Contacts of the helix formed by residues 287 - 306 (chain A) in PDB entry 3CMM
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 287 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ALA 4.5 3.6 - - - +
285A LYS* 3.6 14.7 - - - -
286A PHE* 1.3 92.7 + - + +
288A ARG* 1.3 66.5 + - - +
289A ALA 3.5 0.6 + - - -
290A ALA* 4.4 6.1 + - - +
291A GLN* 3.3 23.0 + - - +
344A ASN* 5.2 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LYS* 3.3 42.6 - - + +
286A PHE 3.0 1.6 - - - -
287A ASP* 1.3 89.1 + - - +
289A ALA* 1.3 59.0 + - - +
290A ALA 3.4 0.2 - - - -
291A GLN* 3.2 8.2 + - - +
292A LEU* 2.8 39.3 + - + +
344A ASN* 5.5 6.1 - - - +
347A LEU* 3.9 27.5 - - + +
392A ASP* 2.6 47.5 + - - +
394A LEU* 4.1 15.9 - - - +
395A GLU* 4.7 6.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PHE* 4.1 21.3 - - + -
279A VAL 6.1 0.2 - - - +
280A PHE* 4.0 24.0 - - + -
285A LYS 4.2 1.2 + - - +
286A PHE 3.3 14.0 + - - +
288A ARG* 1.3 74.4 - - - +
290A ALA* 1.3 60.7 + - - +
291A GLN 3.2 0.2 + - - -
292A LEU 3.2 0.9 + - - -
293A HIS* 2.8 31.7 + - - +
390A TYR* 3.9 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PHE* 4.0 20.4 - - + -
286A PHE 4.6 1.0 + - - +
287A ASP 4.4 6.9 + - - +
289A ALA* 1.3 78.6 - - - +
291A GLN* 1.3 62.2 + - - +
293A HIS* 3.5 3.1 + - - +
294A LEU* 3.2 20.8 + - - +
336A VAL* 3.3 25.7 - - - +
337A LEU* 3.6 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASP 3.3 19.2 + - - +
288A ARG* 3.4 9.9 - - - +
289A ALA 3.1 0.6 - - - -
290A ALA* 1.3 78.3 - - + +
292A LEU* 1.3 57.1 + - - +
294A LEU* 3.4 4.9 + - - +
295A GLY* 2.8 22.3 + - - -
326A VAL* 4.9 2.6 - - - +
337A LEU* 3.4 25.5 - - + +
341A VAL* 4.1 7.5 - - - +
342A ASP 3.1 24.4 + - - -
343A VAL* 3.8 5.0 - - - +
344A ASN* 2.8 39.7 + - + +
347A LEU* 3.8 15.0 - - + -
348A ILE* 3.7 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PHE* 3.7 32.3 - - + -
288A ARG* 2.8 33.0 + - + +
289A ALA 4.0 0.9 - - - +
291A GLN* 1.3 69.6 - - - +
293A HIS* 1.3 57.2 + - - +
294A LEU 3.2 0.4 - - - -
295A GLY* 3.9 2.5 - - - +
296A PHE* 2.7 44.1 + - + -
347A LEU* 3.9 19.1 - - + -
348A ILE* 4.9 2.9 - - + -
351A LEU* 4.6 13.9 - - + -
390A TYR* 3.8 29.6 - - + -
391A PHE 4.1 23.6 - - - +
392A ASP* 4.6 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A GLN 3.7 1.1 - - - -
273A LEU* 2.8 32.8 + - + -
276A PRO* 3.4 38.7 - - + +
278A PHE* 4.0 6.1 - + + -
289A ALA 2.8 18.2 + - - +
290A ALA* 3.5 5.8 - - - +
292A LEU* 1.3 78.4 - - - +
294A LEU* 1.3 70.0 + - + +
296A PHE* 4.3 0.9 - - - +
297A GLN* 3.0 47.9 + - - +
336A VAL* 4.8 3.8 - - + -
388A PHE* 3.6 21.0 - + - -
390A TYR* 2.7 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ALA 3.2 10.6 + - - +
291A GLN 3.6 7.6 - - - +
292A LEU 3.2 0.4 - - - -
293A HIS* 1.3 79.5 - - + +
295A GLY* 1.3 66.4 + - - +
297A GLN* 3.3 18.5 + - - +
298A ALA* 3.0 22.2 + - - +
326A VAL* 4.0 17.5 - - + +
329A LEU* 3.7 33.0 - - + +
330A SER* 4.0 14.4 - - - +
333A GLN* 5.0 2.9 - - - +
336A VAL* 3.6 42.6 - - + -
337A LEU* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLN 2.8 15.7 + - - -
292A LEU 3.0 4.2 + - - -
294A LEU* 1.3 76.9 - - - +
296A PHE* 1.3 56.2 + - - +
298A ALA* 3.0 6.2 + - - +
299A LEU* 3.0 26.9 + - - +
322A LEU* 5.0 1.6 - - - +
326A VAL* 3.9 15.2 - - - +
348A ILE* 4.0 5.2 - - - -
351A LEU* 3.6 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 5.5 0.2 - - - -
155A GLU* 3.6 36.8 - - + -
157A ARG* 3.8 16.6 - - + -
160A PHE* 4.0 18.6 - - + -
161A GLY* 4.0 27.4 - - - -
162A ASN* 3.0 26.0 - - - +
292A LEU* 2.7 40.3 + - + +
293A HIS 4.3 2.0 - - - +
