Contacts of the helix formed by residues 288 - 309 (chain B) in PDB entry 3QEL
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 GLY 288 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B GLU 4.3 8.3 + - - -
285B TRP 4.7 1.5 + - - -
286B ASP 3.8 3.2 + - - -
287B TYR* 1.3 79.5 - - - +
289B LEU* 1.3 67.6 + - - -
290B PRO* 3.4 7.9 - - - -
291B ALA* 3.1 9.1 + - - +
292B ARG* 3.0 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 4.5 17.9 - - + -
45B SER* 4.6 17.3 - - - -
46B ASP 5.8 1.3 - - - +
50B ILE* 6.0 4.0 - - + -
100B ALA* 3.8 25.1 - - + -
126B ILE* 4.1 10.5 - - + -
127B HIS* 3.9 31.9 + - + +
288B GLY* 1.3 70.3 - - - -
290B PRO* 1.3 72.5 - - + +
292B ARG* 2.9 9.6 + - - +
293B VAL* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASP* 5.4 1.6 - - + +
49B ALA* 3.4 44.2 - - + +
50B ILE* 4.0 17.3 - - + +
52B ASP 5.8 2.8 - - - +
288B GLY* 3.4 6.7 - - - -
289B LEU* 1.3 95.5 - - + +
291B ALA* 1.3 60.1 + - - +
293B VAL* 3.7 5.5 + - + +
294B ARG* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ASP 5.8 0.4 - - - +
287B TYR* 3.6 18.4 - - + -
288B GLY* 3.1 15.1 + - - +
290B PRO* 1.3 80.8 - - - +
292B ARG* 1.3 58.4 + - - +
294B ARG* 3.0 53.1 + - - +
295B ASP* 3.1 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ILE* 2.6 46.2 + - + +
127B HIS* 3.9 18.5 + - - +
131B SER* 5.1 1.8 + - - -
146B PHE* 3.7 19.4 + - + +
282B TYR* 3.4 40.1 + - - -
283B ASP 4.2 1.8 + - - -
284B GLU* 3.5 32.6 - - - +
287B TYR* 2.9 45.4 + - + -
288B GLY 3.0 17.8 + - - +
289B LEU* 2.9 15.7 + - - +
291B ALA* 1.3 72.8 - - - +
293B VAL* 1.3 60.2 + - - +
295B ASP 3.3 1.0 + - - -
296B GLY* 2.8 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 4.0 31.0 - - + -
41B LEU* 4.8 7.2 - - + -
50B ILE* 5.2 17.5 - - + +
70B LEU* 5.8 2.9 - - + -
98B VAL* 4.5 4.3 - - + -
126B ILE* 3.7 21.1 - - + -
289B LEU* 2.9 30.6 + - + +
290B PRO* 4.1 6.1 - - + +
292B ARG* 1.3 75.1 - - - +
294B ARG* 1.3 63.9 + - - +
296B GLY* 3.1 1.1 + - - +
297B ILE* 2.9 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP 5.7 3.4 - - - +
287B TYR* 4.4 3.8 - - - -
290B PRO 3.1 13.6 + - - +
291B ALA* 3.0 38.2 + - - +
293B VAL* 1.3 78.0 - - - +
295B ASP* 1.3 86.2 + - - +
297B ILE* 3.1 8.2 + - - +
298B ALA* 3.0 24.8 + - - +
344B PHE* 3.7 30.0 - - + -
345B GLU* 5.2 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B PHE* 4.3 7.4 - - + -
287B TYR* 2.5 36.7 + - - +
291B ALA 3.1 6.6 + - - -
292B ARG 3.8 3.1 - - - +
294B ARG* 1.3 102.7 + - - +
296B GLY* 1.3 66.4 + - - +
298B ALA* 3.6 8.2 - - - +
299B ILE* 3.0 34.8 + - + +
344B PHE* 4.0 9.8 - - + -
349B LEU* 5.3 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B VAL* 3.9 16.2 - - - -
124B LEU* 3.5 25.6 - - - +
126B ILE* 4.9 0.7 - - - -
146B PHE* 4.4 6.9 - - - -
292B ARG 2.8 15.6 + - - -
293B VAL 3.5 4.5 - - - -
294B ARG 3.1 0.6 - - - -
295B ASP* 1.3 80.2 - - - +
297B ILE* 1.3 61.0 + - - +
299B ILE* 3.3 6.5 + - - -
300B ILE* 3.4 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 3.9 16.9 - - + +
39B VAL* 4.3 13.9 - - + -
66B PRO* 3.9 30.3 - - + -
68B VAL* 3.2 34.8 - - + -
98B VAL* 4.1 2.4 - - + +
293B VAL* 2.9 30.6 + - + +
294B ARG* 3.6 8.1 - - - +
296B GLY* 1.3 75.0 - - - +
298B ALA* 1.3 60.0 + - - +
300B ILE 3.6 0.3 + - - -
301B THR* 2.8 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 6.3 0.4 - - - -
294B ARG 3.0 12.6 + - - +
295B ASP* 3.6 12.3 - - - +
296B GLY 3.1 0.2 - - - -
297B ILE* 1.3 78.4 - - - +
299B ILE* 1.3 56.6 + - + +
301B THR* 3.2 4.6 + - - -
302B THR* 2.6 40.5 + - - -
342B VAL* 4.9 0.2 - - - -
344B PHE* 3.8 44.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 4.7 8.7 - - + -
146B PHE* 4.3 16.6 - - + -
