Contacts of the helix formed by residues 263 - 285 (chain D) in PDB entry 7C17
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 263 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ARG* 4.3 16.5 - - - +
251D PRO* 4.7 2.1 + - - -
262D THR* 1.3 91.5 + - - +
264D ASP* 1.3 71.8 + - - +
265D LEU* 3.2 16.9 + - - +
266D ASN* 3.3 29.1 + - - +
267D ASP* 3.6 4.5 + - - +
330D MET* 4.6 9.7 - - - +
449F THR* 5.5 0.5 - - - +
506F SER* 4.6 2.5 - - - -
507F MET* 3.8 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D SER* 1.3 77.3 + - - +
265D LEU* 1.3 66.7 + - - +
267D ASP* 3.0 11.8 + - - +
268D LEU* 3.0 30.2 + - - +
324D LEU* 3.4 31.4 - - + +
325D LYS* 2.5 45.3 + - - +
330D MET* 5.7 1.2 - - - +
506F SER* 4.0 18.9 - - - -
507F MET* 4.3 2.4 + - - +
508F GLU* 3.9 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D LEU* 3.7 29.4 - - + -
250D ARG* 5.1 2.9 - - - -
263D SER* 3.2 11.1 + - - +
264D ASP* 1.3 79.9 + - - +
266D ASN* 1.3 59.0 + - - +
268D LEU* 3.4 23.4 + - + -
269D TYR* 2.9 48.3 + - + -
306D LEU* 4.1 24.9 - - + +
325D LYS 3.8 10.3 - - - +
326D SER 4.2 5.4 - - - -
327D LEU* 3.8 22.4 - - + +
330D MET* 3.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D THR* 5.6 7.5 - - + +
56D LEU* 5.1 4.3 - - - +
57D PHE* 3.3 17.6 - - + -
250D ARG* 2.4 70.8 + - - +
252D LEU* 4.6 2.5 - - + +
262D THR* 3.8 9.7 + - - +
263D SER* 3.3 23.4 + - - +
264D ASP 3.2 0.2 - - - -
265D LEU* 1.3 78.4 - - - +
267D ASP* 1.3 56.5 + - - +
269D TYR* 3.4 4.3 + - - +
270D ARG* 2.9 29.5 + - - +
449F THR* 5.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D SER 3.6 2.8 + - - +
264D ASP* 3.0 17.7 + - - +
266D ASN* 1.3 76.4 - - - +
268D LEU* 1.3 60.6 + - - +
270D ARG* 3.1 32.8 + - - +
271D ARG* 2.9 64.6 + - - +
317D THR 4.8 0.3 - - - +
318D GLY* 5.2 2.4 - - - -
324D LEU* 3.7 18.5 - - + +
449F THR* 5.3 10.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
264D ASP 3.0 16.2 + - - +
265D LEU* 3.8 18.2 - - + +
266D ASN 3.4 0.2 - - - -
267D ASP* 1.3 78.1 - - - +
269D TYR* 1.3 57.2 + - - +
271D ARG* 3.3 7.1 + - - +
272D VAL* 2.9 32.9 + - - +
302D ALA 5.5 1.1 - - - +
305D ALA* 3.7 23.1 - - + +
306D LEU* 3.6 19.1 - - + +
316D ILE* 3.8 37.7 - - + -
324D LEU* 3.8 22.0 - - + +
325D LYS 3.5 26.0 - - - +
326D SER* 4.2 1.6 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
1332C SER* 3.8 9.0 + - - -
56D LEU* 4.4 16.4 - - + +
105D ILE* 5.5 2.2 - - + -
242D LEU* 4.0 14.9 - - + +
243D PRO 3.2 17.6 + - - -
244D VAL* 3.6 36.7 - - + -
245D LEU* 3.7 14.8 + - + +
250D ARG* 4.7 10.5 - - - +
265D LEU* 2.9 49.2 + - + +
266D ASN* 3.9 6.3 - - - +
268D LEU* 1.3 73.4 - - - +
270D ARG* 1.3 60.9 + - - +
272D VAL* 3.4 4.8 + - + +
273D ILE* 2.9 31.8 + - - +
306D LEU* 3.6 35.2 - - + +
327D LEU* 3.8 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PRO* 3.6 25.1 - - + +
43D THR* 5.1 7.2 - - + -
56D LEU* 5.1 4.6 - - + +
