Contacts of the helix formed by residues 299 - 325 (chain A) in PDB entry 5AQX
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 ARG 299 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 2.8 39.9 + - + +
275A SER 3.7 5.7 + - - -
276A SER 3.2 8.3 + - - -
277A SER* 3.0 32.8 + - - +
278A THR* 2.5 38.5 + - + +
298A THR* 1.3 70.4 - - - +
300A ALA* 1.4 53.7 + - - +
302A PHE* 3.0 10.1 + - + +
303A GLU* 2.8 62.1 + - + +
343A ILE* 6.6 0.4 - - + -
344A PRO* 4.0 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A THR* 3.7 8.9 - - - +
299A ARG* 1.4 77.8 - - - +
301A ARG* 1.4 57.8 + - - +
303A GLU* 3.4 15.2 + - - +
304A GLU* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A HIS* 4.2 27.8 - - + +
297A ILE* 4.0 14.4 - - + -
298A THR* 3.0 22.6 + - + +
300A ALA* 1.4 73.8 - - - +
302A PHE* 1.4 57.3 + - - +
304A GLU* 3.1 26.8 + - - +
305A LEU* 2.9 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 4.1 8.5 - - + -
237A LEU* 3.6 36.1 - - + -
271A LYS* 3.6 27.4 - - + -
274A LEU* 3.5 36.6 - - + -
297A ILE* 4.1 4.8 - - + +
298A THR 2.9 7.1 + - - +
299A ARG* 3.3 11.0 - - + +
301A ARG* 1.4 74.6 - - - +
303A GLU* 1.3 63.7 + - + +
305A LEU* 3.0 13.8 + - + +
306A CYS* 3.0 42.4 + - - +
310A PHE* 3.9 26.2 - + - -
343A ILE* 4.1 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ARG* 2.8 48.5 + - + +
300A ALA* 3.5 13.9 - - - +
302A PHE* 1.3 75.8 - - + +
304A GLU* 1.3 53.6 + - - +
306A CYS 3.6 0.5 - - - -
307A SER* 2.8 35.2 + - - -
310A PHE* 4.1 13.2 - - + -
343A ILE* 5.6 1.7 - - + +
344A PRO* 5.1 0.9 - - - +
345A LYS* 3.8 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA 2.9 13.7 + - - +
301A ARG* 3.1 31.0 + - - +
303A GLU* 1.3 72.2 - - - +
305A LEU* 1.4 67.4 + - - +
306A CYS 3.1 2.3 + - - -
307A SER* 3.5 16.9 + - - -
308A ASP* 5.3 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ARG* 2.8 52.3 + - + +
237A LEU* 3.9 13.0 - - + -
240A HIS* 3.5 46.0 - - + +
297A ILE* 3.6 29.2 - - + -
301A ARG* 2.9 22.1 + - + +
302A PHE* 3.0 6.9 + - - +
304A GLU* 1.4 79.7 - - - +
306A CYS* 1.4 52.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 3.7 29.4 - - + -
236A ARG* 3.8 17.9 - - - +
302A PHE* 3.0 37.0 + - - +
303A GLU 3.6 0.9 - - - -
305A LEU* 1.4 81.6 - - - +
307A SER* 1.3 56.6 + - - +
308A ASP* 3.3 5.2 - - - -
309A LEU* 2.9 22.2 + - + +
310A PHE* 3.1 37.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLU 2.8 22.6 + - - -
304A GLU* 3.5 15.4 + - - -
306A CYS* 1.3 69.8 - - - +
308A ASP* 1.3 63.3 + - - +
310A PHE* 3.6 7.6 + - - +
311A ARG* 3.2 47.0 + - - +
345A LYS* 5.8 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ARG* 2.8 44.6 + - - -
304A GLU 5.3 0.7 - - - +
305A LEU 4.4 0.3 - - - +
