Contacts of the helix formed by residues 274 - 296 (chain A) in PDB entry 5IYB
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 ASP 274 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ARG* 3.9 3.7 - - - +
262A PRO* 2.5 52.7 - - + +
264A VAL* 4.6 5.4 - - + +
266A MET* 3.9 4.6 - - + +
272A ASN 3.4 0.6 + - - -
273A GLN* 1.3 82.7 + - - +
275A ASP* 1.3 74.4 + - - +
276A LEU* 3.1 23.3 + - - +
277A THR* 3.4 17.9 + - - +
278A HIS* 2.8 28.9 + - - -
342A ARG* 3.2 9.8 + - - -
67M VAL* 3.0 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ASP* 1.3 75.4 + - - +
276A LEU* 1.3 80.2 + - - +
277A THR 3.3 1.3 - - - -
278A HIS* 3.4 10.8 - - - +
279A LYS* 3.0 28.1 + - - +
330A GLN* 3.7 15.3 - - - +
334A ARG* 3.6 11.1 + - - +
336A LEU* 3.6 23.6 - - + +
337A LYS* 3.2 34.8 + - - +
342A ARG* 2.9 20.9 + - - -
67M VAL* 3.1 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PRO* 4.0 15.9 - - + -
260A VAL* 5.5 4.5 - - + +
261A ARG* 3.7 31.4 - - + -
262A PRO* 5.5 0.7 - - + -
274A ASP* 3.1 12.3 + - - +
275A ASP* 1.3 82.1 + - - +
277A THR* 1.3 57.1 + - - +
279A LYS* 4.1 6.0 - - - +
280A LEU* 3.2 22.4 + - + +
317A MET* 4.4 21.8 - - + +
336A LEU* 5.6 1.3 - - - -
337A LYS 5.2 2.5 - - - +
338A SER 5.5 0.2 - - - -
339A LEU* 3.9 37.9 - - + +
342A ARG* 3.7 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 3.5 26.2 - - + -
58A MET* 5.7 1.3 - - + -
261A ARG* 3.2 37.6 + - - +
264A VAL* 5.0 0.3 - - - +
273A GLN* 3.9 24.3 + - + +
274A ASP* 3.4 23.8 + - - +
276A LEU* 1.3 76.7 - - - +
278A HIS* 1.3 64.5 + - - +
279A LYS 3.3 0.4 - - - -
280A LEU* 3.6 6.3 - - + -
281A ALA* 2.9 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLN* 3.8 29.2 - - + +
274A ASP 2.8 29.9 + - - -
275A ASP* 3.3 13.5 + - - +
277A THR* 1.3 74.8 - - - +
279A LYS* 1.3 62.8 + - - +
281A ALA* 3.4 5.7 + - - +
282A ASP* 3.2 19.4 + - - +
330A GLN* 3.9 11.0 + - - -
331A LYS* 6.2 0.7 - - - -
69M ASP* 4.1 23.6 - - + -
71M GLN* 3.4 20.1 + - - -
79M ASP 4.5 4.1 + - - -
80M LEU* 2.9 28.3 - - - +
81M SER* 4.0 7.5 - - - -
82M THR* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ASP 3.0 16.4 + - - +
276A LEU* 4.1 6.7 - - - +
278A HIS* 1.3 77.6 - - - +
280A LEU* 1.3 55.4 + - - +
282A ASP* 3.5 10.4 + - + +
283A ILE* 3.2 25.6 + - + +
312A PHE* 4.4 1.8 - - - -
313A HIS* 3.0 52.5 + - - +
316A THR* 3.0 28.4 + - - -
317A MET* 4.0 24.2 - - + +
328A ALA* 3.7 15.4 - - + +
336A LEU* 3.5 26.7 - - + +
82M THR* 4.9 8.8 + - - +
84M ILE* 4.8 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 4.1 21.8 - - + -
88A ILE* 3.8 25.1 - - + -
253A LEU* 4.9 4.3 - - + -
254A PRO 5.6 0.4 - - - +
255A VAL* 3.8 33.4 - - + -
