Contacts of the helix formed by residues 281 - 297 (chain D) in PDB entry 1Z1G
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 SER 281 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D CYS* 4.9 1.6 - - - -
280D LEU* 1.3 74.9 - - - +
282D SER* 1.3 68.7 + - - +
283D GLY* 3.0 3.8 - - - -
284D THR* 2.7 36.8 + - - -
285D VAL* 3.4 4.9 + - - +
3L T 4.4 12.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D VAL* 3.9 10.7 - - - +
214D GLY* 4.5 8.5 - - - -
217D CYS* 3.8 24.1 - - - +
280D LEU 3.9 3.0 + - - -
281D SER* 1.3 70.4 - - - +
283D GLY* 1.3 64.5 + - - -
285D VAL* 3.2 14.0 + - - +
286D SER* 3.4 11.3 + - - -
22I G 4.4 17.1 + - - -
23I T 5.8 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D SER* 2.8 5.9 + - - -
282D SER* 1.3 77.4 + - - +
284D THR* 1.3 60.3 + - - +
286D SER* 3.6 3.0 + - - -
287D ARG* 2.9 31.6 + - - +
23I T 4.5 13.2 - - - +
24I T 3.8 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D TRP* 5.6 4.3 - - + -
280D LEU* 4.3 20.3 - - + +
281D SER* 2.7 33.9 + - - -
283D GLY* 1.3 71.9 - - - -
285D VAL* 1.3 54.8 + - - -
287D ARG* 2.8 31.7 + - + +
288D TYR* 2.8 36.1 + - + +
2L A 6.1 4.5 - - + -
3L T 5.2 9.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D TRP* 5.0 17.3 - - + -
199D LEU* 4.4 6.2 - - + +
202D ALA* 4.6 17.3 - - + -
213D VAL* 3.4 27.8 - - + -
217D CYS* 4.9 10.1 - - - -
272D ILE* 4.8 14.1 - - + -
280D LEU* 5.1 10.5 - - + +
281D SER 3.4 3.6 + - - +
282D SER* 3.2 10.6 + - - +
284D THR* 1.3 79.6 - - - +
286D SER* 1.3 65.9 + - - +
288D TYR* 3.4 1.7 + - - +
289D PHE* 3.1 19.9 + - - +
307D PHE* 3.4 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 286 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D VAL* 5.4 0.9 - - - -
282D SER 3.4 7.5 + - - -
283D GLY* 4.1 8.1 - - - -
285D VAL* 1.3 84.2 - - - +
287D ARG* 1.3 58.3 + - - +
289D PHE* 3.1 5.2 + - - +
290D MSE 2.9 28.2 + - - +
306D THR* 4.9 0.5 - - - -
307D PHE* 3.9 15.4 + - - +
22I G 5.7 0.4 - - - -
23I T 3.2 59.0 + - - +
24I T 4.7 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D GLY 2.9 18.5 + - - +
284D THR* 2.8 25.3 + - - +
286D SER* 1.3 76.4 - - - +
288D TYR* 1.3 65.9 + - + +
290D MSE 3.1 41.7 - - + +
291D ARG* 3.4 25.3 + - - +
23I T 6.4 0.7 - - - -
24I T 3.9 29.6 + - + +
25I G 3.6 20.2 + - - -
26I G 2.8 28.5 + - - -
3L T 5.0 12.4 - - - +
4L C 3.3 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 288 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D SER* 5.0 5.5 + - - -
196D PRO* 4.2 25.6 - - + -
198D TRP* 4.1 30.1 - + + -
199D LEU* 4.3 11.3 - - + +
284D THR* 2.8 34.9 + - + +
285D VAL 4.3 1.6 - - - +
287D ARG* 1.3 79.9 - - + +
289D PHE* 1.3 66.7 + - - +
290D MSE 3.0 1.8 - - - -
291D ARG* 2.8 62.3 + - + +
