Contacts of the helix formed by residues 350 - 366 (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 THR 350 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348F ASN 5.6 0.9 - - - +
349F LEU* 1.3 73.8 - - - +
351F LYS* 1.3 65.1 + - - +
352F LYS* 3.3 25.0 - - - +
353F GLN* 2.9 43.4 + - - +
354F ARG* 2.9 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 351 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349F LEU 3.7 1.0 + - - -
350F THR* 1.3 72.9 - - - +
352F LYS* 1.3 74.5 + - + +
354F ARG* 3.3 14.8 + - - +
355F GLN* 3.1 48.5 + - + +
311G ASN* 5.6 7.0 + - - +
449G MET* 5.9 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 352 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350F THR* 3.1 22.6 - - - +
351F LYS* 1.3 99.6 - - + +
353F GLN* 1.3 61.9 + - + +
355F GLN* 3.3 15.4 + - - +
356F SER* 3.0 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232F PHE* 4.3 20.1 - - - -
285F LEU* 3.7 27.8 - - + +
348F ASN 4.7 0.9 - - - +
349F LEU* 3.4 19.7 - - + +
350F THR* 2.9 51.4 + - - +
352F LYS* 1.3 74.5 - - + +
354F ARG* 1.3 61.9 + - - +
356F SER* 3.2 2.0 + - - -
357F LEU* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 354 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344F ASP* 3.7 18.3 + - - -
346F PHE* 2.7 45.8 + - + +
347F GLN* 3.5 10.6 + - - +
349F LEU* 3.5 30.0 - - + +
350F THR 2.9 14.5 + - - +
351F LYS* 3.6 14.8 - - - +
352F LYS 3.3 0.2 - - - -
353F GLN* 1.3 75.4 - - - +
355F GLN* 1.3 62.7 + - + +
357F LEU* 3.9 6.8 - - - +
358F ARG* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 355 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351F LYS* 3.1 45.9 + - + +
352F LYS* 3.5 14.8 + - - +
354F ARG* 1.3 77.3 - - + +
356F SER* 1.3 61.3 + - - +
358F ARG* 3.4 6.3 + - - +
359F LYS* 3.0 22.5 + - - +
311G ASN* 5.2 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 356 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285F LEU* 3.9 16.7 - - - +
352F LYS* 3.0 14.8 + - - +
353F GLN* 3.7 6.0 - - - -
355F GLN* 1.3 72.7 - - - +
357F LEU* 1.3 66.6 + - - +
359F LYS* 3.1 6.5 + - - +
360F MET* 2.9 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 357 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285F LEU* 3.9 13.2 - - + +
288F LEU* 3.6 36.8 - - + -
289F ALA* 3.7 18.6 - - + +
292F PHE* 4.6 2.0 - - + -
335F PHE* 5.3 2.9 - - + -
346F PHE* 3.4 40.4 - - + -
349F LEU* 4.9 1.8 - - + -
353F GLN 2.9 17.3 + - - +
354F ARG* 3.9 6.1 - - - +
356F SER* 1.3 76.7 - - - +
358F ARG* 1.3 60.1 + - + +
360F MET* 3.8 8.6 - - - +
361F VAL* 2.8 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 358 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335F PHE* 3.2 60.8 - - + +
354F ARG 3.0 19.3 + - - +
355F GLN* 3.7 5.8 - - - +
357F LEU* 1.3 76.3 - - - +
359F LYS* 1.3 64.1 + - - +
361F VAL* 3.8 0.9 - - - +
362F ILE* 3.0 39.4 + - + +
310G ILE* 5.8 0.2 - - - +
313G ASN* 6.0 2.0 - - - -
317G ALA* 3.0 27.9 + - - +
318G LEU* 3.5 18.6 + - - +
321G ASN* 3.7 8.9 - - - +
322G ASP* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 359 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355F GLN 3.0 14.2 + - - +
