Contacts of the helix formed by residues 324 - 342 (chain A) in PDB entry 3MEK
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 ASN 324 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ASP 4.4 1.3 - - - -
275A MSE 3.3 16.4 + - - -
276A LEU* 3.9 3.2 - - - +
277A THR 2.9 29.6 + - - +
283A TRP* 3.3 29.4 - - - +
320A LEU* 3.9 9.0 - - + +
321A PRO* 3.1 17.7 + - + +
322A ASP 3.7 0.2 - - - +
323A ILE* 1.3 81.1 - - - +
325A ILE* 1.3 59.7 + - - +
326A TYR* 3.0 23.9 + - - +
327A GLN* 3.2 14.2 + - + +
328A LEU* 2.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.7 40.6 - - + +
244A MSE 4.0 1.1 - - - -
245A THR* 3.9 16.8 - - + +
248A GLU* 3.7 22.7 - - - +
275A MSE 3.0 49.1 + - + +
276A LEU* 4.7 0.2 - - + -
323A ILE 3.3 0.4 + - - -
324A ASN* 1.3 70.8 + - - +
326A TYR* 1.3 83.7 + - + +
328A LEU* 3.3 7.0 + - - +
329A LYS* 3.0 35.2 + - - +
361A PHE* 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A THR* 4.4 1.0 - - - +
248A GLU* 2.4 32.1 + - - -
276A LEU* 3.7 20.0 - - + +
283A TRP* 3.7 40.4 - + + +
286A VAL* 3.9 16.2 - - + -
287A GLN* 3.2 34.0 + - + +
290A LEU* 3.6 28.0 - - + +
324A ASN* 3.0 13.5 + - - +
325A ILE* 1.3 92.5 - - + +
327A GLN* 1.3 65.6 + - - +
328A LEU 3.4 0.2 + - - -
329A LYS* 3.4 10.0 + - + -
330A VAL* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A VAL* 4.8 0.7 - - - -
312A ILE* 4.0 22.1 + - - +
313A ILE* 4.6 14.1 + - - +
319A ARG* 5.8 2.2 - - - +
320A LEU* 3.6 40.0 + - + +
321A PRO 3.4 22.2 - - - +
322A ASP* 3.3 26.1 + - - +
324A ASN* 3.2 13.3 + - - +
326A TYR* 1.3 74.5 - - - +
328A LEU* 1.3 58.3 + - - +
330A VAL* 3.2 8.8 + - - +
331A LEU* 3.0 38.0 + - + +
353A ARG* 3.7 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.7 24.7 - - + -
322A ASP 3.6 16.4 - - - +
324A ASN 2.8 16.5 + - - +
325A ILE* 3.6 7.4 - - - +
326A TYR 3.2 0.4 - - - -
327A GLN* 1.3 77.4 - - - +
329A LYS* 1.3 57.0 + - - +
331A LEU* 3.1 10.4 + - + +
332A ASP* 2.9 26.7 + - - +
354A THR* 3.9 31.4 - - + -
357A PRO* 3.8 26.7 - - + -
358A TYR* 3.9 16.6 - - + -
361A PHE* 3.9 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ASP* 4.0 17.9 + - - +
243A LEU* 3.2 49.8 + - + -
244A MSE 5.0 3.8 - - - +
290A LEU* 3.9 23.6 - - + -
294A GLU* 4.0 21.2 + - - +
325A ILE* 3.0 23.3 + - - +
326A TYR* 3.7 13.8 - - + +
328A LEU* 1.3 72.9 - - - +
330A VAL* 1.3 60.7 + - - +
332A ASP* 3.3 8.0 + - - +
333A CYS* 2.9 35.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A VAL* 3.6 22.4 - - + -
290A LEU* 3.9 18.2 - - + -
293A ILE* 4.4 3.6 - - + -
309A CYS* 3.6 27.1 - - + +
312A ILE* 3.9 20.6 - - + -
313A ILE* 3.8 25.6 - - + -
326A TYR 3.1 18.2 + - - +
327A GLN* 3.2 10.1 + - - +
329A LYS* 1.3 75.4 - - - +
331A LEU* 1.3 58.8 + - - +
333A CYS* 3.3 1.2 + - - -
334A ALA* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ILE* 3.8 27.1 - - + -
322A ASP* 3.3 38.4 - - + +
327A GLN* 3.0 24.8 + - + +
328A LEU* 3.1 13.0 + - + +
330A VAL* 1.3 78.1 - - - +
332A ASP* 1.3 57.5 + - - +
334A ALA* 3.4 1.7 + - - +
335A MSE 2.9 30.8 + - - +
350A TYR* 3.7 25.5 - - + +
353A ARG* 4.2 26.7 - - + +
354A THR* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 6.2 0.9 - - + -
297A LYS* 5.0 8.1 + - - -
328A LEU 2.9 12.9 + - - +
329A LYS* 3.6 11.2 - - - +
331A LEU* 1.3 77.1 - - - +
333A CYS* 1.3 64.3 + - - +
335A MSE 3.3 14.0 + - - +