306A CYS 3.7 2.6 - - - -
307A SER* 1.3 72.7 + - - +
309A LEU* 1.3 71.1 + - - +
311A ARG* 3.3 12.9 + - - +
312A SER* 3.1 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 4.4 17.9 - - + +
232A ASP* 4.2 15.7 - - + -
233A PHE* 3.9 30.6 - - + -
236A ARG* 3.5 55.6 - - + +
306A CYS* 2.9 8.6 + - - +
308A ASP* 1.3 78.5 - - - +
310A PHE* 1.3 64.6 + - - +
312A SER* 2.4 27.2 + - - +
313A THR* 3.7 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 3.5 40.6 - + - -
302A PHE* 3.9 22.7 - + - -
303A GLU* 4.1 20.2 - - - -
306A CYS* 3.1 32.8 + - + -
307A SER* 3.9 7.0 - - - +
308A ASP 3.3 0.2 - - - -
309A LEU* 1.3 75.7 - - - +
311A ARG* 1.3 57.8 + - - +
313A THR* 2.7 31.1 + - + -
314A LEU* 5.0 0.7 - - - +
343A ILE* 4.1 9.9 - - + -
345A LYS* 3.9 27.4 - - + -
346A VAL* 3.6 19.9 - - + +
349A LEU* 3.5 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A SER* 3.2 31.2 + - - +
308A ASP* 3.4 12.9 - - - +
309A LEU 3.2 0.6 - - - -
310A PHE* 1.3 79.5 - - - +
312A SER* 1.3 61.2 + - - +
313A THR 3.2 0.7 + - - -
314A LEU* 3.3 23.8 + - + +
315A GLU* 4.3 1.6 + - - +
349A LEU* 4.6 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 3.9 18.1 - - - +
308A ASP 3.1 11.5 + - - -
309A LEU* 2.4 35.9 + - - +
311A ARG* 1.3 75.3 - - - +
313A THR* 1.3 49.6 + - - +
315A GLU* 3.2 9.8 + - - +
316A PRO* 2.7 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PHE* 3.5 29.3 - - + -
200A LEU* 4.7 14.8 - - + -
205A PHE* 3.4 29.4 - - + -
228A LEU* 4.5 9.9 - - + -
233A PHE* 5.8 2.0 - - + -
309A LEU 3.8 10.1 - - - +
310A PHE* 2.7 27.1 + - + +
312A SER* 1.3 76.6 - - - +
314A LEU* 1.3 65.1 + - - +
316A PRO* 2.9 15.4 - - - +
317A VAL* 3.5 9.3 - - - +
346A VAL* 5.0 6.0 - - + +
349A LEU* 5.2 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PHE* 5.3 1.1 - - + -
310A PHE 5.0 0.9 - - - +
311A ARG* 3.3 15.6 + - - +
312A SER 3.2 0.4 - - - -
313A THR* 1.3 87.1 + - - +
315A GLU* 1.3 65.1 + - - +
317A VAL* 3.0 9.7 + - + +
318A GLU* 2.9 26.2 + - + +
349A LEU* 4.0 36.1 - - + +
350A LEU* 4.3 19.3 - - + -
353A PHE* 3.9 43.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ARG 4.3 1.4 + - - +
312A SER* 3.2 11.6 + - - +
314A LEU* 1.3 75.3 - - - +
316A PRO* 1.3 74.5 - - + +
318A GLU* 3.1 14.7 + - - +
319A LYS* 3.0 30.0 + - - +
322A ARG* 4.1 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PHE* 3.4 32.3 - - + -
207A VAL* 4.1 6.1 - - + -
223A ALA* 3.2 16.3 - - + +
224A GLY* 3.8 26.0 - - - +
225A ASP* 5.6 2.2 - - + -
228A LEU* 6.1 0.2 - - + -
312A SER 2.7 28.3 - - - +
313A THR 2.9 5.6 - - - +
315A GLU* 1.3 88.1 - - + +
317A VAL* 1.3 56.0 + - - +
319A LYS* 3.4 4.4 + - + -
320A ALA* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 4.0 12.8 - - + -
