Contacts of the helix formed by residues 290 - 310 (chain D) in PDB entry 4H3K
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 ALA 290 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D THR 3.4 3.6 + - - -
289D LEU* 1.3 74.9 - - - +
291D LYS* 1.3 67.2 + - - +
292D SER 3.4 1.1 - - - +
293D GLN* 2.8 19.9 + - - +
294D VAL* 2.9 20.9 + - - +
177E GLN* 3.1 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D LEU 3.9 0.2 + - - -
290D ALA* 1.3 74.0 - - - +
292D SER* 1.3 62.3 + - - +
294D VAL* 3.3 10.2 + - + +
295D SER* 3.1 27.2 + - - +
180E GLU* 6.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ALA* 3.4 1.0 - - - +
291D LYS* 1.3 79.6 - - - +
293D GLN* 1.3 55.7 + - - +
295D SER* 3.5 9.9 - - - -
296D SER* 2.7 36.7 + - - -
177E GLN* 3.4 13.7 + - - -
180E GLU* 2.7 33.5 + - - -
186E THR* 4.3 16.6 - - - -
187E PHE 3.7 14.0 + - - -
188E LEU* 3.7 4.3 - - - +
189E HIS 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D SER* 3.6 28.1 + - - +
288D THR 4.0 3.8 - - - +
289D LEU* 3.6 14.5 - - + +
290D ALA* 2.8 33.2 + - + +
292D SER* 1.3 77.9 - - - +
294D VAL* 1.3 54.8 + - - +
296D SER* 3.2 3.5 + - - -
297D VAL* 2.8 41.9 + - - +
173E ASP* 3.9 27.6 + - - +
177E GLN* 3.7 32.6 + - - +
189E HIS* 6.1 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D LEU* 5.0 19.3 - - + -
286D PRO 5.4 0.4 - - - +
289D LEU* 3.7 32.7 - - + +
290D ALA 2.9 18.7 + - - +
291D LYS* 3.6 10.1 - - - +
293D GLN* 1.3 75.6 - - - +
295D SER* 1.3 58.6 + - - +
297D VAL* 3.3 2.1 + - - +
298D ARG* 2.8 67.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D LYS* 3.1 13.2 + - - +
292D SER* 3.5 11.6 - - - -
294D VAL* 1.3 80.2 - - - +
296D SER* 1.3 62.0 + - - -
298D ARG* 3.3 7.6 + - - +
299D LYS* 3.0 29.5 + - - +
188E LEU* 3.6 18.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
250D SER* 4.4 3.8 - - - -
254D THR* 4.7 1.1 - - - -
292D SER 2.7 25.3 + - - -
293D GLN* 3.2 7.9 + - - -
295D SER* 1.3 73.7 - - - +
297D VAL* 1.3 63.6 + - - +
299D LYS* 3.4 7.4 + - - +
300D ASN* 3.2 30.6 + - - +
116E TYR* 4.2 7.2 + - - -
188E LEU* 3.5 10.5 - - - +
189E HIS* 3.0 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D SER* 3.7 36.1 - - - +
253D LEU* 3.5 30.7 - - + -
254D THR* 3.8 11.0 - - + -
257D LEU* 4.0 14.2 - - + +
281D LEU* 4.4 7.6 - - + -
286D PRO* 6.2 0.2 - - + -
289D LEU* 4.4 10.5 - - + -
293D GLN 2.8 21.9 + - - +
294D VAL* 3.8 4.0 - - - +
296D SER* 1.3 71.6 - - - +
298D ARG* 1.3 60.7 + - + +
300D ASN* 3.1 4.0 + - - +
301D LEU* 2.9 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D HIS* 5.1 15.2 + - + -
285D LEU* 4.1 26.9 - - - +
294D VAL* 2.8 44.9 + - + +
295D SER* 3.8 6.3 - - - +
297D VAL* 1.3 80.2 - - + +
299D LYS* 1.3 62.1 + - + +
301D LEU* 3.3 11.0 + - + +
302D LYS* 3.1 23.2 + - - +
328D LEU* 4.1 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D SER* 3.0 24.7 + - - +
296D SER* 3.7 6.1 - - - +
297D VAL 3.3 0.2 - - - -
298D ARG* 1.3 76.0 - - + +
300D ASN* 1.3 61.1 + - - +
302D LYS* 3.5 10.1 - - + +
303D LEU* 3.0 25.8 + - - +
113E GLU* 2.6 29.8 + - - +
116E TYR* 3.6 25.8 - - + -
117E ASP* 2.8 36.2 + - - -
188E LEU* 4.1 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D THR* 3.3 24.3 - - - +
257D LEU* 4.6 3.6 - - + -
296D SER 3.2 12.8 + - - +
297D VAL 3.1 8.4 + - - +
299D LYS* 1.3 80.4 - - - +
301D LEU* 1.3 65.5 + - - +
303D LEU* 3.9 20.2 - - - +
304D HIS* 2.8 44.7 + - + -
116E TYR* 5.1 2.4 + - - -
120E VAL* 4.2 12.1 - - - +
190E THR* 2.8 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D LEU* 4.2 17.8 - - + +
278D TYR* 3.9 38.6 - - + +
281D LEU* 4.4 14.4 - - + -