295B ASP* 3.0 25.1 + - + +
296B GLY* 3.3 4.9 + - - +
298B ALA* 1.3 76.6 - - + +
300B ILE* 1.3 58.5 + - - +
303B ALA* 3.0 31.5 + - - +
339B LEU* 3.7 35.4 - - + +
342B VAL* 3.8 27.6 - - + +
344B PHE* 6.2 0.2 - - + -
349B LEU* 3.7 30.7 - - + +
351B PHE* 4.1 17.9 - - + -
357B GLN* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 4.3 5.8 - - + -
37B ILE* 3.6 26.9 - - + -
95B GLN* 4.7 6.1 - - + +
96B GLY* 3.7 20.6 - - - +
97B VAL 3.6 28.3 - - - +
98B VAL* 3.8 14.6 - - + -
122B PRO* 4.9 7.2 - - + -
124B LEU* 3.7 30.5 - - + -
296B GLY 3.4 4.7 + - - +
298B ALA 3.3 0.4 - - - -
299B ILE* 1.3 77.6 - - - +
301B THR* 1.3 58.0 + - - +
303B ALA* 4.0 1.0 - - - +
304B ALA* 3.2 26.0 + - - +
335B LEU* 5.6 4.5 - - + +
339B LEU* 4.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 3.8 9.5 - - + +
37B ILE* 3.5 6.9 - - - +
62B LEU* 3.5 20.9 - - + -
64B VAL* 3.6 22.9 - - + +
66B PRO* 3.4 37.5 - - + +
297B ILE* 2.8 23.0 + - - -
298B ALA* 3.7 3.6 - - - -
300B ILE* 1.3 74.9 - - - +
302B THR* 1.3 65.8 + - - +
303B ALA 3.2 0.9 - - - -
304B ALA 3.3 0.9 + - - -
305B SER* 2.9 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 3.9 25.5 - - + +
298B ALA* 2.6 30.4 + - - +
301B THR* 1.3 72.3 - - - +
303B ALA* 1.3 64.1 + - - +
305B SER* 3.2 3.1 + - - -
306B ASP* 2.9 41.3 + - - +
342B VAL* 3.6 35.1 - - + +
343B THR 4.9 6.6 + - - +
344B PHE* 4.8 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ILE 3.0 19.6 + - - +
300B ILE 4.0 2.0 - - - +
302B THR* 1.3 80.3 - - - +
304B ALA* 1.3 63.2 + - - +
306B ASP* 3.4 5.4 + - - +
307B MET* 3.3 22.2 + - - +
335B LEU* 3.8 6.9 - - + +
338B TYR* 3.7 13.3 - - + +
339B LEU* 3.7 40.8 - - + +
342B VAL* 4.1 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 4.1 15.9 - - + -
64B VAL* 4.0 11.9 - - + -
95B GLN* 5.3 5.6 - - + -
300B ILE 3.2 16.6 + - - +
301B THR 3.3 4.0 + - - +
303B ALA* 1.3 79.5 - - - +
305B SER* 1.3 62.8 + - - +
307B MET 3.0 9.9 + - - -
308B LEU* 3.1 4.3 + - - +
314B ILE* 3.1 38.2 - - + +
335B LEU* 4.1 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 3.3 27.3 - - - +
63B SER* 3.4 22.0 + - - -
64B VAL* 3.4 18.9 - - - +
301B THR 2.9 13.1 + - - -
302B THR 3.2 8.5 + - - -
304B ALA* 1.3 75.6 - - - +
306B ASP* 1.3 68.0 + - - +
307B MET 2.9 1.4 + - - -
308B LEU* 3.0 15.0 + - - +
309B SER* 3.0 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 5.2 2.3 - - - +
302B THR* 2.9 40.5 + - - +
303B ALA* 3.7 7.3 - - - +
305B SER* 1.3 78.8 + - - +
307B MET* 1.3 58.1 + - - +
309B SER* 3.4 18.1 + - - -
310B GLU* 3.5 15.8 + - - +
338B TYR* 3.9 24.5 - - + +
341B ASN 4.9 7.8 - - - +
342B VAL* 5.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA 3.3 4.9 + - - +
304B ALA 3.0 8.6 + - - +
305B SER 3.0 1.0 - - - -
306B ASP* 1.3 77.9 - - - +
308B LEU* 1.3 62.5 + - - +
309B SER 3.2 0.9 - - - -
310B GLU 4.0 1.3 - - - +
311B HIS* 3.2 22.6 + - - +
313B PHE* 3.1 34.4 - - + +
314B ILE* 3.7 4.7 - - + -
315B PRO* 3.6 36.6 - - + -
334B MET* 3.6 36.3 - - + -
335B LEU* 4.0 16.2 - - + -
338B TYR* 3.3 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B SER* 5.2 8.3 - - - -
64B VAL* 6.0 4.5 - - + -
304B ALA 3.1 9.6 + - - +
305B SER* 3.0 10.5 + - - +
307B MET* 1.3 76.2 - - - +
309B SER* 1.3 57.9 + - - +
310B GLU 3.1 2.5 + - - -
312B SER* 2.8 28.6 + - - -
313B PHE* 3.6 16.8 - - - +
314B ILE* 3.7 9.1 - - + +
329D ILE* 5.5 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B SER* 4.8 13.0 - - - -
305B SER* 3.0 14.8 + - - -
306B ASP* 3.4 14.7 + - - -
307B MET 3.2 0.2 - - - -
308B LEU* 1.3 77.4 - - - +
310B GLU* 1.3 57.7 + - - +
----------------------------------------------------------
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