Contacts of the helix formed by residues 295 - 314 (chain D) in PDB entry 3QKJ
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 LEU 295 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D TRP* 4.7 11.0 - - + -
291D THR* 2.8 37.5 + - + +
292D PHE 3.7 6.6 - - - +
293D ASN 3.7 0.4 - - - -
294D LYS* 1.3 93.8 - - + +
296D VAL* 1.3 64.1 + - - +
297D SER* 3.7 20.6 - - - +
298D TYR* 3.2 15.2 + - + +
299D ARG* 3.3 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D LYS 4.2 1.0 + - - -
295D LEU* 1.3 71.0 - - - +
297D SER* 1.4 60.9 + - - +
299D ARG* 3.2 39.1 + - - +
300D LYS* 2.9 30.1 + - + +
325D LEU* 4.5 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D TRP* 3.8 18.5 - - - -
265D GLY* 5.1 2.1 - - - -
295D LEU* 3.7 17.3 - - - +
296D VAL* 1.4 83.1 - - - +
298D TYR* 1.3 57.4 + - - +
300D LYS* 3.6 6.6 + - - +
301D ALA* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D TRP* 3.6 10.9 - - - -
237D SER* 4.6 3.8 - - - -
238D TRP 3.6 20.4 + - - -
239D TRP* 3.7 30.3 - + + -
240D PRO* 5.0 0.9 - - + -
287D PHE* 3.7 9.0 - + - -
288D ASN* 3.0 40.6 + - + +
291D THR* 3.6 31.9 - - + +
292D PHE* 3.5 27.4 - + + -
295D LEU* 3.2 11.7 + - + +
297D SER* 1.3 79.5 + - - +
299D ARG* 1.3 57.7 + - - +
301D ALA* 3.3 2.5 + - - +
302D MET* 2.9 59.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D PHE* 3.1 57.4 + - + +
293D ASN* 4.1 16.1 + - - +
294D LYS 4.8 3.2 + - - -
295D LEU 3.3 3.9 + - - +
296D VAL* 3.2 50.6 + - - +
298D TYR* 1.3 77.2 - - - +
300D LYS* 1.4 56.1 + - - +
302D MET* 3.2 1.9 + - - +
303D TYR* 3.0 24.1 + - - +
325D LEU* 4.0 15.5 - - + +
326D GLU* 3.8 40.4 + - - +
329D LEU* 3.3 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D GLY* 4.5 6.5 - - - +
296D VAL* 2.9 17.2 + - + +
297D SER* 3.8 7.2 - - - +
299D ARG* 1.4 71.6 - - - +
301D ALA* 1.4 66.1 + - - +
303D TYR* 3.2 6.8 + - - +
304D HIS* 3.1 39.1 + - + +
325D LEU* 4.1 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D TRP* 3.4 22.0 - - + +
240D PRO* 4.1 11.4 - - + -
264D PHE* 3.3 36.2 - - - +
265D GLY* 3.9 2.4 - - - +
297D SER 3.0 19.8 + - - +
298D TYR* 3.5 5.6 - - + +
300D LYS* 1.4 74.9 - - - +
302D MET* 1.3 57.5 + - - +
305D ALA* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D TRP* 3.7 28.5 - - + -
240D PRO* 3.7 21.1 - - + -
280D LEU* 5.7 0.9 - - - -
283D PHE* 3.9 16.4 - - - -
287D PHE* 4.1 9.4 - - + -
292D PHE* 4.3 4.3 - - + -
298D TYR* 2.9 50.7 + - + +
299D ARG* 3.4 8.7 - - - +
301D ALA* 1.3 73.9 - - - +
303D TYR* 1.4 58.2 + - - +
305D ALA* 3.4 2.9 + - - +
306D LEU* 2.9 39.3 + - + +
329D LEU* 4.0 7.6 - - + -
333D LEU* 4.1 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D ARG 3.0 8.6 + - - +
300D LYS* 3.6 7.4 - - - +
302D MET* 1.4 75.6 - - - +
304D HIS* 1.3 86.2 + + - +
306D LEU* 3.8 0.9 - - - +
307D GLU* 2.9 58.4 + - + +
325D LEU* 3.7 30.5 - - + -
328D GLN* 3.3 40.7 + - + -
329D LEU* 3.6 13.4 - - + +
332D MET* 3.2 34.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D PHE* 3.6 27.1 - - + -
265D GLY* 4.2 17.0 - - - +
300D LYS* 3.1 34.2 + - + +
301D ALA 4.1 2.2 - - - +
303D TYR* 1.3 98.3 - + - +
305D ALA* 1.3 62.5 + - - +
307D GLU* 3.8 4.6 - - - +