282D HIS* 4.1 31.4 - - + -
297D VAL* 2.9 13.8 + - + +
298D ARG* 3.6 13.2 - - + +
300D ASN* 1.3 75.8 - - - +
302D LYS* 1.3 65.0 - - - +
304D HIS* 3.8 2.5 - - - +
305D LEU* 2.9 47.6 + - + +
324D LEU* 5.5 1.1 - - + -
328D LEU* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D ARG 3.1 13.4 + - - +
299D LYS* 3.5 12.8 - - - +
301D LEU* 1.3 78.0 - - - +
303D LEU* 1.3 62.5 + - - +
305D LEU 3.4 0.2 + - - -
306D LEU* 3.0 30.6 + - + +
325D LEU* 3.7 8.1 - - + +
328D LEU* 4.0 24.1 - - + +
329D GLY 4.6 2.6 + - - -
330D THR* 3.5 28.1 - - - +
331D PRO* 3.8 16.8 - - - +
334D GLU* 3.1 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D LYS 3.0 12.0 + - - +
300D ASN* 3.4 16.2 - - - +
302D LYS* 1.3 81.8 - - - +
304D HIS* 1.3 74.9 + - + +
306D LEU* 3.4 10.5 + - + +
307D SER* 3.1 21.9 + - - -
120E VAL* 3.8 25.8 - - + -
121E GLU* 4.8 23.6 - - + -
124E ASN* 3.7 36.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
254D THR 4.4 4.4 + - - -
257D LEU* 3.9 8.5 - - + +
258D GLY* 3.4 38.0 + - - -
261D ALA* 3.9 9.1 - - + +
265D ARG* 5.7 1.8 + - - -
278D TYR* 3.7 22.0 - - + +
300D ASN* 2.8 42.6 + - + +
301D LEU* 4.1 2.7 - - - +
303D LEU* 1.3 86.4 - - + +
305D LEU* 1.3 61.4 + - - +
307D SER* 3.2 8.1 + - - -
308D VAL* 2.9 33.4 + - - +
124E ASN* 3.3 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D ILE* 4.7 2.7 - - + -
278D TYR* 3.5 28.7 - - + -
301D LEU* 2.9 40.3 + - + +
304D HIS* 1.3 76.2 - - - +
306D LEU* 1.3 57.9 + - - +
308D VAL* 3.3 5.3 + - - +
309D LEU* 2.8 31.4 + - - +
321D ILE* 3.9 29.8 - - + +
324D LEU* 3.8 31.6 - - + -
325D LEU* 3.6 18.2 - - + -
328D LEU* 3.8 17.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
302D LYS* 3.0 36.0 + - + +
303D LEU* 3.7 10.5 - - + +
305D LEU* 1.3 75.2 - - - +
307D SER* 1.3 62.1 + - - +
309D LEU* 3.4 6.4 + - + +
310D LYS* 3.3 18.7 + - - +
325D LEU* 3.7 25.8 - - + -
330D THR* 4.3 9.0 - - + -
334D GLU* 3.5 37.2 - - - +
335D ILE* 4.3 3.1 - - - -
338D ASN* 3.5 43.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D ALA* 4.1 7.1 - - - +
265D ARG* 3.6 44.5 + - - -
303D LEU* 3.1 17.0 + - - -
304D HIS* 3.3 8.8 + - - -
305D LEU 3.2 0.4 - - - -
306D LEU* 1.3 77.9 - - - +
308D VAL* 1.3 61.6 + - - +
310D LYS* 3.5 18.5 + - - +
311D HIS 3.9 2.3 + - - -
338D ASN* 5.5 0.7 - - - -
124E ASN* 5.0 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D ALA* 3.8 34.1 - - + +
264D ALA* 4.3 7.2 - - + -
265D ARG* 4.8 5.6 - - + -
271D MET* 3.4 34.1 - - + -
274D VAL* 4.9 0.4 - - + -
275D ILE* 4.0 17.3 - - + -
278D TYR* 4.4 9.9 - - + -
304D HIS 2.9 21.2 + - - +
305D LEU* 3.8 5.6 - - - +
307D SER* 1.3 74.9 + - - +
309D LEU* 1.3 65.0 + - - +
310D LYS 3.1 2.0 - - - -
311D HIS* 3.1 15.8 + - - +
314D SER* 3.3 9.1 - - - -
321D ILE* 4.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D LEU 2.8 21.0 + - - +
306D LEU 3.6 5.8 - - - +
307D SER 3.4 0.2 - - - -
308D VAL* 1.3 71.3 - - - +
310D LYS* 1.3 61.0 + - - +
314D SER* 2.7 28.7 + - - +
318D GLN* 4.3 18.8 - - + +
321D ILE* 4.0 23.5 - - + +
322D THR* 4.5 3.1 - - - +
325D LEU* 3.9 21.1 - - + -
335D ILE* 3.7 23.6 - - + +
338D ASN* 3.4 18.8 - - + +
339D MET* 4.1 25.8 - - + -
340D PRO* 3.4 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D LEU 3.3 6.1 + - - +
307D SER* 3.6 13.2 - - - +
308D VAL 3.1 0.8 - - - -
309D LEU* 1.3 78.4 - - - +
311D HIS* 1.3 60.0 + - - +
312D PRO* 3.6 3.6 - - - +
337D ARG 4.8 8.7 - - - -
338D ASN* 3.2 36.0 + - - +
339D MET 4.2 9.9 - - - +
340D PRO* 3.3 20.4 - - + +
----------------------------------------------------------
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