292D ALA* 3.1 11.4 + - - +
2L A 3.8 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D LEU* 5.0 6.1 - - + -
185D TYR* 5.7 0.4 - + - -
188D ILE* 3.7 25.7 - - + +
199D LEU* 3.9 10.1 - - + +
203D MSE 3.5 50.0 - - + -
285D VAL 3.1 12.9 + - - +
286D SER* 3.1 12.5 + - - +
288D TYR* 1.3 74.4 - - - +
290D MSE 1.3 63.7 - - - +
292D ALA* 3.2 7.5 + - + +
293D ARG* 3.0 26.7 + - + +
305D PRO* 5.3 1.3 - - + -
306D THR* 3.6 11.4 - - - -
307D PHE* 3.2 47.1 - + + -
309D GLU* 5.2 1.3 - - + -
310D LEU* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D SER* 2.9 11.2 + - - +
287D ARG* 3.1 44.2 - - + +
289D PHE* 1.3 76.9 - - - +
291D ARG* 1.3 79.2 + - - +
293D ARG* 2.8 57.7 - - - +
294D LYS* 3.1 19.6 + - + +
24I T 3.8 38.8 - - + +
25I G 5.0 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D SER* 6.0 1.3 - - - +
287D ARG* 3.5 28.1 + - - +
288D TYR* 2.8 63.9 + - + +
290D MSE 1.3 93.0 - - - +
292D ALA* 1.3 59.0 + - - +
294D LYS* 3.2 7.6 + - - +
295D ALA* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ILE* 4.0 19.3 - - + +
191D ALA* 3.7 7.0 - - - +
192D ALA* 4.2 29.6 - - + +
195D SER* 4.6 3.8 + - - +
199D LEU* 4.5 6.3 - - + -
288D TYR 3.1 6.9 + - - +
289D PHE* 3.5 9.9 - - + +
291D ARG* 1.3 76.1 - - - +
293D ARG* 1.3 58.9 + - - +
295D ALA* 4.2 6.3 - - - -
296D SER* 2.9 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ILE* 4.6 20.4 - - + +
289D PHE* 3.0 17.6 + - + +
290D MSE 2.8 43.8 + - - +
292D ALA* 1.3 72.5 - - - +
294D LYS* 1.3 68.1 + - - +
296D SER* 3.1 21.6 + - - -
297D GLY* 3.4 4.3 + - - -
298D LEU 4.5 3.1 + - - +
300D PHE* 5.0 16.8 - - + -
304D PRO* 3.2 25.5 + - - +
305D PRO* 2.3 44.7 + - + -
306D THR* 3.3 10.9 - - - +
24I T 2.1 51.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D MSE 3.1 18.1 + - + +
291D ARG* 3.5 9.6 - - - +
293D ARG* 1.3 79.0 - - - +
295D ALA* 1.3 57.3 + - - +
297D GLY* 3.0 21.3 + - - -
25I G 5.5 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D ALA* 4.2 14.2 - - + +
194D SER* 5.6 4.3 - - - +
291D ARG 2.9 16.6 + - - +
292D ALA* 3.7 8.5 - - - +
294D LYS* 1.3 75.9 - - - +
296D SER* 1.3 60.1 + - - +
297D GLY* 3.3 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D LYS* 4.0 28.9 - - - +
188D ILE* 4.3 14.3 - - - +
191D ALA* 4.0 7.4 - - - -
292D ALA 2.9 17.2 + - - -
293D ARG 3.1 7.2 + - - -
295D ALA* 1.3 77.1 - - - +
297D GLY* 1.3 61.2 + - - +
298D LEU* 3.4 30.0 + - - +
300D PHE* 5.5 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D ARG 3.4 2.4 + - - -
294D LYS 3.0 16.7 + - - -
295D ALA 3.3 0.6 - - - -
296D SER* 1.3 78.5 + - - +
298D LEU* 1.3 67.2 + - - +
299D SER* 3.9 4.2 + - - -
----------------------------------------------------------
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