295A GLY* 1.3 69.2 - - - -
297A GLN* 1.3 64.5 + - + +
299A LEU* 3.2 17.9 - - + +
300A HIS* 3.1 25.0 + - + +
351A LEU* 4.2 14.6 - - + -
390A TYR* 3.8 21.1 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 4.4 15.6 - - + +
273A LEU* 3.6 45.6 + - + +
293A HIS* 3.0 44.8 + - + +
294A LEU* 3.3 17.9 + - - +
295A GLY 3.2 0.4 - - - -
296A PHE* 1.3 79.0 - - + +
298A ALA* 1.3 63.2 + - - +
300A HIS* 3.2 7.1 + - - +
301A GLN* 3.1 25.9 + - + +
329A LEU* 4.5 13.5 - - + +
333A GLN* 5.6 4.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU 3.0 14.1 + - - +
295A GLY 3.0 8.5 + - - +
297A GLN* 1.3 77.1 - - - +
299A LEU* 1.3 57.7 + - - +
301A GLN* 3.1 6.5 + - - +
302A PHE* 2.9 27.9 + - - +
322A LEU* 3.8 8.7 - - + -
325A LEU* 3.6 24.8 - - + +
326A VAL* 3.6 23.6 - - + +
329A LEU* 4.1 7.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
155A GLU* 4.6 5.6 - - - +
157A ARG* 4.5 12.3 - - - +
295A GLY 3.0 12.0 + - - +
296A PHE* 3.2 55.4 - - + +
298A ALA* 1.3 76.2 - - - +
300A HIS* 1.3 59.6 + - + +
302A PHE* 3.5 3.9 - - - +
303A ALA* 3.2 24.3 + - - +
309A GLU 5.3 0.2 - - - +
310A LEU* 5.4 6.7 - - + +
311A PRO* 4.5 11.1 - - + +
322A LEU* 3.7 20.8 - - + +
351A LEU* 3.8 29.8 - - + +
355A ALA* 3.8 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASP 6.0 0.2 + - - -
132A VAL 4.7 2.4 + - - -
133A SER* 4.4 10.7 - - - -
134A LEU* 3.4 56.9 + - + +
137A LYS* 4.9 0.4 - - - -
155A GLU* 2.8 41.8 + - - -
157A ARG* 4.5 6.1 + - - -
296A PHE* 3.1 21.0 + - + -
297A GLN 3.2 8.8 + - - +
298A ALA 3.2 0.6 - - - -
299A LEU* 1.3 78.4 - - + +
301A GLN* 1.3 63.5 + - + +
302A PHE 3.2 1.6 - - - -
303A ALA* 3.3 9.5 + - + +
304A VAL* 3.1 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 6.5 0.2 - - + -
297A GLN* 3.1 16.3 + - + +
298A ALA* 3.1 6.1 + - - +
300A HIS* 1.3 75.0 - - + +
302A PHE* 1.3 61.7 + - - +
304A VAL* 3.5 8.4 + - - +
305A ARG* 3.1 23.9 + - - +
325A LEU* 3.7 32.5 + - + +
328A ASP* 6.1 0.8 - - - +
329A LEU* 3.9 36.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
298A ALA 2.9 12.8 + - - +
299A LEU* 3.5 15.0 - - - +
301A GLN* 1.3 73.6 - - - +
303A ALA* 1.3 59.3 + - - +
305A ARG* 3.2 5.5 + - - +
306A HIS* 2.9 58.9 + + + -
309A GLU* 3.6 12.1 - - + -
310A LEU 3.8 4.3 - - - -
311A PRO* 3.6 33.9 - - + -
318A ASP* 3.7 45.3 - - + -
321A GLU* 3.6 33.9 - - + -
322A LEU* 4.1 11.0 - - + -
325A LEU* 3.9 8.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
299A LEU 3.2 14.9 + - - +
300A HIS* 3.3 13.4 + - + +
302A PHE* 1.3 75.0 - - - +
304A VAL* 1.3 66.1 + - + +
306A HIS 3.0 8.5 + - - -
307A ASN 3.1 0.2 + - - -
308A GLY* 2.7 41.8 + - - +
309A GLU 3.3 20.0 - - - +
310A LEU* 5.0 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLU* 5.3 12.8 - - + +
300A HIS* 3.1 17.7 + - + +
301A GLN* 3.8 7.6 - - - +
303A ALA* 1.3 79.1 - - + +
305A ARG* 1.3 61.9 + - - +
306A HIS 3.4 0.2 + - - -
307A ASN* 3.7 7.4 + - - -
308A GLY* 4.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A GLN 3.1 17.2 + - - +
302A PHE* 3.5 5.4 - - - +
303A ALA 3.1 0.6 - - - -
304A VAL* 1.3 80.2 - - + +
306A HIS* 1.3 63.3 + - + +
307A ASN 3.6 1.1 + - - -
321A GLU* 3.1 39.9 + - - +
324A LYS* 6.3 0.4 - - - +
325A LEU* 3.5 35.4 - - - +
328A ASP* 5.9 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A PHE* 2.9 49.4 + + + +
303A ALA 3.0 2.6 + - - -
305A ARG* 1.3 85.7 + - + +
307A ASN* 1.3 66.9 + - - +
309A GLU* 3.1 33.1 + - + +
312A ARG* 6.1 0.9 - - - -
318A ASP* 5.2 4.3 - - - -
321A GLU* 3.0 37.8 + - - -
----------------------------------------------------------
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