266D ASN 2.9 18.3 + - - +
267D ASP* 3.1 31.5 + - - +
269D TYR* 1.3 77.4 - - - +
271D ARG* 1.3 62.8 - - - +
273D ILE* 3.3 8.0 - - - +
274D ASN* 2.7 56.3 + - - +
398F GLY 5.1 0.2 + - - -
399F LEU* 3.4 20.8 - - - +
445F ASP 5.2 1.6 - - - -
446F GLN* 4.2 4.7 - - - +
447F ALA* 3.2 26.0 - - - +
448F ARG 3.1 44.0 + - - +
449F THR* 3.8 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D ASP* 2.9 51.2 + - - +
268D LEU* 3.3 6.9 + - - +
270D ARG* 1.3 87.6 - - - +
272D VAL* 1.3 60.6 + - + +
274D ASN* 3.6 7.0 - - - +
275D ARG* 2.9 36.0 + - - +
302D ALA* 5.0 6.1 - - + -
316D ILE* 3.7 17.1 - - - +
317D THR 4.6 8.1 + - - -
318D GLY* 5.3 3.8 - - - -
397F ARG 5.6 0.2 + - - -
398F GLY 2.8 27.9 + - - -
399F LEU* 3.4 16.0 - - + +
400F GLN* 3.3 58.1 - - - +
403F ASP* 4.5 5.1 - - - +
446F GLN* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ILE* 5.5 5.6 - - + -
107D LEU* 5.1 8.1 - - + -
242D LEU* 3.8 24.0 - - + -
268D LEU 2.9 20.4 + - - +
269D TYR* 3.8 8.5 - - + +
270D ARG 3.3 0.2 - - - -
271D ARG* 1.3 76.1 - - - +
273D ILE* 1.3 59.5 + - + +
275D ARG 3.4 0.9 + - - -
276D ASN* 2.9 26.5 + - - +
299D LEU* 3.7 17.1 - - + +
302D ALA* 3.7 40.2 - - + +
303D VAL* 4.0 6.3 - - + +
306D LEU* 3.8 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D VAL* 3.7 18.2 - - + -
39D LYS* 3.6 6.7 - - - -
40D LYS 3.4 37.0 - - - +
41D PRO* 3.7 21.1 - - + -
56D LEU* 4.0 7.0 - - + -
105D ILE* 3.8 28.5 - - + -
269D TYR 2.9 17.7 + - - +
270D ARG* 3.3 17.3 - - - +
272D VAL* 1.3 77.4 - - - +
274D ASN* 1.3 56.5 + - - +
276D ASN* 4.1 9.2 - - - +
277D ASN* 2.9 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PRO* 3.3 24.5 - - - +
270D ARG* 2.7 50.0 + - - +
271D ARG* 3.6 7.0 - - - +
272D VAL 3.2 0.2 - - - -
273D ILE* 1.3 74.6 - - - +
275D ARG* 1.3 59.8 + - + +
277D ASN* 3.3 6.1 + - - +
278D ARG* 2.9 33.7 + - - +
281D ARG* 4.3 3.8 + - - -
403F ASP* 6.2 0.4 - - - +
445F ASP* 5.6 0.9 - - - +
446F GLN* 3.4 49.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D ARG* 2.9 19.1 + - - +
272D VAL 3.9 3.6 - - - +
274D ASN* 1.3 74.9 - - - +
276D ASN* 1.3 58.9 + - - +
278D ARG* 3.4 17.7 + - - +
279D LEU* 2.9 25.6 + - - +
295D GLU* 2.9 18.8 - - - +
298D MET* 2.4 65.6 + - - +
299D LEU* 4.1 14.8 - - + +
301D GLU* 4.3 5.5 - - - +
302D ALA* 3.5 25.0 - - - +
400F GLN* 2.8 41.0 + - - +
402F LEU* 4.3 10.9 - - - +
403F ASP* 2.6 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D VAL 5.7 0.6 + - - -
39D LYS* 5.9 2.8 + - - +
105D ILE* 3.4 18.5 - - + +
106D GLU 2.7 30.2 + - - +
107D LEU* 3.4 19.5 - - + +
108D ALA* 3.1 19.9 + - - +
272D VAL 2.9 18.0 + - - +
273D ILE* 3.7 12.1 - - - +
274D ASN 3.2 0.2 - - - -
275D ARG* 1.3 74.3 - - - +
277D ASN* 1.3 63.7 + - - +
279D LEU* 3.3 5.8 + - - +
280D LYS* 2.9 33.7 + - - +
299D LEU* 4.1 6.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LYS* 3.0 29.3 + - - +
40D LYS* 4.0 0.6 - - - +
41D PRO* 3.4 26.1 - - - +
