Contacts of the helix formed by residues 274 - 292 (chain D) in PDB entry 3GZN
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 274 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D ASP* 3.0 29.7 + - + +
273D ASP* 1.3 74.8 - - - +
275D PRO* 1.3 74.0 - - - +
276D GLU* 3.0 33.3 + - - +
277D HIS* 3.0 43.1 + - - +
278D ILE* 3.2 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D ASP 3.2 11.4 - - - +
274D ASP* 1.3 90.0 - - - +
276D GLU* 1.3 60.6 + - + +
278D ILE* 4.0 4.3 - - + -
279D GLN* 3.1 27.4 + - - +
299D TYR* 3.6 18.8 + - - +
303D GLN* 6.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D PHE* 3.6 37.6 - - + -
274D ASP* 3.0 22.1 + - - +
275D PRO* 1.3 80.9 - - + +
277D HIS* 1.3 67.0 + - - +
279D GLN* 3.1 9.6 + - - +
280D TRP 3.0 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D TRP* 3.2 28.2 - + + -
264D PHE* 3.9 36.3 - + + +
268D VAL* 4.8 8.0 - - + +
269D PRO 3.8 10.9 + - - -
270D LEU* 3.8 10.8 - - + -
271D ASP* 3.3 34.9 + - + +
274D ASP* 3.0 38.4 + - + +
276D GLU* 1.3 77.3 - - - +
278D ILE* 1.3 61.7 + - - +
280D TRP* 3.2 3.6 + - - +
281D ILE* 3.1 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D LEU* 5.4 2.0 - - + -
271D ASP 4.6 1.1 - - - +
272D GLY* 3.3 35.7 - - - +
273D ASP 4.9 0.9 - - - -
274D ASP 3.2 17.0 + - - +
275D PRO* 3.9 3.1 - - + +
277D HIS* 1.3 76.4 - - + +
279D GLN* 1.3 57.6 + - - +
281D ILE* 3.5 6.1 + - + +
282D PHE* 2.9 32.2 + - - +
299D TYR* 3.6 34.8 - - + +
302D THR* 4.0 16.5 - - + +
303D GLN* 4.3 25.8 - - + +
306D VAL* 4.4 20.0 - - + -
307D LYS* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D PRO 3.1 15.5 + - - +
276D GLU* 3.1 14.7 + - - +
278D ILE* 1.3 76.5 - - - +
280D TRP* 1.3 61.9 + - - +
282D PHE* 3.2 23.4 + - - +
283D GLN* 3.2 45.9 + - - +
299D TYR* 4.3 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D VAL* 3.5 27.4 - - + -
257D GLN* 4.0 22.0 - - - -
258D TRP* 3.6 35.2 - + + -
261D GLU* 3.9 15.9 + - + -
263D PRO* 3.6 30.5 - - + +
264D PHE* 3.6 26.5 - + + -
276D GLU 3.0 5.9 + - - -
277D HIS 3.2 6.5 + - - +
279D GLN* 1.3 73.9 - - - +
281D ILE* 1.3 82.2 + - + +
282D PHE 3.3 0.2 + - - -
283D GLN* 4.1 2.2 - - - +
284D LYS* 3.0 62.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ILE* 3.7 30.1 - - + +
253D VAL* 3.9 23.6 - - + +
254D ARG* 5.1 1.6 - - - +
258D TRP* 3.7 18.8 - - + -
270D LEU* 3.5 34.3 - - + -
277D HIS 3.1 27.5 + - - +
278D ILE* 4.0 5.4 - - - +
280D TRP* 1.3 89.6 - - + +
282D PHE* 1.3 59.4 + - - +
284D LYS* 3.8 1.0 - - - +
285D SER* 2.6 35.6 + - - +
302D THR* 3.7 9.0 - - + -
306D VAL* 4.2 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D ILE 2.9 19.0 + - - +
279D GLN* 3.4 19.5 - - - +
280D TRP 3.2 0.4 - - - -
281D ILE* 1.3 76.4 - - - +
283D GLN* 1.3 69.9 + - + +
285D SER* 3.2 13.0 + - - -
286D LEU* 3.2 34.6 + - + +
297D VAL* 3.2 26.6 - - + +
298D THR* 3.4 16.2 - - - -
299D TYR* 3.8 32.3 - + + -
