Contacts of the helix formed by residues 297 - 321 (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 ASP 297 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296D LYS* 1.3 73.2 - - - +
298D THR* 1.3 66.9 + - - +
299D THR* 3.8 13.7 + - - +
300D THR* 2.6 38.6 + - - +
301D SER* 3.0 26.9 + - - -
420D LEU* 4.7 3.0 - - + +
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Residues in contact with THR 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D GLY* 5.6 4.3 - - - +
291D ALA* 3.6 26.6 - - + +
292D SER* 5.1 4.3 - - - +
296D LYS 3.1 5.5 + - - +
297D ASP* 1.3 75.6 + - - +
299D THR* 1.3 65.4 + - - +
301D SER* 3.5 2.9 + - - -
302D VAL* 3.2 32.4 + - - +
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Residues in contact with THR 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D ASP* 3.2 12.6 + - - +
298D THR* 1.3 82.0 + - - +
300D THR* 1.3 66.9 + - - +
302D VAL* 3.5 5.6 + - - +
303D ARG* 3.1 25.9 + - + +
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Residues in contact with THR 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D ASP* 2.6 35.0 + - - +
299D THR* 1.3 77.8 - - - +
301D SER* 1.3 63.5 + - - +
303D ARG* 3.5 23.4 + - - +
304D ILE* 3.2 36.6 + - + +
416D GLU* 5.6 0.9 - - - +
420D LEU* 4.4 13.5 - - + -
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Residues in contact with SER 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D SER 5.7 0.2 - - - -
285D LEU* 3.7 27.7 - - - +
288D GLY* 6.2 1.3 - - - -
290D PHE* 4.3 1.9 - - - -
291D ALA* 3.6 23.4 - - - +
296D LYS* 4.2 1.6 - - - +
297D ASP 3.0 14.3 + - - -
298D THR 3.5 10.3 - - - -
299D THR 3.2 0.2 - - - -
300D THR* 1.3 78.5 - - - +
302D VAL* 1.3 63.5 + - - +
304D ILE* 3.4 2.8 + - - +
305D GLY 3.0 17.8 + - - -
420D LEU* 3.7 27.5 - - - +
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Residues in contact with VAL 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D LEU 3.6 17.3 - - - +
286D LEU* 4.5 14.3 - - - +
288D GLY* 5.5 6.1 - - - +
298D THR* 3.2 18.2 + - - +
299D THR* 3.5 6.3 + - - +
301D SER* 1.3 72.9 - - - +
303D ARG* 1.3 67.8 + - - +
305D GLY* 3.3 0.9 + - - +
306D LEU* 2.9 45.4 + - + +
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Residues in contact with ARG 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D THR* 3.1 21.4 + - + +
300D THR* 3.7 30.9 + - - +
301D SER 3.3 0.2 - - - -
302D VAL* 1.3 77.3 - - - +
304D ILE* 1.3 70.6 + - - +
306D LEU* 3.6 5.9 + - - +
307D MET* 3.1 56.6 + - + +
413D LEU* 4.7 0.2 - - - +
416D GLU* 2.7 41.2 + - - -
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Residues in contact with ILE 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D LEU* 4.3 3.4 - - + -
300D THR* 3.2 29.1 + - + +
301D SER* 3.8 4.0 - - - +
303D ARG* 1.3 91.6 - - - +
305D GLY* 1.3 61.5 + - - +
307D MET* 3.3 1.8 + - - +
308D MET* 2.8 32.6 + - + +
413D LEU* 3.7 24.1 - - + +
416D GLU* 4.0 31.2 - - + +
417D LEU* 3.9 29.4 - - + +
420D LEU* 4.0 19.1 - - + -
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Residues in contact with GLY 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D PHE* 3.6 6.4 - - - -
285D LEU* 3.9 19.9 - - - +
286D LEU* 3.3 19.3 - - - -
301D SER 3.0 14.8 + - - -
302D VAL 3.3 1.7 + - - -
304D ILE* 1.3 78.6 - - - +
306D LEU* 1.3 50.8 + - - +
308D MET* 3.3 4.3 + - - +
309D GLU* 2.7 34.5 + - - +
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Residues in contact with LEU 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D LEU* 3.3 11.9 - - + +
