Contacts of the helix formed by residues 290 - 308 (chain A) in PDB entry 3SF4
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 290 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A TYR* 2.8 27.7 + - + +
288A LEU* 4.6 5.8 - - + +
289A GLN* 1.3 76.4 - - - +
291A TYR* 1.3 60.5 + - - +
292A GLU* 3.6 10.7 + - - +
293A LYS* 3.1 45.6 + - - +
294A ALA* 3.1 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A THR* 3.9 36.4 + - + -
289A GLN* 3.6 44.9 + - + +
290A ASP* 1.3 70.2 - - - +
292A GLU* 1.3 59.5 + - - +
294A ALA* 3.4 5.7 - - - +
295A ILE* 2.8 36.2 + - - +
324A ALA* 4.1 13.5 - - + +
327A ALA* 3.8 41.0 - - + +
328A LEU* 3.6 27.8 - - + +
24D GLN 5.9 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ASP* 3.2 8.4 + - - +
291A TYR* 1.3 75.9 - - - +
293A LYS* 1.3 64.6 + - + +
295A ILE* 3.3 11.6 + - - +
296A ASP* 3.1 26.7 + - - +
328A LEU* 4.1 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LYS* 4.6 7.3 - - - +
285A TYR* 3.6 49.3 + - + -
290A ASP* 3.1 33.1 + - - +
292A GLU* 1.3 77.7 - - + +
294A ALA* 1.3 66.1 + - - +
296A ASP* 3.1 12.7 + - - +
297A TYR* 3.0 34.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLY* 3.4 29.7 - - - +
285A TYR* 3.9 2.8 - - - +
286A THR* 3.4 19.1 - - - +
290A ASP 3.1 12.1 + - - +
291A TYR* 3.4 14.6 - - - +
292A GLU 3.2 0.2 - - - -
293A LYS* 1.3 76.5 - - - +
295A ILE* 1.3 52.3 + - - +
297A TYR* 3.8 0.7 - - - -
298A HIS* 2.8 46.0 + - + -
324A ALA* 4.6 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A TYR 2.8 28.1 + - - +
292A GLU* 3.3 10.1 - - - +
294A ALA* 1.3 75.0 - - - +
296A ASP* 1.3 55.5 + - - +
298A HIS* 3.2 2.5 + - - +
299A LEU* 2.8 52.0 + - + +
321A LEU* 3.9 6.9 - - + +
324A ALA* 3.2 32.8 - - + +
325A TYR* 3.3 56.1 - - + +
328A LEU* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLU* 3.1 17.9 + - - +
293A LYS* 3.1 17.6 + - + +
295A ILE* 1.3 81.9 - - - +
297A TYR* 1.3 61.3 + - + +
299A LEU* 3.2 11.3 + - - +
300A LYS* 3.0 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LYS* 4.0 22.2 - - - +
262A LEU* 3.9 14.3 - - + +
266A ARG* 5.7 0.7 - - - -
278A CYS* 3.3 34.1 - - - +
281A LEU* 3.7 30.5 - - + -
282A GLY* 3.7 8.7 - - - +
285A TYR* 3.6 34.5 - + - -
293A LYS* 3.0 29.9 + - + +
296A ASP* 1.3 80.5 - - + +
298A HIS* 1.3 63.9 + - - +
300A LYS* 3.3 25.6 + - + -
301A HIS* 3.0 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR* 3.7 27.2 + + - -
282A GLY* 3.4 22.1 + - - -
283A ASN* 3.6 24.1 + - - -
286A THR* 4.5 4.7 + - - -
294A ALA* 2.8 35.6 + - + +
295A ILE* 5.1 0.4 - - - -
297A TYR* 1.3 73.2 - - - +
299A LEU* 1.3 56.4 + - - +
301A HIS* 3.3 7.1 + - - +
302A LEU* 2.8 27.7 + - - +
317A ALA* 4.6 3.7 + - - +
320A SER* 3.5 41.7 - - - -
321A LEU* 3.6 25.5 - - + +
324A ALA* 5.1 2.9 - - + -
28D VAL* 6.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ILE* 2.8 36.1 + - + +
296A ASP* 3.4 11.4 - - - +