273D ILE* 2.9 23.5 + - - +
274D ASN* 3.8 6.7 - - - +
276D ASN* 1.3 78.1 + - - +
278D ARG* 1.3 60.7 + - - +
280D LYS* 3.4 15.7 + - - +
281D ARG* 2.9 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D ASN* 2.9 22.7 + - - +
275D ARG* 3.4 20.0 - - - +
277D ASN* 1.3 74.8 - - - +
279D LEU* 1.3 59.1 + - - +
281D ARG* 3.4 21.2 + - - +
282D LEU* 2.9 31.9 + - - +
295D GLU* 3.3 27.9 + - - +
298D MET* 3.8 9.5 - - - +
403F ASP* 3.4 38.3 + - - +
406F GLN* 3.7 26.0 + - - +
407F GLU* 2.8 22.7 + - - +
410F ILE* 4.6 11.2 - - + -
446F GLN* 3.2 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ALA* 4.3 13.9 - - + -
109D SER* 5.6 4.5 - - - +
275D ARG 2.9 17.1 + - - +
276D ASN* 3.3 8.5 + - - +
278D ARG* 1.3 77.7 - - - +
280D LYS* 1.3 57.1 + - - +
282D LEU* 3.0 5.5 + - - +
283D LEU* 2.9 36.9 + - + +
292D VAL* 6.3 2.0 - - + -
295D GLU* 3.7 21.9 - - + -
296D LYS* 6.1 2.7 - - + -
299D LEU* 5.3 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LYS* 4.5 13.9 - - - +
106D GLU* 3.4 39.7 + - - +
108D ALA* 4.3 15.4 - - + +
276D ASN* 2.9 23.0 + - - +
277D ASN* 3.7 17.2 + - - +
278D ARG 3.3 0.2 - - - -
279D LEU* 1.3 76.3 - - - +
281D ARG* 1.3 57.6 + - + +
282D LEU 3.6 0.2 + - - -
283D LEU* 3.7 9.1 + - + +
284D ASP* 2.9 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D ASN* 4.3 4.4 + - - -
277D ASN* 2.9 26.1 + - + +
278D ARG* 3.5 40.0 - - - +
280D LYS* 1.3 75.5 - - + +
282D LEU* 1.3 59.2 + - + +
284D ASP* 2.9 19.1 - - - +
285D LEU* 3.3 25.5 - - + +
407F GLU* 3.4 26.8 + - - -
410F ILE* 4.3 16.4 - - + +
441F ARG* 4.4 19.4 - - - +
446F GLN* 5.0 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D ARG 2.9 14.9 + - - +
279D LEU* 3.0 6.7 + - - +
281D ARG* 1.3 80.3 - - - +
283D LEU* 1.3 64.0 + - - +
285D LEU* 3.8 3.5 + - + -
286D ALA 3.9 0.2 + - - -
287D ALA* 3.3 45.2 + - + +
291D ILE* 3.8 28.5 - - + +
292D VAL* 4.4 10.0 - - + +
295D GLU* 3.4 37.0 - - + +
406F GLN* 4.5 0.4 - - - +
410F ILE* 3.8 28.5 - - + -
413F MET* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ALA* 3.8 33.2 - - + +
109D SER* 6.3 1.1 - - - -
279D LEU* 2.9 22.1 + - + +
280D LYS* 3.7 7.4 + - + +
281D ARG 3.5 0.2 - - - -
282D LEU* 1.3 79.6 - - - +
284D ASP* 1.3 61.8 + - - +
285D LEU 3.5 0.2 + - - -
286D ALA* 3.7 8.3 + - - -
287D ALA 5.0 0.2 + - - -
292D VAL* 4.3 23.3 - - + -
296D LYS* 5.4 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D LYS* 2.9 22.2 - - - +
281D ARG* 2.9 20.7 - - - +
283D LEU* 1.3 76.3 - - - +
285D LEU* 1.3 68.9 + - - +
286D ALA* 3.3 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D ARG* 3.3 28.0 + - + +
282D LEU* 3.8 4.7 + - + +
283D LEU 3.3 1.0 - - - -
284D ASP* 1.3 93.0 + - - +
286D ALA* 1.3 69.3 + - - +
287D ALA 3.6 1.1 - - - -
413F MET* 4.1 22.8 - - + +
414F LYS* 4.8 21.5 - - + +
----------------------------------------------------------
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