302D VAL* 2.9 38.3 + - + +
303D ARG* 4.0 6.1 - - - +
305D GLY* 1.3 71.6 - - - +
307D MET* 1.3 67.4 + - + +
309D GLU* 3.2 23.2 + - - +
310D GLU* 3.0 23.4 + - - +
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Residues in contact with MET 307 (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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303D ARG* 3.1 46.9 + - + +
304D ILE 3.7 3.6 - - - +
306D LEU* 1.3 76.3 - - + +
308D MET* 1.3 61.2 + - - +
310D GLU* 3.3 10.2 + - - +
311D MET* 3.1 27.5 + - + +
409D THR* 4.6 20.9 - - + -
413D LEU* 4.0 29.4 - - + -
416D GLU* 5.5 1.6 - - - +
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Residues in contact with MET 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D PHE* 4.1 8.5 - - + -
285D LEU* 5.7 1.3 - - + -
304D ILE* 2.8 20.4 + - + +
305D GLY* 3.6 4.9 - - - +
307D MET* 1.3 73.6 - - - +
309D GLU* 1.3 67.8 + - - +
311D MET* 3.2 9.0 + - - +
312D ILE* 3.1 63.8 + - + +
410D TRP* 5.3 6.1 - - - -
413D LEU* 3.7 23.7 - - + +
414D ARG* 5.3 6.3 - - - -
417D LEU* 5.1 7.2 - - + -
460D LEU* 4.6 16.6 - - + +
461D TYR* 2.9 46.9 - - + +
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Residues in contact with GLU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D PHE* 3.7 21.1 - - + -
283D HIS* 6.1 0.2 - - - -
286D LEU* 3.8 21.0 - - + +
305D GLY 2.7 18.5 + - - +
306D LEU* 3.2 28.5 + - - +
308D MET* 1.3 76.5 - - - +
310D GLU* 1.3 62.3 + - - +
312D ILE* 3.1 7.0 + - - +
313D PHE* 3.1 51.8 + - + +
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Residues in contact with GLU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D LEU 3.0 12.3 + - - +
307D MET* 3.4 13.1 - - - +
309D GLU* 1.3 78.0 - - - +
311D MET* 1.3 62.6 + - + +
313D PHE* 3.4 5.3 + - - +
314D ASN* 2.8 56.9 + - + +
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Residues in contact with MET 311 (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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307D MET 3.1 17.2 + - - +
308D MET* 3.2 10.5 + - - +
310D GLU* 1.3 79.3 - - + +
312D ILE* 1.3 57.7 + - - +
314D ASN* 4.2 4.3 - - - +
315D LEU* 3.2 27.2 + - - +
402D ILE* 4.7 4.7 - - + +
406D LYS* 3.5 39.0 - - + +
409D THR* 4.6 11.7 - - + -
410D TRP* 3.6 35.7 - - + +
413D LEU* 3.9 17.7 - - - -
460D LEU* 3.4 16.1 - - + +
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Residues in contact with ILE 312 (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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282D PHE* 3.9 17.9 - - + -
308D MET* 3.1 42.2 - - + +
309D GLU 3.1 6.0 + - - +
310D GLU 3.1 0.2 - - - -
311D MET* 1.3 76.2 - - - +
313D PHE* 1.3 75.3 + - + +
315D LEU* 3.1 4.5 + - - +
316D ALA* 2.8 29.8 + - - +
453D PRO* 3.9 6.7 - - + +
456D ALA* 3.5 21.5 - - + +
457D LYS* 3.4 35.2 - - + -
460D LEU* 3.5 16.8 - - + -
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Residues in contact with PHE 313 (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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309D GLU* 3.1 42.5 + - + +
310D GLU* 4.2 4.5 - - - +
312D ILE* 1.3 92.4 - - + +
314D ASN* 1.3 58.4 + - - +
316D ALA* 3.7 6.4 - - + +
317D ASP* 2.8 43.5 + - - +
322D PHE* 4.7 23.3 - + + -
453D PRO* 4.8 13.5 - - + -
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Residues in contact with ASN 314 (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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310D GLU* 2.8 41.7 + - + +