256A PRO* 5.2 2.9 - - + -
261A ARG* 4.2 13.0 - - - +
276A LEU 3.2 19.0 + - - +
277A THR* 3.8 5.8 - - + +
278A HIS 3.3 0.4 - - - -
279A LYS* 1.3 77.6 - - - +
281A ALA* 1.3 59.3 + - - +
283A ILE* 3.3 10.8 + - + +
284A VAL* 3.0 29.3 + - + +
317A MET* 4.3 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PRO* 3.6 13.7 - - + +
57A LEU* 3.6 24.8 - - + +
277A THR 2.9 17.9 + - - +
278A HIS* 3.7 5.8 - - - +
280A LEU* 1.3 76.2 - - - +
282A ASP* 1.3 58.2 - - - +
284A VAL* 3.4 1.4 + - - -
285A LYS* 2.9 35.8 + - - +
80M LEU* 4.6 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A HIS 3.2 8.6 + - - +
279A LYS* 3.5 16.6 + - + +
280A LEU 3.3 0.2 - - - -
281A ALA* 1.3 75.5 - - - +
283A ILE* 1.3 64.5 + - - +
285A LYS* 3.3 6.4 + - - +
286A ILE* 3.2 31.7 + - - +
313A HIS* 3.1 33.9 + - + -
81M SER* 3.3 32.3 + - - -
82M THR* 4.0 14.6 + - - +
84M ILE* 5.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 4.9 8.3 - - + -
90A LEU* 4.9 3.8 - - + -
253A LEU* 4.3 15.5 - - + -
279A LYS 3.2 12.9 + - - +
280A LEU* 3.3 8.9 + - + +
282A ASP* 1.3 77.6 - - - +
284A VAL* 1.3 59.2 + - - +
286A ILE* 3.4 7.1 - - - +
287A ASN* 2.9 35.6 + - + +
310A LEU* 4.2 14.8 - - + -
313A HIS* 3.5 40.6 - - + +
314A VAL* 3.7 22.0 - - + +
317A MET* 3.9 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLY 5.3 2.9 - - - +
42A LYS* 3.8 27.4 - - - +
44A PRO* 3.4 32.1 - - + -
57A LEU* 5.1 7.0 - - + -
88A ILE* 3.7 31.9 - - + -
280A LEU* 3.0 20.0 + - + +
281A ALA* 3.7 3.4 - - - +
282A ASP 3.3 0.2 - - - -
283A ILE* 1.3 75.5 - - - +
285A LYS* 1.3 54.3 + - - +
287A ASN* 3.8 6.2 - - - +
288A ASN* 2.7 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TYR* 2.9 32.9 + - + -
44A PRO* 3.7 18.4 - - + -
281A ALA 2.9 26.2 + - - +
282A ASP* 3.3 8.0 + - - +
284A VAL* 1.3 76.6 - - - +
286A ILE* 1.3 59.6 + - + +
288A ASN* 3.9 4.2 + - - +
289A GLN* 2.9 29.7 + - - +
80M LEU* 3.3 19.7 - - + +
81M SER* 4.2 20.4 - - - -
107M MET* 4.4 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ASP* 3.2 22.4 + - - +
283A ILE 3.4 11.0 - - - +
285A LYS* 1.3 75.0 - - + +
287A ASN* 1.3 61.7 + - - +
289A GLN* 3.6 6.0 - - - +
290A LEU* 2.7 38.1 + - - +
306A ASP* 4.6 9.0 - - - +
309A LEU* 3.7 27.1 - - + -
310A LEU* 3.5 46.9 - - + +
313A HIS* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 4.0 11.1 - - + +
89A GLU 3.2 21.6 + - - -
90A LEU* 3.2 18.8 - - + +
91A ALA* 2.9 29.4 + - - +
283A ILE* 2.9 23.7 + - + +
284A VAL* 3.8 5.1 + - - +
286A ILE* 1.3 80.2 - - - +
288A ASN* 1.3 58.4 + - - +
290A LEU* 3.9 5.7 - - - +
291A ARG* 3.1 27.1 + - - +
310A LEU* 4.2 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLY 4.7 7.8 - - - +
