Contacts of the helix formed by residues 324 - 337 (chain F) in PDB entry 1MKD
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 SER 324 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ASN* 4.2 3.7 - - - +
322F ASP 3.8 2.8 + - - -
323F SER* 1.3 73.1 - - - +
325F VAL* 1.3 66.2 + - - +
326F LEU 3.3 2.4 + - - -
327F GLU* 3.3 23.2 + - - -
328F ASN* 2.8 30.6 + - - -
366F LEU* 4.3 8.2 + - - +
369F ASP* 2.7 27.4 + - - +
372F LYS* 3.7 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 325 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ASN* 3.4 13.7 + - - +
309F LEU* 4.1 13.9 - - + -
310F ILE* 4.3 9.6 - - + -
316F LEU* 3.5 42.2 - - + +
317F ALA* 3.7 17.0 - - + +
320F TYR* 3.7 14.3 - - + -
322F ASP* 3.6 33.9 - - - +
323F SER 3.1 3.8 - - - +
324F SER* 1.3 76.7 - - - +
326F LEU* 1.3 64.8 + - - +
329F HIS* 3.2 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300F ASP 5.3 0.7 - - - +
301F HIS* 3.6 17.0 - - - +
302F PRO* 3.4 30.3 - - + -
304F VAL 3.4 23.8 - - - +
305F SER* 4.5 1.1 - - - -
306F ASN* 2.7 36.0 + - - +
309F LEU* 3.6 17.0 - - + -
316F LEU* 4.7 7.9 - - + -
325F VAL* 1.3 69.7 - - - +
327F GLU* 1.3 64.5 + - - +
329F HIS* 2.9 9.0 + - + +
330F HIS* 2.8 56.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 327 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ASN* 2.9 28.3 + - - -
324F SER* 3.3 20.5 + - - +
326F LEU* 1.3 78.7 - - - +
328F ASN* 1.3 62.5 + - - +
330F HIS* 3.4 11.0 + - - +
331F LEU* 3.2 27.2 + - - +
365F VAL* 3.8 13.1 - - - +
366F LEU* 4.2 9.6 - - + -
368F THR* 3.6 20.9 - - - +
369F ASP* 3.6 32.6 - - + +
370F MET 4.7 0.9 + - - -
2012F MG 3.7 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 328 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320F TYR* 3.5 32.9 + - + -
323F SER* 2.9 27.5 + - - -
324F SER* 2.8 21.9 + - - +
325F VAL 3.7 1.3 - - - +
327F GLU* 1.3 76.9 - - - +
329F HIS* 1.3 62.4 + - - +
331F LEU 3.3 1.4 + - - -
332F ALA* 3.0 20.8 + - - +
366F LEU* 3.8 14.7 - - - +
320G TYR* 4.4 5.6 - - - +
321G ASN* 2.9 35.9 + - - +
323G SER* 5.7 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 329 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F VAL 4.6 1.8 - - - -
300F ASP* 2.7 42.2 + - + -
316F LEU* 3.7 36.9 - - + +
320F TYR* 4.0 16.6 + - + -
325F VAL 3.2 10.6 + - - +
326F LEU* 2.9 15.1 + - + +
328F ASN* 1.3 77.4 - - - +
330F HIS* 1.3 69.2 + - - +
332F ALA* 3.2 4.1 + - - +
333F VAL* 3.0 43.9 + - + +
319G MET* 5.7 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 330 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296F ILE* 3.6 19.3 - - - +
297F HIS 3.0 23.1 - - - +
298F ASP* 3.2 32.5 + - - -
299F VAL* 2.7 34.7 + - - +
300F ASP 4.7 0.9 - - - -
301F HIS* 3.9 21.7 - + + -
326F LEU* 2.8 50.6 + - + +
327F GLU* 3.5 12.3 - - - +
328F ASN 3.3 0.2 - - - -
