Contacts of the helix formed by residues 248 - 266 (chain D) in PDB entry 6IY6
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 248 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D GLY* 1.3 76.3 - - - -
249D SER* 1.3 62.3 + - - +
250D LYS* 3.0 33.7 + - - +
251D GLU* 3.2 26.8 + - - -
252D LYS* 3.2 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D SER* 1.3 70.0 - - - +
250D LYS* 1.3 65.4 - - - +
252D LYS* 3.9 16.7 + - - +
253D ALA* 3.3 22.0 + - - +
292D SER* 4.8 11.5 + - - -
293D VAL* 4.1 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D SER* 3.4 19.3 - - - +
249D SER* 1.3 80.7 - - - +
251D GLU* 1.3 65.6 + - + +
253D ALA* 3.4 6.2 + - - +
254D ALA* 3.4 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D GLN* 3.2 39.7 - - + +
246D GLU 4.5 1.7 - - - +
247D GLY* 3.4 7.5 - - - -
248D SER* 3.2 28.2 + - - +
250D LYS* 1.3 79.0 - - + +
252D LYS* 1.3 60.1 + - - +
254D ALA* 3.1 10.2 + - - +
255D VAL* 2.9 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D GLN 5.3 0.2 + - - -
244D LEU* 4.0 40.1 - - + +
245D LYS 4.9 4.0 - - - -
247D GLY 3.5 20.4 + - - +
248D SER* 3.2 12.5 + - - +
249D SER* 3.9 9.3 + - - +
251D GLU* 1.3 76.8 - - - +
253D ALA* 1.3 61.0 - - - +
255D VAL* 3.2 5.2 + - - +
256D PHE* 3.1 34.8 + - + -
288D ILE* 4.5 24.9 - - + +
292D SER* 4.0 16.3 + - - +
293D VAL* 3.9 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D SER 3.3 16.4 + - - +
250D LYS* 3.5 6.7 - - - +
251D GLU 3.3 0.4 - - - -
252D LYS* 1.3 77.2 - - - +
254D ALA* 1.3 61.6 + - - +
256D PHE* 3.4 7.7 + - - +
257D ARG* 3.3 28.0 + - - +
293D VAL* 4.1 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D LYS 3.4 9.0 + - - +
251D GLU* 3.1 13.8 + - - +
253D ALA* 1.3 74.9 - - - +
255D VAL* 1.3 65.5 + - + +
257D ARG* 3.4 15.3 + - - +
258D SER* 3.4 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D TRP* 4.6 2.8 - - + -
239D ILE* 4.0 29.8 - - + -
243D GLN* 4.9 9.2 - - + +
244D LEU* 4.1 39.7 - - + +
251D GLU* 2.9 21.2 + - + +
252D LYS 3.5 7.9 - - - +
254D ALA* 1.3 70.7 - - + +
256D PHE* 1.3 60.8 + - + +
258D SER* 3.4 7.2 + - - -
259D MET* 3.0 48.0 + - + +
281D LEU* 4.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D LEU* 5.2 3.4 - - + -
252D LYS* 3.1 35.2 + - + -
253D ALA* 3.5 11.9 - - - +
254D ALA 3.3 0.4 - - - -
255D VAL* 1.3 74.1 - - + +
257D ARG* 1.3 54.5 + - + +
259D MET* 3.3 8.4 + - - +
260D ASN* 2.6 38.5 + - - +
285D LEU* 3.6 33.2 - - + -
288D ILE* 5.9 1.3 - - + -
293D VAL* 4.2 23.8 - - + -
294D THR 4.4 5.6 - - - +
295D VAL* 4.2 18.6 - - + -
296D PRO* 3.9 27.9 - - + +
299D VAL* 4.1 24.2 - - + +
303D MET* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D ALA* 3.3 14.8 + - - +
254D ALA* 3.5 15.0 - - - +
255D VAL 3.3 0.2 - - - -
256D PHE* 1.3 76.8 - - + +
258D SER* 1.3 53.7 + - - +
260D ASN* 3.2 8.3 + - - +
261D SER* 2.8 38.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D TRP* 3.9 17.7 - - - -
239D ILE* 6.2 1.8 - - - -
254D ALA 3.4 11.2 + - - -
255D VAL* 3.4 9.6 + - - -
257D ARG* 1.3 76.3 - - - +
259D MET* 1.3 55.6 + - - +
261D SER* 4.0 5.4 - - - -
262D ALA* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D TRP* 3.6 25.1 - - + -
244D LEU* 5.3 0.4 - - - -
255D VAL* 3.0 31.8 + - - +
256D PHE* 3.5 15.5 - - - +
258D SER* 1.3 73.3 - - - +
260D ASN* 1.3 55.9 - - - +
262D ALA* 3.1 3.0 + - - +
263D LEU* 2.6 47.8 + - + +
269D LEU* 4.3 4.7 - - + -
281D LEU* 3.6 27.4 - - + -
285D LEU* 3.9 12.1 - - + -
299D VAL* 4.0 14.1 - - + -
302D TRP* 3.5 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D PHE 2.6 23.2 + - - +
257D ARG* 3.5 7.7 - - - +
259D MET* 1.3 71.0 - - - +
261D SER* 1.3 53.6 + - - +
264D GLY* 2.9 15.9 + - - -
296D PRO* 3.5 27.9 - - + +
297D ALA* 4.3 1.6 + - - +
298D ASN* 2.6 71.5 + - - +
299D VAL* 4.3 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D ARG 2.8 20.2 + - - -
258D SER* 4.0 6.1 - - - -
260D ASN* 1.3 70.8 - - - +
262D ALA* 1.3 63.2 + - - +
264D GLY* 3.3 10.2 + - - -
265D LYS* 3.5 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D TRP* 4.2 17.5 - - + +
258D SER 3.1 17.5 + - - +
259D MET* 3.1 5.3 + - - +
261D SER* 1.3 78.4 - - - +
263D LEU* 1.3 55.7 + - - +
264D GLY 3.1 0.2 - - - -
265D LYS* 3.1 11.1 + - - +
266D SER* 2.9 33.1 + - - +
268D TRP 4.9 0.7 - - - -
269D LEU* 4.6 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D MET* 2.6 28.7 + - + +
260D ASN 3.7 0.2 - - - -
262D ALA* 1.3 70.8 - - - +
264D GLY* 1.3 60.2 - - - +
265D LYS 3.3 0.2 - - - -
266D SER* 2.8 17.8 - - - +
267D PRO 4.0 7.2 - - - +
268D TRP 3.7 23.6 - - - -
269D LEU* 3.9 13.2 - - + -
298D ASN* 3.8 13.7 - - + -
299D VAL* 4.0 25.4 - - + -
301D ARG* 3.0 23.2 + - - +
302D TRP* 3.6 52.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D ASN 2.9 11.6 + - - -
261D SER 3.3 4.5 + - - -
262D ALA 3.1 0.8 - - - -
263D LEU* 1.3 78.2 - - - +
265D LYS* 1.3 60.3 + - - +
298D ASN* 3.2 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D SER* 3.5 32.1 + - - +
262D ALA* 3.1 8.8 + - - +
264D GLY* 1.3 79.5 - - - +
266D SER* 1.3 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D ALA* 2.9 14.7 + - - +
263D LEU* 2.8 25.4 - - - +
265D LYS* 1.3 77.5 - - - +
267D PRO* 1.4 69.9 - - - +
268D TRP 2.7 17.2 + - - -
269D LEU 4.7 3.6 + - - -
270D ALA 4.8 0.6 - - - -
271D GLY* 3.3 24.3 + - - -
----------------------------------------------------------
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