - + +
391D TYR* 1.3 66.8 + - - +
393D THR* 3.4 7.4 + - - -
394D TYR* 2.9 41.1 + - + +
401D LEU* 4.5 22.1 - - + +
459D LEU* 6.0 0.2 - - - -
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Residues in contact with TYR 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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320D LEU* 6.1 0.2 - - - +
387D VAL* 2.9 14.3 + - + +
388D LYS 3.5 8.7 - - - +
390D MET* 1.3 78.0 - - - +
392D ASN* 1.3 66.4 + - - +
395D LYS* 2.8 40.0 + - + +
455D LEU* 4.1 27.8 - - + -
458D VAL* 3.4 21.6 - - + +
459D LEU* 3.6 37.2 - - + -
464D GLY* 3.0 27.2 - - - -
467D PHE* 2.5 32.3 + - - +
468D PRO* 4.8 0.4 - - + -
469D ILE* 3.7 33.7 - - + -
472D ILE* 3.8 2.4 - - + +
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Residues in contact with ASN 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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388D LYS* 3.0 38.2 + - - +
389D GLU* 4.0 6.2 - - - +
390D MET 3.2 0.4 - - - -
391D TYR* 1.3 90.0 - - - +
393D THR* 1.3 65.1 + - + +
394D TYR 3.5 0.2 + - - -
395D LYS* 3.4 42.0 + - - +
396D ASN 5.2 0.2 + - - -
468D PRO* 5.9 0.5 - - - +
469D ILE* 4.3 10.6 + - - +
470D GLU* 5.5 1.0 - - - +
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Residues in contact with THR 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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389D GLU* 2.9 25.2 + - + +
390D MET* 3.4 4.0 + - - -
392D ASN* 1.3 79.0 - - + +
394D TYR* 1.3 96.4 + - - +
395D LYS 3.7 0.2 - - - -
396D ASN 4.9 1.2 + - - -
397D ASN* 4.1 10.6 + - - +
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Residues in contact with TYR 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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386D ARG* 6.1 0.9 - - - -
390D MET* 2.9 27.7 + - + +
391D TYR 3.7 1.3 - - - -
393D THR* 1.3 104.0 - - - +
395D LYS* 1.3 63.0 + - - +
396D ASN 3.2 2.2 - - - -
397D ASN* 3.3 45.4 + - - +
398D VAL* 3.4 15.6 + - - +
400D GLY* 4.0 5.2 + - - -
401D LEU* 3.5 56.7 - - + +
459D LEU* 4.2 4.9 - - + +
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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
----------------------------------------------------------
391D TYR* 2.8 28.9 + - + +
392D ASN* 3.4 40.1 + - - +
393D THR 3.7 0.2 - - - -
394D TYR* 1.3 75.0 - - - +
396D ASN* 1.3 86.2 + - - +
397D ASN 3.4 0.7 + - - -
398D VAL* 4.1 10.2 - - - +
459D LEU* 3.7 11.9 - - + +
462D GLY* 5.5 4.2 - - - -
464D GLY* 3.6 37.1 + - - +
465D SER* 4.3 10.4 + - - +
468D PRO* 5.9 4.2 - - - +
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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