Contacts of the helix formed by residues 257 - 277 (chain D) in PDB entry 4U0Z
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 257 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D GLY 4.4 0.4 + - - -
256D LYS* 1.3 73.0 - - - +
258D LEU* 1.4 64.0 + - - +
259D GLU* 4.0 7.4 + - - +
260D GLU* 3.2 39.2 + - - +
261D GLN* 3.2 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D ALA* 5.6 9.6 - - + -
256D LYS 3.9 1.0 + - - +
257D SER* 1.4 69.3 - - - +
259D GLU* 1.4 55.6 + - - +
261D GLN* 3.1 15.2 + - + +
262D ASN* 2.9 52.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D SER* 3.4 8.0 + - - +
258D LEU* 1.4 76.2 - - - +
260D GLU* 1.3 57.2 - - + +
262D ASN* 3.3 6.6 + - - +
263D GLU* 3.0 41.3 + - - +
301D VAL* 3.4 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D GLY 4.0 2.9 - - - +
236D ASN* 3.4 41.4 + - - +
237D THR* 2.7 46.5 + - - +
238D LEU* 3.4 13.6 - - + +
256D LYS* 4.1 7.1 - - + +
257D SER* 3.2 35.2 + - - +
258D LEU 3.3 0.6 - - - -
259D GLU* 1.3 76.7 - - + +
261D GLN* 1.3 61.5 + - + +
263D GLU* 3.5 11.2 - - - +
264D VAL* 3.7 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D LEU* 4.0 13.0 - - + -
246D ILE* 3.6 27.4 - - + +
252D ALA* 3.6 12.7 - - - +
253D VAL* 2.9 39.7 + - - +
256D LYS* 2.9 32.5 + - + +
257D SER 3.2 12.2 + - - +
258D LEU* 3.1 13.9 + - + +
260D GLU* 1.3 77.3 - - - +
262D ASN* 1.3 59.6 + - - +
263D GLU 3.3 0.2 - - - -
264D VAL* 3.3 6.2 + - - +
265D ILE* 3.2 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D LEU* 2.9 36.4 + - - +
259D GLU* 3.7 7.0 - - - +
261D GLN* 1.3 75.6 - - - +
263D GLU* 1.4 57.0 + - - +
264D VAL 3.3 0.4 - - - -
265D ILE* 3.3 22.3 - - - +
266D GLY* 3.0 24.8 + - - -
297D VAL 4.9 0.7 - - - +
300D TYR* 3.3 44.6 + - + +
301D VAL* 3.7 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D VAL* 4.1 19.4 - - + +
234D GLU* 5.8 1.9 - - - -
236D ASN* 3.1 26.4 + - - +
259D GLU* 3.0 29.9 + - - +
260D GLU* 3.5 11.0 - - - +
261D GLN 3.3 0.2 - - - -
262D ASN* 1.4 75.1 - - - +
264D VAL* 1.4 54.9 + - - +
266D GLY* 3.5 1.9 + - - -
267D MET* 3.1 32.2 + - - +
297D VAL 4.5 5.1 - - - +
301D VAL* 3.5 15.7 - - + +
371D ARG* 3.6 34.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
227D ILE* 4.3 16.9 - - + +
231D VAL* 4.3 12.3 - - + -
238D LEU* 4.0 9.9 - - + -
243D ILE* 3.8 35.4 - - + -
246D ILE* 3.9 21.3 - - + -
247D LEU* 3.9 20.2 - - + -
260D GLU 3.7 13.0 - - - +
261D GLN* 3.3 10.5 + - - +
262D ASN 3.3 0.4 - - - -
263D GLU* 1.4 73.4 - - - +
265D ILE* 1.4 64.1 + - - +
267D MET* 3.4 4.5 + - - +
268D HIS* 3.3 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D ILE* 4.4 16.2 - - + +
247D LEU* 4.5 5.6 - - + -
250D ARG* 5.2 13.9 - - - +
261D GLN* 3.2 16.0 + - + +
262D ASN* 3.3 30.3 - - - +
263D GLU 3.6 0.2 - - - -
264D VAL* 1.4 73.7 - - - +
266D GLY* 1.3 56.8 + - - +
268D HIS* 3.4 9.6 + - + +
269D ALA* 3.1 27.4 + - - +
300D TYR* 3.7 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D ASN 3.0 15.1 + - - -
263D GLU 3.7 2.2 - - - -
264D VAL 3.2 0.2 - - - -
265D ILE* 1.3 73.5 - - - +
267D MET* 1.3 63.8 + - - +
269D ALA* 3.4 1.9 + - - +
270D ALA* 3.1 20.4 + - - +
296D ARG 3.2 27.9 - - - +
297D VAL* 3.7 11.0 - - - -
300D TYR* 3.5 12.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D HIS* 4.4 1.6 - - + -