198A PHE* 3.9 19.7 - - + -
207A VAL* 3.8 25.8 - - + -
209A ILE* 4.9 0.3 - - - +
313A THR 3.5 14.6 - - - +
314A LEU* 3.0 13.4 + - + +
316A PRO* 1.3 75.1 - - - +
318A GLU* 1.3 64.7 + - - +
320A ALA* 3.3 3.6 + - - +
321A LEU* 3.2 22.4 + - + +
350A LEU* 4.5 5.6 - - + -
353A PHE* 3.9 24.9 - - + -
354A PHE* 4.0 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LEU* 2.9 11.8 + - + +
315A GLU* 3.6 19.2 - - - +
317A VAL* 1.3 75.6 - - - +
319A LYS* 1.3 64.1 + - - +
321A LEU* 3.3 9.0 + - + +
322A ARG* 3.2 38.6 + - - +
353A PHE* 3.4 37.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A THR 5.8 1.3 - - - -
223A ALA* 4.4 13.0 - - + +
315A GLU* 3.0 20.2 + - - +
316A PRO* 3.7 10.1 - - + +
318A GLU* 1.3 78.4 - - - +
320A ALA* 1.3 61.7 + - - +
322A ARG* 3.2 30.5 + - - +
323A ASP* 3.0 49.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A VAL* 3.8 18.6 - - + +
209A ILE* 3.7 18.6 - - + -
221A ALA* 3.3 20.5 - - + +
223A ALA* 4.1 12.9 - - + +
316A PRO 3.0 17.4 + - - +
317A VAL 3.6 5.4 - - - +
318A GLU 3.3 0.2 - - - -
319A LYS* 1.3 75.6 - - - +
321A LEU* 1.3 59.3 + - - +
323A ASP* 4.6 1.3 - - - -
324A ALA* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 4.9 0.4 - - + -
209A ILE* 3.7 19.7 - - + -
317A VAL* 3.2 14.2 + - + +
318A GLU* 3.6 9.6 - - + +
319A LYS 3.2 0.2 - - - -
320A ALA* 1.3 79.5 - - - +
322A ARG* 1.3 56.1 + - + +
324A ALA* 3.6 1.1 + - - -
325A LYS 3.0 6.6 + - - -
326A LEU* 2.8 50.8 + - + +
327A ASP 3.9 6.5 - - - +
328A LYS* 4.0 22.4 - - + +
331A ILE* 3.8 25.4 - - + -
353A PHE* 4.0 28.9 - - + -
354A PHE* 4.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLU* 4.1 19.6 + - - -
318A GLU* 3.2 23.0 + - - +
319A LYS* 3.2 44.4 + - - +
321A LEU* 1.3 74.5 - - + +
323A ASP* 1.4 65.1 + - - +
325A LYS* 2.9 28.8 + - - +
326A LEU 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LYS 4.5 4.8 - - - +
221A ALA* 3.9 17.0 - - + -
222A THR 4.5 10.9 - - - +
223A ALA* 5.5 0.2 - - - +
319A LYS* 3.0 42.9 + - - +
320A ALA* 4.9 1.1 - - - -
322A ARG* 1.4 79.1 + - - +
324A ALA* 1.4 59.9 + - - +
325A LYS* 3.5 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ILE* 4.1 6.7 - - + -
220A LYS* 3.8 32.9 + - + +
221A ALA* 3.8 14.5 - - + +
320A ALA 2.9 19.4 + - - +
321A LEU 4.1 1.6 - - - +
323A ASP* 1.4 72.2 - - - +
325A LYS* 1.4 69.3 + - - +
326A LEU* 3.7 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU 3.0 1.2 + - - -
322A ARG* 2.9 21.6 + - - +
323A ASP 4.3 8.3 - - - +
324A ALA* 1.4 79.7 - - - +
326A LEU* 1.3 63.5 + - - +
330A GLN* 4.1 3.1 - - - +
----------------------------------------------------------
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