297A TYR 3.2 0.2 - - - -
298A HIS* 1.3 75.8 - - - +
300A LYS* 1.3 66.1 + - + +
302A LEU* 3.0 16.9 + - + +
303A ALA* 3.0 23.9 + - - +
321A LEU* 3.9 25.4 - - + -
325A TYR* 4.2 7.4 - - - +
337A PHE* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ARG* 4.2 20.7 - - - +
278A CYS* 3.8 17.5 - - - -
296A ASP* 3.0 32.1 + - - +
297A TYR* 3.3 36.3 + - + +
299A LEU* 1.3 76.2 - - + +
301A HIS* 1.3 61.8 + - - +
303A ALA* 3.5 5.8 + - - +
304A ILE* 3.3 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ALA* 3.3 41.9 - - + +
276A GLN* 5.0 0.7 - - - -
278A CYS* 4.0 7.3 - - + +
279A TYR* 3.5 36.6 - + + +
297A TYR 3.0 13.6 + - - +
298A HIS* 3.5 10.4 + - - +
300A LYS* 1.3 76.9 - - - +
302A LEU* 1.3 66.5 + - - +
304A ILE* 3.5 1.6 + - - +
305A ALA* 2.9 28.6 + - + +
310A ASP* 5.9 0.4 + - - -
313A GLY* 3.1 35.5 + - - -
316A ARG* 5.1 0.2 - - + -
317A ALA* 3.6 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A HIS 2.8 14.5 + - - +
299A LEU* 3.0 19.9 + - + +
301A HIS* 1.3 81.8 + - - +
303A ALA* 1.3 64.4 + - - +
305A ALA* 3.1 5.6 + - - +
306A GLN* 2.9 45.7 + - - +
314A GLU* 3.6 31.2 - - + +
317A ALA* 4.0 16.6 - - + -
318A CYS* 4.5 7.4 - - - -
321A LEU* 3.9 20.0 - - + -
337A PHE* 4.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ARG* 5.7 1.3 - - - +
299A LEU 3.0 11.3 + - - +
300A LYS* 3.7 11.4 - - - +
301A HIS 3.3 0.2 - - - -
302A LEU* 1.3 74.2 - - - +
304A ILE* 1.3 66.1 + - + +
306A GLN* 2.9 19.9 + - - +
307A GLU* 2.8 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ARG* 3.5 57.9 - - + +
274A GLU* 3.6 41.5 - - + +
275A ALA* 3.7 22.0 - - + +
278A CYS* 5.2 2.5 - - - -
300A LYS* 3.3 19.5 + - + +
301A HIS 4.0 0.4 - - - +
303A ALA* 1.3 76.5 - - + +
305A ALA* 1.3 56.4 + - - +
307A GLU* 3.3 8.2 + - - +
308A LEU* 2.9 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ALA* 5.1 3.1 - - + +
301A HIS* 2.9 33.1 + - + +
302A LEU* 3.2 11.0 - - - +
304A ILE* 1.3 78.5 - - - +
306A GLN* 1.3 59.1 - - - +
308A LEU* 3.3 2.9 + - - -
309A ASN 3.0 3.8 + - - -
310A ASP* 2.7 51.4 + - + +
313A GLY* 4.4 1.3 - - - -
314A GLU* 4.3 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 2.9 36.7 + - - +
303A ALA* 2.9 19.9 + - - +
305A ALA* 1.3 73.5 - - - +
307A GLU* 1.3 57.4 + - - +
309A ASN* 2.7 26.4 + - - +
314A GLU* 3.6 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ARG* 2.8 48.6 + - - +
303A ALA 2.8 11.7 + - - +
304A ILE* 3.3 10.8 - - - +
306A GLN* 1.3 77.6 - - - +
308A LEU* 1.3 67.5 + - + +
309A ASN* 3.0 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ARG* 4.2 16.2 - - + -
272A ALA* 4.0 35.0 - - + +
275A ALA* 5.6 1.3 - - + -
304A ILE* 2.9 33.5 + - + +
305A ALA* 4.1 3.1 - - - +
307A GLU* 1.3 78.2 - - + +
309A ASN* 1.3 71.1 + - - +
310A ASP* 3.2 9.5 + - + +
----------------------------------------------------------
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