336A ASP* 3.1 31.8 + - - +
354A THR* 4.3 6.4 - - + +
358A TYR* 3.7 20.1 + - + +
372A GLN* 3.1 24.8 + - - +
375A LYS* 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU* 4.8 6.1 - - - -
293A ILE* 3.9 20.2 - - + -
294A GLU* 4.9 8.5 - - - -
297A LYS* 3.6 29.2 - - + +
302A TRP* 4.9 1.0 - - - -
305A VAL* 3.8 10.3 - - + +
309A CYS* 3.9 14.1 - - - -
329A LYS* 2.9 24.1 + - - +
330A VAL* 3.8 4.3 - - - +
332A ASP* 1.3 78.1 - - - +
334A ALA* 1.3 58.1 + - - +
336A ASP* 3.4 5.9 + - - +
337A ALA* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A VAL* 5.2 0.2 - - - -
306A LEU* 4.5 4.5 - - + -
309A CYS* 3.7 15.2 - - + -
313A ILE* 3.6 17.9 - - + -
330A VAL 2.9 18.8 + - - +
331A LEU 3.6 2.7 - - - +
333A CYS* 1.3 75.3 - - - +
335A MSE 1.3 59.2 - - - +
337A ALA* 3.4 6.0 + - - +
338A CYS* 2.9 34.3 + - - -
350A TYR* 3.5 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU 2.9 17.6 + - - +
332A ASP* 3.3 15.7 + - - +
334A ALA* 1.3 76.7 - - - +
336A ASP* 1.3 80.0 + - - +
338A CYS* 3.3 3.1 + - - +
339A ILE* 2.9 39.9 + - + +
347A ALA* 3.5 21.7 - - + +
350A TYR* 3.9 14.9 - - + -
351A GLY* 3.6 20.6 - - - +
354A THR* 5.7 0.2 - - + -
372A GLN* 3.5 33.4 - - - +
375A LYS* 3.8 19.7 - - + +
376A VAL* 4.7 8.3 - - - -
379A LEU* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU* 5.0 2.0 - - - +
191A GLN* 5.3 1.1 - - - +
297A LYS* 4.0 17.7 + - - -
302A TRP* 4.1 17.3 - - + -
332A ASP* 3.1 28.8 + - - +
333A CYS 3.8 3.8 - - - +
335A MSE 1.3 82.3 - - - +
337A ALA* 1.3 65.5 + - - +
339A ILE* 3.3 8.1 + - - +
340A ASN* 2.9 35.4 + - - +
375A LYS* 2.9 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TRP* 3.5 43.6 - - + +
305A VAL* 4.0 2.7 - - + -
306A LEU* 3.9 19.7 - - + +
333A CYS 2.9 17.8 + - - +
334A ALA 3.8 3.6 - - - +
336A ASP* 1.3 76.1 - - - +
338A CYS* 1.3 56.9 + - - +
340A ASN* 3.3 2.9 + - - +
341A LEU* 2.9 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LEU* 3.6 27.1 - - - -
334A ALA 2.9 20.7 + - - +
337A ALA* 1.3 73.2 - - - +
339A ILE* 1.3 62.8 + - - +
341A LEU* 3.3 2.4 + - - -
342A GLY 3.0 4.0 + - - -
343A LEU* 2.8 52.4 + - - +
346A GLU* 3.7 31.2 - - - -
347A ALA* 3.4 13.5 - - + -
350A TYR* 3.9 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU* 6.6 0.2 - - + -
335A MSE 2.9 38.2 + - + +
336A ASP* 3.3 18.8 + - - +
338A CYS* 1.3 72.0 - - - +
340A ASN* 1.3 69.2 + - - +
342A GLY* 3.2 12.6 + - - -
344A LEU* 4.3 11.8 - - + +
347A ALA* 4.0 13.7 - - + -
375A LYS* 4.2 26.9 - - + -
379A LEU* 4.2 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TRP* 5.1 6.8 - - - -
302A TRP* 3.4 54.6 + - + +
336A ASP* 2.9 32.1 + - - +
337A ALA 3.9 0.2 - - - +
339A ILE* 1.3 82.0 - - - +
341A LEU* 1.3 62.0 + - - +
342A GLY 3.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TRP* 3.8 38.1 - - + +
303A GLU* 3.8 33.9 - - + +
306A LEU* 3.9 24.2 - - + -
337A ALA 2.9 20.7 + - - +
338A CYS 4.1 2.7 - - - +
339A ILE 3.3 0.4 - - - -
340A ASN* 1.3 78.5 - - - +
342A GLY* 1.3 61.0 + - - +
343A LEU* 3.3 19.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A CYS 3.0 4.1 + - - -
339A ILE 3.2 10.8 + - - -
340A ASN 3.3 1.0 + - - -
341A LEU* 1.3 78.2 - - - +
343A LEU* 1.3 61.9 + - - +
344A LEU* 3.2 23.9 + - - +
345A GLU* 4.8 1.7 - - - +
----------------------------------------------------------
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