302D THR* 3.6 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D GLN* 3.2 32.9 + - - +
280D TRP* 4.3 2.0 - - - +
282D PHE* 1.3 87.9 - - + +
284D LYS* 1.3 58.8 + - + +
285D SER 2.9 5.4 - - - -
286D LEU* 2.8 18.7 + - + +
287D GLU* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D VAL* 3.5 29.2 - - + +
257D GLN* 3.3 30.3 + - - +
261D GLU* 4.1 13.0 - - - -
280D TRP* 3.0 52.5 + - + +
281D ILE 4.0 0.2 - - - +
282D PHE 3.4 0.2 - - - -
283D GLN* 1.3 75.1 - - + +
285D SER* 1.3 57.9 + - - +
287D GLU* 4.2 15.4 - - + +
288D ARG* 3.7 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D CYS* 4.1 4.0 - - - +
250D ILE* 3.5 26.2 - - - +
253D VAL* 3.3 18.2 - - - +
281D ILE 2.6 19.5 + - - -
282D PHE* 3.3 10.3 - - - -
283D GLN 2.9 0.8 - - - -
284D LYS* 1.3 77.5 - - - +
286D LEU* 1.3 55.7 + - - +
287D GLU 3.3 1.3 - - - -
288D ARG* 3.6 4.5 - - - +
289D ALA* 2.7 36.6 + - - +
297D VAL* 3.7 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D PHE* 3.2 44.1 + - + +
283D GLN* 2.8 20.3 + - + +
285D SER* 1.3 74.5 - - - +
287D GLU* 1.3 63.4 + - - +
289D ALA* 4.2 4.4 - - + +
290D SER* 3.2 26.2 + - - -
297D VAL* 3.6 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D GLN 2.8 13.9 + - - +
284D LYS* 4.2 19.3 - - + +
286D LEU* 1.3 78.8 - - - +
288D ARG* 1.3 61.0 + - - +
290D SER* 3.8 3.3 + - - -
291D GLN* 3.4 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 288 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D ILE 3.4 21.6 + - - -
240D ALA 4.5 7.3 + - - -
243D PRO* 3.6 24.7 - - - +
249D CYS* 4.1 21.1 - - + +
252D TYR* 3.3 60.7 + - + +
257D GLN* 5.3 2.2 - - - +
284D LYS 3.7 14.7 + - - +
285D SER* 3.4 6.9 + - - +
286D LEU 3.3 0.4 - - - -
287D GLU* 1.3 79.8 - - - +
289D ALA* 1.3 62.1 + - - +
291D GLN* 3.2 18.9 + - - +
292D TYR* 3.0 48.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D CYS* 3.8 16.8 - - - -
285D SER 2.7 22.0 + - - +
286D LEU* 4.2 5.4 - - + +
287D GLU 3.4 0.4 - - - -
288D ARG* 1.3 71.9 - - - +
290D SER* 1.3 58.1 + - - +
292D TYR* 3.3 2.6 + - - -
293D ASN 3.0 8.1 + - - -
294D ILE* 2.6 49.8 + - + +
297D VAL* 3.6 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D LEU 3.2 16.5 + - - -
287D GLU* 4.1 3.8 - - - -
289D ALA* 1.3 75.3 - - - +
291D GLN* 1.3 64.6 + - - +
293D ASN* 3.2 21.7 - - - +
294D ILE 4.5 1.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D GLU 3.4 12.5 + - - +
288D ARG* 3.2 24.7 + - - +
290D SER* 1.3 79.6 - - - +
292D TYR* 1.3 86.6 + - + +
293D ASN* 3.4 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C SER* 3.3 34.4 - - - -
347C ILE* 3.3 19.2 - - - +
240D ALA 5.0 2.9 + - - -
241D SER 4.4 8.5 + - - -
243D PRO* 4.0 16.2 - - + +
288D ARG* 3.0 69.8 + - + -
289D ALA 3.3 2.0 + - - +
291D GLN* 1.3 103.0 + - + +
293D ASN* 1.3 70.0 + - - +
294D ILE* 3.5 18.1 - - + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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