Contacts of the helix formed by residues 258 - 273 (chain D) in PDB entry 3NDM
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 GLU 258 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D MET* 4.0 8.9 - - - +
244D GLU* 4.5 0.2 - - - +
256D GLY* 3.6 19.0 + - - +
257D ARG* 1.3 86.6 + - + +
259D CYS* 1.3 58.0 + - + +
261D TRP* 2.9 38.7 + - + +
262D TRP 3.4 0.9 + - - -
320D ARG* 2.7 58.8 + - + +
323D ARG* 3.2 23.7 + - + +
325D GLY 5.3 0.2 - - - -
326D ARG* 4.0 29.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D ILE* 3.7 20.9 - - - -
197D ARG* 4.5 5.6 - - - -
242D SER* 3.5 22.8 - - - +
244D GLU* 3.6 17.0 - - + +
245D VAL* 4.2 9.0 - - + -
255D TYR* 3.8 17.3 - - + -
256D GLY 3.6 16.4 - - - +
257D ARG 2.7 5.3 + - - -
258D GLU* 1.3 77.9 - - + +
260D ASP* 1.3 68.2 + - - -
262D TRP* 3.4 16.1 - - - +
263D SER* 3.6 10.2 + - - -
323D ARG* 3.7 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D LEU* 4.1 10.0 - - + +
190D HIS* 3.1 24.7 - - + +
195D ILE* 3.0 14.9 - - - +
196D HIS* 2.5 35.5 + - - +
197D ARG* 2.7 28.0 + - - -
199D VAL* 3.7 18.3 - - + +
257D ARG 2.8 15.1 + - - +
259D CYS* 1.3 75.5 - - - +
261D TRP* 1.3 64.2 + - - +
263D SER* 3.7 2.6 + - - -
264D VAL* 3.3 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D VAL* 3.5 44.0 - - + -
186D LEU* 4.1 19.7 - - + -
187D ASP* 4.4 3.8 - - + -
190D HIS* 4.0 22.4 + + - -
257D ARG* 4.6 13.1 - - - +
258D GLU* 2.9 27.1 + - - +
260D ASP* 1.3 78.1 - - - +
262D TRP* 1.3 58.5 + - - +
263D SER 3.1 2.0 - - - -
264D VAL* 2.6 64.3 + - + +
265D GLY 3.1 2.6 + - - -
316D PHE* 3.6 24.5 - + + -
323D ARG* 4.7 2.5 - - + -
324D LEU 3.7 8.5 - - - +
325D GLY* 4.1 14.3 + - - -
329D VAL* 4.6 17.3 - - + +
332D ILE* 3.2 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D TYR 3.0 28.9 + - - -
241D ILE 3.1 7.7 + - - -
242D SER* 3.2 19.7 - - - +
243D PRO* 3.3 27.1 - - + -
258D GLU 3.4 3.8 + - - -
259D CYS 3.4 11.2 - - - +
261D TRP* 1.3 75.6 - - - +
263D SER* 1.3 59.2 - - - +
265D GLY* 3.0 18.9 + - - -
266D VAL* 3.3 20.2 + - + +
278D PHE* 4.4 11.4 - + - -
290D ILE* 2.9 27.5 - - + +
293D HIS* 3.4 29.2 - + + -
316D PHE 3.4 28.3 - - - -
317D LEU* 3.4 32.2 - - + +
318D THR 3.7 5.2 - - - -
323D ARG* 3.8 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D ARG 6.0 0.5 - - - -
198D ASP* 5.6 0.9 + - - -
199D VAL* 3.4 44.3 + - - +
240D TYR* 3.7 23.1 + - - +
241D ILE* 5.3 0.5 - - - -
242D SER 5.1 1.4 + - - -
259D CYS 3.6 11.2 + - - -
260D ASP* 3.9 2.0 + - - -
261D TRP 3.1 0.6 - - - -
262D TRP* 1.3 77.3 - - - +
264D VAL* 1.3 66.8 + - - +
266D VAL* 3.0 10.0 + - - +
267D PHE* 2.8 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D THR* 5.0 11.2 - - + +
182D VAL* 5.0 8.5 - - + -
183D VAL* 4.8 12.3 - - + -
186D LEU* 4.2 10.3 - - + -
199D VAL* 4.6 3.5 - - + +
260D ASP 3.3 9.1 + - - +
261D TRP* 2.6 51.8 + - + +
263D SER* 1.3 71.5 - - - +
265D GLY* 1.3 60.7 + - - -
267D PHE* 2.9 12.5 + - + +
268D LEU* 2.9 23.2 + - + +
312D LEU* 5.6 0.4 - - + -
316D PHE* 3.2 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D TRP 3.1 2.2 + - - -
262D TRP 3.0 6.3 + - - -
264D VAL* 1.3 81.3 - - - +
266D VAL* 1.3 56.2 + - - +
268D LEU* 3.2 7.1 + - - +
269D TYR* 2.8 30.7 + - - +
313D ILE* 4.3 4.1 - - - +
316D PHE* 3.9 13.6 - - - -
317D LEU* 3.3 28.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D ASP 3.3 26.9 - - - +