227D ILE* 4.1 13.7 - - + -
230D THR* 3.5 28.3 - - + +
231D VAL* 3.8 21.1 - - + -
263D GLU 3.1 16.7 + - - +
264D VAL 3.4 9.4 + - - +
266D GLY* 1.3 74.9 - - - +
268D HIS* 1.3 52.6 + - - +
270D ALA* 2.9 8.5 + - - +
271D MET* 2.9 49.8 + - - +
297D VAL* 4.5 8.7 + - + -
371D ARG* 4.0 27.4 - - - +
375D LEU* 3.6 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D TYR* 2.7 43.6 + + - -
227D ILE* 4.8 2.6 - - + +
247D LEU* 3.5 31.1 - - + +
250D ARG* 3.4 39.8 + - - -
264D VAL 3.3 2.5 + - - +
265D ILE* 3.5 10.3 - - + +
267D MET* 1.3 78.4 - - - +
269D ALA* 1.4 52.4 + - - +
271D MET* 3.5 3.3 + - - -
272D LYS* 2.9 64.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D ILE* 3.1 14.5 + - + +
266D GLY 3.6 9.0 - - - +
268D HIS* 1.4 76.9 - - - +
270D ALA* 1.4 58.6 + - - +
272D LYS* 4.0 4.5 - - - +
273D TYR* 3.1 28.6 + - - +
296D ARG* 3.4 21.9 + - + +
300D TYR* 3.9 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D GLY 3.1 12.1 + - - +
267D MET* 2.9 10.9 + - - +
269D ALA* 1.4 76.8 - - - +
271D MET* 1.4 58.1 + - - +
273D TYR* 3.3 5.4 + - - +
274D ILE* 3.0 32.3 + - - +
293D ILE* 4.1 5.6 - - + +
296D ARG* 3.6 15.2 - - + +
297D VAL* 3.7 15.9 - - + -
375D LEU* 3.6 24.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
223D TYR* 3.3 47.3 - - + +
226D HIS* 3.5 36.3 - - + +
227D ILE* 3.8 24.9 - - - -
267D MET* 2.9 30.4 + - - +
268D HIS* 3.9 1.1 - - - +
270D ALA* 1.4 72.8 - - - +
272D LYS* 1.4 60.8 + - - +
273D TYR 3.2 0.2 - - - -
274D ILE* 4.0 7.1 - - + +
275D ASN* 3.0 46.3 + - - +
375D LEU* 4.4 11.7 - - + -
378D ASN* 5.8 1.8 - - - +
388D PRO* 6.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D TYR* 3.6 30.2 + - - +
268D HIS* 2.9 45.6 + - + +
269D ALA* 4.1 5.8 - - - +
271D MET* 1.4 76.6 - - - +
273D TYR* 1.3 59.3 + - - +
275D ASN* 4.1 9.4 - - - +
276D THR* 2.6 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D ALA 3.1 19.5 + - - +
270D ALA 3.4 6.3 - - - +
272D LYS* 1.3 74.5 - - - +
274D ILE* 1.4 63.2 + - + +
276D THR* 3.4 2.0 + - - -
277D THR* 2.9 65.3 + - + +
278D LEU* 3.8 31.9 - - + +
289D ASP* 4.5 4.3 + - - -
292D GLU* 3.2 39.0 - - + +
293D ILE* 4.6 4.3 - - + -
296D ARG* 3.4 42.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ALA 3.0 24.5 + - - +
271D MET* 3.5 6.7 + - + +
273D TYR* 1.4 72.9 - - + +
275D ASN* 1.3 59.0 + - - +
278D LEU* 3.1 31.8 + - + -
279D VAL* 2.8 40.8 + - + -
293D ILE* 4.0 17.5 - - + -
375D LEU* 3.8 45.8 - - + +
379D LEU* 3.7 31.9 - - + -
382D MET* 6.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D TYR* 5.1 8.9 - - - -
271D MET* 3.0 35.9 + - - +
272D LYS* 4.3 11.4 - - - +
274D ILE* 1.3 78.9 - - - +
276D THR* 1.3 59.3 + - - +
279D VAL* 3.4 28.4 + - - +
280D SER* 4.8 5.9 + - - -
382D MET* 3.7 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D LYS* 2.6 28.9 + - - +
273D TYR* 4.2 1.3 - - - -
275D ASN* 1.3 78.8 - - - +
277D THR* 1.3 67.7 + - - +
279D VAL 5.5 0.2 - - - -
280D SER* 5.7 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D TYR* 2.9 54.1 + - + +
276D THR* 1.3 78.0 - - - +
278D LEU* 1.3 65.8 + - + +
280D SER* 5.3 1.2 - - - -
281D ARG* 3.3 30.0 + - - +
----------------------------------------------------------
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