311D MET* 4.2 5.6 - - - +
313D PHE* 1.3 75.9 - - - +
315D LEU* 1.3 61.0 + - - +
317D ASP* 4.7 4.0 + - - -
318D THR* 2.8 42.7 + - - -
406D LYS* 3.9 26.3 + - + +
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Residues in contact with LEU 315 (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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311D MET 3.2 16.7 + - - +
312D ILE 3.1 5.3 + - - +
314D ASN* 1.3 75.9 - - - +
316D ALA* 1.3 58.5 + - - +
319D HIS* 2.8 43.0 + - + +
320D LEU* 3.3 28.1 + - + -
398D VAL* 5.5 1.1 - - + -
401D LEU* 4.2 13.5 - - + -
402D ILE* 4.1 21.1 - - + -
456D ALA* 3.9 12.6 - - - +
459D LEU* 4.6 11.7 - - + -
460D LEU* 3.4 38.8 - - + -
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Residues in contact with ALA 316 (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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312D ILE 2.8 15.8 + - - +
313D PHE* 3.7 11.7 - - + +
315D LEU* 1.3 78.4 - - - +
317D ASP* 1.3 56.8 + - - +
320D LEU* 3.0 27.2 + - - -
322D PHE* 2.9 43.1 + - + +
452D ILE* 4.3 8.3 - - + +
453D PRO* 5.0 4.0 - - + -
456D ALA* 4.3 11.6 - - + +
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Residues in contact with ASP 317 (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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313D PHE* 2.8 30.1 + - - +
314D ASN* 4.4 4.2 + - - +
316D ALA* 1.3 75.2 - - - +
318D THR* 1.3 68.2 + - - +
321D PHE* 3.9 10.9 + - - -
322D PHE* 3.6 25.0 + - - +
323D ASN* 3.2 39.0 + - - +
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Residues in contact with THR 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D ASN* 2.8 33.2 + - - -
317D ASP* 1.3 82.3 - - - +
319D HIS* 1.3 85.4 + - + +
321D PHE* 5.1 1.6 + - - -
406D LYS* 6.2 0.6 - - - -
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Residues in contact with HIS 319 (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 ASN 5.1 0.2 - - - -
315D LEU* 2.8 34.7 + - + +
318D THR* 1.3 100.2 - - + +
320D LEU* 1.3 64.2 + - + +
321D PHE* 3.5 9.8 + - - -
390D MET* 3.1 29.6 - - - +
401D LEU* 2.9 54.4 + - + -
402D ILE* 4.1 17.3 - - + -
406D LYS* 6.4 1.6 - - + -
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Residues in contact with LEU 320 (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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315D LEU* 3.5 29.4 - - + +
316D ALA* 3.0 19.2 + - - +
319D HIS* 1.3 89.3 - - + +
321D PHE* 1.3 75.2 + - - +
322D PHE 3.0 3.6 + - - -
325D LEU* 3.7 12.5 - - - +
387D VAL* 3.9 30.9 - - + +
390D MET* 4.3 13.0 - - + -
391D TYR 6.1 0.2 - - - +
401D LEU* 5.5 2.2 - - + -
452D ILE* 3.8 32.9 - - + +
455D LEU* 4.8 7.4 - - + -
456D ALA* 4.1 13.2 - - - +
459D LEU* 4.8 8.3 - - + -
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Residues in contact with PHE 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D ALA 3.3 1.2 + - - -
317D ASP 3.9 7.8 + - - -
318D THR 6.1 1.1 - - - -
319D HIS 3.5 8.0 - - - -
320D LEU* 1.3 79.1 - - - +
322D PHE* 1.3 62.7 + - - +
323D ASN* 3.1 4.5 - - - -
324D ASP* 3.0 20.7 + - + +
325D LEU* 3.1 15.5 + - + +
350D PHE* 3.6 38.6 - + + -
383D ARG* 3.4 55.4 - - + +
386D ARG* 3.9 29.8 - - + -
387D VAL* 4.0 3.6 - - + -
390D MET* 4.1 12.1 - - + -
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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