329F HIS* 1.3 74.4 - + - +
331F LEU* 1.3 65.0 + - - +
334F GLY* 2.9 21.5 + - - -
365F VAL* 4.5 2.9 - - + -
2012F MG 4.2 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296F ILE* 4.2 6.1 - - + -
327F GLU 3.2 10.2 + - - +
328F ASN 3.6 4.3 - - - +
329F HIS 3.2 0.2 - - - -
330F HIS* 1.3 79.7 - - - +
332F ALA* 1.3 63.4 + - - +
334F GLY* 3.3 0.5 + - - -
335F PHE* 3.0 51.4 + - + -
361F VAL* 3.7 14.4 - - + +
362F ILE* 3.7 15.5 - - + +
365F VAL* 3.5 36.1 - - + -
366F LEU* 3.7 32.3 - - + -
321G ASN* 3.1 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320F TYR* 3.7 17.5 - - - +
328F ASN 3.0 13.6 + - - +
329F HIS* 3.5 9.6 - - - +
331F LEU* 1.3 74.8 - - - +
333F VAL* 1.3 60.6 + - + +
336F LYS* 2.9 32.3 + - - +
318G LEU* 3.6 22.1 - - + +
319G MET* 3.9 21.3 - - + +
321G ASN* 3.7 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 333 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249F HIS* 4.5 13.2 - - + -
299F VAL* 4.0 25.4 - - + -
300F ASP* 4.3 10.1 - - + +
329F HIS* 3.0 47.7 + - + +
330F HIS 3.8 2.7 - - - +
332F ALA* 1.3 76.0 - - + +
334F GLY* 1.3 63.7 + - - +
336F LYS* 3.3 6.2 + - + +
337F LEU* 3.0 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 334 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242F TYR* 2.7 32.4 + - - -
246F LEU* 4.7 4.3 - - - -
292F PHE* 4.3 1.2 - - - -
296F ILE* 4.1 21.8 - - - -
299F VAL* 4.1 3.8 - - - +
330F HIS 2.9 16.1 + - - -
331F LEU 3.8 1.1 - - - -
333F VAL* 1.3 79.3 - - - +
335F PHE* 1.3 62.6 + - - +
337F LEU* 3.8 4.3 + - - +
338F LEU* 3.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 335 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F PHE* 4.2 15.7 - + - -
296F ILE* 4.9 1.1 - - + -
331F LEU* 3.0 50.5 + - + +
332F ALA* 4.0 2.7 - - - +
334F GLY* 1.3 74.4 - - - +
336F LYS* 1.3 67.3 + - - +
338F LEU* 3.1 38.6 + - + +
339F GLN* 4.0 5.9 + - - +
357F LEU* 5.3 5.2 - - + -
358F ARG* 3.2 55.6 - - + +
361F VAL* 3.5 27.1 - - + -
362F ILE* 3.8 9.0 - - + -
318G LEU* 4.2 10.8 - - + -
321G ASN* 4.3 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 336 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332F ALA 2.9 20.2 + - - +
333F VAL* 3.6 7.9 - - + +
335F PHE* 1.3 76.5 - - - +
337F LEU* 1.3 66.3 + - + +
339F GLN* 3.0 48.2 + - - +
340F GLU* 4.2 3.3 + - - +
315G GLU* 3.1 26.7 + - - +
318G LEU* 4.1 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242F TYR* 3.7 15.7 - - + -
245F THR* 3.8 12.3 - - + +
246F LEU* 3.7 44.0 - - + +
249F HIS* 3.6 42.4 - - + +
333F VAL* 3.0 27.7 + - + +
334F GLY 4.0 0.9 - - - +
335F PHE 3.2 0.4 - - - -
336F LYS* 1.3 80.0 - - + +
338F LEU* 1.3 62.0 + - - +
339F GLN 3.3 0.5 + - - -
340F GLU* 3.4 23.0 + - - +
343F CYS* 3.3 19.4 - - - +
----------------------------------------------------------
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