41A ILE* 4.6 15.4 + - - +
42A LYS 5.5 3.1 - - - -
43A TYR* 5.4 12.7 - - - +
44A PRO* 5.9 2.2 - - + -
284A VAL* 2.7 28.5 + - + +
285A LYS* 3.9 4.7 + - - +
287A ASN* 1.3 73.4 - - - +
289A GLN* 1.3 64.4 + - - +
291A ARG* 3.3 10.4 + - - +
292A ARG* 3.0 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LYS 2.9 19.8 + - - +
286A ILE* 3.6 7.9 - - - +
288A ASN* 1.3 76.9 + - - +
290A LEU* 1.3 54.4 + - - +
292A ARG* 3.3 23.2 + - - +
293A ASN* 2.7 40.2 + - + +
306A ASP* 5.3 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA* 3.6 23.8 - - + -
92A LYS* 5.0 7.0 - - + +
286A ILE 2.7 21.5 + - - +
287A ASN* 3.9 5.4 - - - +
289A GLN* 1.3 72.2 - - - +
291A ARG* 1.3 55.4 + - - +
293A ASN* 3.3 3.7 - - + +
294A GLU* 2.8 31.2 + - + +
303A ILE* 3.5 32.5 - - + -
306A ASP* 3.4 49.0 + - + +
307A VAL* 4.6 10.5 - - + +
310A LEU* 4.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 3.7 23.4 + - - +
90A LEU 2.5 31.8 + - - -
91A ALA* 3.6 29.6 + - + +
287A ASN* 3.1 17.2 + - - +
288A ASN* 3.4 15.5 - - - +
289A GLN 3.2 0.2 - - - -
290A LEU* 1.3 74.7 - - - +
292A ARG* 1.3 60.1 + - - +
294A GLU* 3.4 13.6 + - - +
295A GLN* 3.0 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ASN* 3.0 21.3 + - - +
289A GLN* 3.8 23.7 + - - +
291A ARG* 1.3 76.0 - - - +
293A ASN* 1.3 54.3 + - - +
295A GLN* 3.4 7.0 - - - +
296A ASN* 2.8 60.3 + - - +
26X G 3.5 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLN* 2.7 23.2 + - + +
290A LEU* 3.3 9.4 - - + +
292A ARG* 1.3 75.6 - - - +
294A GLU* 1.3 62.6 + - - +
296A ASN* 3.5 9.4 - - - +
297A GLY 3.5 3.8 + - - +
298A ALA* 2.9 37.0 + - - +
299A ALA 4.8 0.5 + - - -
302A VAL* 3.9 24.1 - - - +
303A ILE* 4.7 7.1 - - - +
306A ASP* 3.7 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA* 4.1 20.4 - - - +
92A LYS* 3.1 29.0 + - - -
290A LEU* 2.8 20.4 + - + +
291A ARG* 3.8 15.6 + - - +
293A ASN* 1.3 69.6 - - - +
295A GLN* 1.3 56.7 + - - +
296A ASN 2.7 27.9 - - - +
298A ALA* 3.6 12.2 + - + +
303A ILE* 4.9 6.6 - - + +
64Q ASN* 4.1 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG* 3.0 30.6 + - + +
292A ARG* 3.4 10.5 - - - +
294A GLU* 1.3 74.8 - - - +
296A ASN* 1.3 65.1 + - - +
61Q SER* 4.0 13.7 - - - +
64Q ASN* 5.9 0.4 - - - -
65Q ASN* 5.8 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ARG* 2.8 52.6 + - - +
293A ASN* 3.5 5.6 - - - +
294A GLU 2.7 20.0 + - - +
295A GLN* 1.3 74.5 - - - +
297A GLY* 1.3 60.6 + - - +
298A ALA 3.5 1.6 + - - -
57Q LYS* 4.5 14.3 - - - +
61Q SER* 2.8 29.2 + - - +
64Q ASN* 4.5 1.0 + - - -
----------------------------------------------------------
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