240D TYR* 3.4 29.7 - - + +
262D TRP* 3.5 34.1 - - + +
263D SER* 3.0 5.5 + - - +
265D GLY* 1.3 75.3 - - - +
267D PHE* 1.3 61.9 + - - +
269D TYR* 3.7 5.6 - - - +
270D GLU* 3.1 23.2 + - - +
276D THR* 4.2 3.1 - - - -
277D PRO* 3.5 26.9 - - + -
278D PHE* 5.0 3.8 - - + -
317D LEU* 4.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D LEU* 3.1 24.5 - - + -
165D MET* 4.6 8.3 - - - -
178D TYR 4.9 2.2 - - - -
179D THR* 5.2 5.2 - - + -
182D VAL* 3.3 26.7 - - + -
199D VAL* 5.2 2.7 - - + -
200D LYS* 6.0 0.2 - - - -
201D PRO* 4.5 19.1 - - + -
204D MET* 3.1 41.7 - - + -
240D TYR* 4.1 8.9 - - + -
263D SER 2.8 11.1 + - - +
264D VAL* 3.0 13.0 - - + +
266D VAL* 1.3 75.5 - - - +
268D LEU* 1.3 68.2 + - - +
269D TYR 3.0 0.7 + - - -
270D GLU* 3.8 2.6 - - + +
271D MET* 2.9 60.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D ALA* 4.7 4.3 - - + -
179D THR* 4.0 23.3 + - + +
264D VAL* 2.9 10.9 + - + +
265D GLY* 3.5 9.6 - - - +
267D PHE* 1.3 76.9 - - - +
269D TYR* 1.3 66.3 + - - +
271D MET* 3.0 21.2 - - - +
272D LEU* 3.1 38.1 + - + +
309D ALA* 4.3 2.0 - - - +
312D LEU* 3.3 34.5 - - + -
313D ILE* 3.3 32.8 - - + +
316D PHE* 5.5 0.9 - - + -
337D PHE* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D GLY 2.8 20.4 + - - +
266D VAL 3.7 0.9 - - - +
267D PHE 3.0 0.6 + - - -
268D LEU* 1.3 71.3 - - - +
270D GLU* 1.3 64.8 + - - +
271D MET 2.7 5.9 + - - -
272D LEU* 4.5 1.3 - - - -
273D VAL* 2.9 54.9 + - + +
275D ASP 3.4 19.1 - - - -
276D THR 4.7 0.4 - - - -
277D PRO* 3.5 43.2 - - + +
297D LEU* 4.6 4.9 - - + -
298D THR* 3.5 30.7 + - - -
299D PHE* 3.8 28.0 - + - -
300D PRO* 4.2 5.0 - - - +
313D ILE* 3.9 29.8 - - + +
317D LEU* 4.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D VAL* 4.7 10.7 - - - +
165D MET* 3.1 24.9 - - + +
201D PRO* 4.2 9.6 - - - +
240D TYR* 2.4 30.8 + - - -
266D VAL 3.1 13.6 + - - +
267D PHE* 4.1 2.9 - - + +
269D TYR* 1.3 78.9 - - - +
271D MET* 1.3 61.8 + - - +
274D GLY* 3.2 35.3 + - - +
275D ASP* 3.8 18.0 - - - -
276D THR* 3.9 21.1 - - - +
277D PRO* 4.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D LEU* 4.0 3.4 - - + -
164D LEU* 5.5 0.2 - - + -
165D MET* 3.2 21.4 - - - +
169D ASP* 5.4 1.9 - - - +
170D VAL* 3.5 39.0 + - + +
175D ALA* 4.2 11.9 - - + -
178D TYR* 3.5 35.9 - - + -
179D THR* 3.7 22.4 - - - -
267D PHE* 2.9 51.9 + - + +
268D LEU* 3.0 13.0 - - - +
269D TYR 2.7 0.8 + - - -
270D GLU* 1.3 81.1 - - - +
272D LEU* 1.3 62.2 + - + +
273D VAL 4.8 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D ASP* 4.7 7.6 - - - +
170D VAL* 4.9 11.2 - - + +
172D GLU* 4.4 27.6 - - + +
175D ALA* 4.2 17.0 - - + -
268D LEU* 3.1 33.7 - - + +
269D TYR* 3.0 3.6 + - - +
271D MET* 1.3 83.2 - - - +
273D VAL* 1.3 73.8 + - + +
299D PHE* 6.4 0.4 - - + -
305D ILE* 4.4 19.5 - - + -
309D ALA* 4.2 11.7 - - + -
313D ILE* 3.4 29.2 - - + -
337D PHE* 5.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D ASP* 4.8 6.1 - - - +
269D TYR* 2.9 54.8 + - + +
271D MET 4.8 0.4 - - - -
272D LEU* 1.3 89.8 - - + +
274D GLY* 1.3 59.7 + - - +
275D ASP* 4.3 6.3 - - + +
299D PHE* 5.7 2.9 - - + -
300D PRO* 4.4 25.6 - - + -
305D ILE* 5.5 5.2 - - + -
313D ILE* 6.1 0.2 - - + -
----------------------------------------------------------
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