356F SER* 3.1 10.3 + - - +
358F ARG* 1.3 78.5 - - - +
360F MET* 1.3 57.9 + - + +
362F ILE* 3.6 7.2 - - + +
363F ASP* 2.9 51.0 + - - +
400F TYR* 3.7 30.8 - - + +
322G ASP* 5.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 360 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285F LEU* 4.0 31.2 - - + +
286F GLU* 3.8 31.9 - - + +
289F ALA* 3.9 11.7 - - + -
356F SER* 2.9 37.2 + - - +
357F LEU* 3.8 9.2 - - - +
359F LYS* 1.3 75.7 - - + +
361F VAL* 1.3 57.4 + - - +
363F ASP* 3.2 1.6 + - - +
364F ILE* 2.9 38.4 + - + +
400F TYR* 3.7 29.8 - - + -
404F ILE* 3.9 17.5 - - + -
407F LEU* 4.9 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 361 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289F ALA* 3.7 28.7 - - + +
292F PHE* 3.8 21.3 - - + -
293F ALA* 4.2 13.7 - - + -
296F ILE* 4.1 14.1 - - + -
331F LEU* 3.8 11.2 - - + -
335F PHE* 3.5 25.4 - - + -
357F LEU* 2.8 28.6 + - + +
360F MET* 1.3 76.2 - - - +
362F ILE* 1.3 62.5 + - - +
364F ILE* 3.3 0.8 + - - -
365F VAL* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 362 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331F LEU* 3.7 9.4 - - + -
335F PHE* 3.8 15.7 - - + -
358F ARG* 3.0 46.1 + - + +
359F LYS* 3.6 5.6 - - + +
361F VAL* 1.3 75.8 - - - +
363F ASP* 1.3 69.0 + - - +
366F LEU* 3.0 45.2 + - + +
321G ASN* 3.4 49.1 - - + +
322G ASP* 3.9 6.1 - - + +
323G SER* 4.5 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 363 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359F LYS* 2.9 37.0 + - - +
360F MET 3.6 3.6 - - - +
362F ILE* 1.3 82.8 - - - +
364F ILE* 1.3 62.6 + - - +
366F LEU* 4.2 6.0 - - - +
367F ALA* 3.5 12.6 + - - +
400F TYR* 2.9 24.3 + - - -
404F ILE* 4.1 12.8 - - + +
408F GLN* 3.0 26.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 364 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289F ALA 4.5 1.1 - - - -
290F ALA* 3.9 28.5 - - + +
293F ALA* 3.9 14.4 - - + -
360F MET* 2.9 28.4 + - + +
361F VAL 3.8 3.4 - - - +
363F ASP* 1.3 74.2 - - - +
365F VAL* 1.3 60.7 + - - +
367F ALA* 2.9 24.3 + - - +
368F THR* 3.5 6.2 + - - +
404F ILE* 4.1 11.9 - - + -
407F LEU* 4.0 29.8 - - + +
408F GLN* 3.9 14.8 - - + +
411F VAL* 3.5 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 365 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293F ALA* 3.7 32.5 - - + +
296F ILE* 4.4 3.8 - - + -
297F HIS* 4.1 27.1 - - + +
327F GLU* 3.8 17.1 - - + +
330F HIS* 4.5 3.6 - - + -
331F LEU* 3.5 36.1 - - + -
361F VAL* 3.0 18.0 + - + +
364F ILE* 1.3 75.1 - - + +
366F LEU* 1.3 57.3 + - - +
368F THR* 2.6 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324F SER* 4.3 7.6 + - - -
327F GLU* 4.2 7.2 - - + -
328F ASN* 3.8 42.0 - - - +
331F LEU* 3.7 15.5 - - + -
362F ILE* 3.0 37.7 + - + +
363F ASP* 4.2 6.7 - - - +
365F VAL* 1.3 76.9 - - - +
367F ALA* 1.3 59.0 + - - +
368F THR 3.2 0.2 - - - -
369F ASP* 3.5 11.5 - - - +
372F LYS* 3.4 26.7 - - - +
321G ASN* 5.3 0.9 - - + -
323G SER* 4.5 13.0 - - - +
----------------------------------------------------------
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