308D LYS* 3.2 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D LEU* 4.6 2.1 - - - +
240D PRO* 3.6 28.3 - - + -
264D PHE* 3.6 22.5 - - + -
280D LEU* 4.5 14.9 - - + +
301D ALA 3.0 18.5 + - - +
302D MET* 3.8 5.4 - - - +
304D HIS* 1.3 76.0 - - - +
306D LEU* 1.3 60.0 + - + +
308D LYS* 3.3 5.4 + - - +
309D ALA* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D LEU* 4.6 6.7 - - + -
283D PHE* 3.9 17.0 - - + -
302D MET* 2.9 23.9 + - + +
303D TYR* 4.3 2.0 - - - +
305D ALA* 1.3 74.7 - - + +
307D GLU* 1.3 55.3 + - - +
309D ALA* 3.5 7.9 - - + +
310D ARG* 2.8 34.6 + - - +
329D LEU* 4.6 3.1 - - + -
332D MET* 3.8 40.0 - - + +
333D LEU* 3.8 29.8 - - + +
335D TRP* 4.0 5.6 - - + -
336D ALA* 3.7 23.3 - - + -
340D PHE* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D TYR* 2.9 49.5 + - + +
304D HIS* 3.8 7.6 - - - +
306D LEU* 1.3 73.7 - - - +
308D LYS* 1.4 62.9 + - - +
310D ARG* 2.9 48.0 + - - +
311D VAL* 3.1 34.2 + - + +
328D GLN* 5.6 0.7 + - - -
332D MET* 4.1 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D LEU* 4.1 12.3 - - + -
242D MET* 3.8 32.1 - - + -
264D PHE* 4.0 12.3 - - + -
304D HIS 3.2 13.6 + - - +
305D ALA 3.3 8.7 + - - +
307D GLU* 1.4 74.0 - - - +
309D ALA* 1.4 62.1 + - - +
311D VAL* 3.4 10.5 + - + +
312D ARG* 3.1 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D LEU* 4.0 17.4 - - + +
280D LEU* 4.7 2.7 - - + -
305D ALA 3.1 13.2 + - - +
306D LEU* 3.5 14.6 - - + +
307D GLU 3.4 0.2 - - - -
308D LYS* 1.4 75.6 - - - +
310D ARG* 1.4 55.8 + - - +
312D ARG* 3.4 4.9 + - - +
313D ALA* 3.0 31.0 + - - +
335D TRP* 3.7 11.8 - - + -
340D PHE* 4.5 6.7 - - + -
348D LEU* 3.6 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D LEU 2.8 20.9 + - - +
307D GLU* 2.9 44.7 + - - +
308D LYS 3.3 0.2 - - - -
309D ALA* 1.4 70.3 - - - +
311D VAL* 1.3 84.3 + - - +
313D ALA 3.5 0.3 + - - -
314D GLY 3.2 2.8 + - - -
315D LYS* 2.8 72.9 + - + +
316D THR* 4.3 9.7 + - - +
317D PHE* 3.5 37.0 - - + +
332D MET* 5.2 2.0 - - - -
335D TRP* 3.7 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D GLU* 3.1 23.7 + - + +
308D LYS* 4.0 10.5 - - + +
310D ARG* 1.3 100.5 - - - +
312D ARG* 1.3 65.7 + - + +
314D GLY* 3.2 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 312 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D GLY* 2.7 35.4 + - - -
228D LEU* 3.6 20.4 - - - +
242D MET* 3.8 15.4 - - - -
308D LYS* 3.1 49.8 + - - +
309D ALA 3.6 4.0 - - - +
311D VAL* 1.3 77.4 - - + +
313D ALA* 1.3 59.9 + - - +
314D GLY* 3.4 1.0 + - - -
347D GLY* 3.2 15.9 - - - +
348D LEU* 3.0 28.8 + - - +
349D LYS 3.8 11.5 - - - +
350D PRO* 3.6 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D ALA 3.0 17.5 + - - +
310D ARG 4.0 2.9 - - - +
312D ARG* 1.3 73.3 - - - +
314D GLY* 1.3 61.2 + - - +
315D LYS* 4.3 3.3 - - + +
335D TRP* 3.8 21.1 - - + -
343D THR* 3.4 38.5 - - + +
347D GLY* 3.1 19.1 + - - +
348D LEU* 4.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D ARG 3.9 0.2 - - - -
311D VAL 3.2 15.4 + - - -
312D ARG 3.2 1.6 + - - -
313D ALA* 1.3 77.6 - - - +
315D LYS* 1.3 61.1 + - - +
316D THR* 4.2 4.4 + - - -
----------------------------------------------------------
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