Contacts of the helix formed by residues 350 - 367 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348H ASN 4.1 1.7 + - - +
349H LEU* 1.3 76.2 - - - +
351H LYS* 1.3 65.3 + - - +
352H LYS* 3.2 26.1 - - - +
353H GLN* 2.9 43.1 + - - +
354H ARG* 2.9 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 351 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349H LEU 3.7 1.0 + - - -
350H THR* 1.3 72.1 - - - +
352H LYS* 1.3 75.5 + - + +
354H ARG* 3.3 15.8 + - + +
355H GLN* 3.1 49.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 352 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350H THR* 3.2 22.9 - - - +
351H LYS* 1.3 98.7 - - + +
353H GLN* 1.3 61.2 + - + +
355H GLN* 3.2 16.3 + - - +
356H SER* 3.0 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232H PHE* 4.3 19.7 - - - -
285H LEU* 3.8 27.7 - - + +
348H ASN 4.7 0.9 - - - +
349H LEU* 3.4 19.8 - - + +
350H THR* 2.9 52.9 + - - +
352H LYS* 1.3 73.4 - - + +
354H ARG* 1.3 62.3 + - - +
356H SER* 3.3 1.6 + - - -
357H LEU* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 354 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344H ASP* 3.6 17.2 + - - -
346H PHE* 2.6 45.6 + - + +
347H GLN* 3.5 10.3 + - - +
349H LEU* 3.5 28.9 - - + +
350H THR 2.9 15.4 + - - +
351H LYS* 3.6 15.5 - - - +
352H LYS 3.3 0.2 - - - -
353H GLN* 1.3 76.0 - - - +
355H GLN* 1.3 63.5 + - + +
357H LEU* 3.9 6.4 - - - +
358H ARG* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 355 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351H LYS* 3.1 45.6 + - + +
352H LYS* 3.5 14.8 - - - +
353H GLN 3.2 0.2 - - - -
354H ARG* 1.3 76.5 - - + +
356H SER* 1.3 63.1 + - - +
358H ARG* 3.4 6.7 + - - +
359H LYS* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 356 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285H LEU* 3.9 16.6 - - - +
352H LYS 3.0 14.1 + - - -
353H GLN* 3.7 6.0 - - - -
355H GLN* 1.3 72.5 - - - +
357H LEU* 1.3 68.0 + - - +
359H LYS* 3.1 6.7 + - - +
360H MET* 2.9 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 357 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285H LEU* 3.9 13.2 - - + +
288H LEU* 3.6 37.2 - - + -
289H ALA* 3.7 18.4 - - + +
292H PHE* 4.6 1.3 - - + -
335H PHE* 5.2 3.6 - - + -
346H PHE* 3.4 41.5 - - + -
349H LEU* 4.7 1.8 - - + -
353H GLN 2.9 18.1 + - - +
354H ARG* 3.9 6.5 - - - +
356H SER* 1.3 76.3 - - - +
358H ARG* 1.3 60.1 + - - +
360H MET* 3.8 9.2 - - - +
361H VAL* 2.8 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 358 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E ALA 3.2 25.3 + - - -
318E LEU* 3.7 17.2 + - - +
321E ASN* 3.7 11.9 + - - +
322E ASP* 3.0 29.8 + - - +
335H PHE* 3.2 61.6 - - + +
354H ARG 3.1 18.5 + - - +
355H GLN* 3.7 7.2 - - - +
357H LEU* 1.3 75.9 - - - +
359H LYS* 1.3 63.7 + - - +
361H VAL* 3.8 0.5 - - - +
362H ILE* 3.0 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 359 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355H GLN 3.1 14.5 + - - +
356H SER* 3.1 9.8 + - - +
358H ARG* 1.3 79.0 - - - +
360H MET* 1.3 57.9 + - + +
362H ILE* 3.3 7.1 + - + +
363H ASP* 2.9 49.7 + - - +
400H TYR* 3.7 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 360 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285H LEU* 4.0 24.9 - - + +
286H GLU* 3.9 30.7 - - + +
289H ALA* 3.9 17.7 - - + -
356H SER* 2.9 35.6 + - - +
357H LEU* 3.9 10.3 - - - +
359H LYS* 1.3 75.7 - - + +
361H VAL* 1.3 57.7 + - - +
363H ASP* 3.2 1.6 + - - +
364H ILE* 2.8 39.5 + - + +
400H TYR* 3.8 30.3 - - + -
404H ILE* 3.9 17.3 - - + -
407H LEU* 5.0 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 361 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289H ALA* 3.7 28.9 - - + +
292H PHE* 3.8 27.1 - - + -
293H ALA* 4.2 13.0 - - + -
296H ILE* 4.0 8.5 - - + -
331H LEU* 3.8 11.0 - - + -
335H PHE* 3.5 25.4 - - + -
357H LEU* 2.8 29.3 + - + +
360H MET* 1.3 76.7 - - - +
362H ILE* 1.3 62.8 + - - +
364H ILE* 3.3 0.5 + - - +
365H VAL* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 362 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321E ASN* 3.6 49.1 - - + +
322E ASP* 4.3 3.8 - - + +
323E SER* 4.9 2.2 - - - +
331H LEU* 3.7 9.8 - - + +
335H PHE* 3.7 15.9 - - + -
358H ARG* 3.0 51.2 + - + +
359H LYS* 3.7 6.5 - - - +
361H VAL* 1.3 76.1 - - - +
363H ASP* 1.3 68.8 + - - +
366H LEU* 3.0 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 363 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359H LYS* 2.9 36.6 + - - +
360H MET 3.6 4.0 - - - +
362H ILE* 1.3 82.9 - - - +
364H ILE* 1.3 61.4 + - - +
366H LEU* 4.2 6.0 - - - +
367H ALA* 3.5 13.0 + - - +
400H TYR* 2.9 23.9 + - - -
404H ILE* 4.1 13.6 - - + +
408H GLN* 3.1 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 364 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289H ALA 4.5 1.6 - - - -
290H ALA* 3.9 27.8 - - - +
293H ALA* 3.9 14.6 - - + -
360H MET* 2.8 30.4 + - + +
361H VAL 3.8 2.9 - - - +
363H ASP* 1.3 71.7 - - - +
365H VAL* 1.3 62.8 + - - +
367H ALA* 2.9 23.9 + - - +
368H THR* 3.5 6.8 + - - +
404H ILE* 4.2 11.9 - - + -
407H LEU* 4.0 29.2 - - + +
408H GLN* 3.9 14.6 - - + +
411H VAL* 3.5 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 365 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293H ALA* 3.7 33.0 - - + +
296H ILE* 4.4 3.1 - - + -
297H HIS* 4.1 24.9 - - + +
327H GLU* 3.8 16.9 - - + +
330H HIS* 4.5 3.8 - - + -
331H LEU* 3.5 37.5 - - + +
361H VAL* 3.0 18.0 + - + +
364H ILE* 1.3 75.5 - - + +
366H LEU* 1.3 62.4 + - - +
368H THR* 2.6 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321E ASN* 5.2 1.6 - - + +
323E SER* 5.0 9.0 - - - +
324H SER* 4.3 7.9 - - - +
327H GLU* 4.2 7.6 - - + -
328H ASN* 3.9 41.5 - - - +
331H LEU* 3.7 15.5 - - + -
362H ILE* 3.0 37.8 + - + +
363H ASP* 4.3 6.3 - - - +
365H VAL* 1.3 77.3 - - - +
367H ALA* 1.3 59.2 + - - +
368H THR 3.2 0.9 - - - -
369H ASP* 3.4 12.2 - - - +
372H LYS* 3.4 26.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 367 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363H ASP 3.5 13.0 + - - +
364H ILE 2.9 13.5 + - - +
366H LEU* 1.3 77.9 - - - +
368H THR* 1.3 57.6 + - - +
369H ASP 3.1 12.9 + - - +
372H LYS* 4.6 9.5 - - - +
376H LEU* 3.6 31.6 - - + +
408H GLN* 3.7 26.5 - - + +
412H HIS* 3.9 7.9 + - - -
----------------------------------------------------------
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