Contacts of the helix formed by residues 275 - 291 (chain H) in PDB entry 6MZL
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 275 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H ASN* 3.7 10.4 + - - +
273H GLN* 4.7 7.4 - - + +
274H ASN* 1.3 75.1 - - - +
276H LEU* 1.3 65.5 + - - +
277H ALA* 3.4 18.9 + - - +
278H LEU* 3.0 48.4 + - + +
279H LEU* 3.2 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274H ASN 3.7 8.5 + - - +
275H ASN* 1.3 74.6 - - - +
277H ALA* 1.3 76.6 + - + +
279H LEU* 3.1 15.4 + - - +
280H ILE* 2.9 30.2 + - + +
318H CYS* 5.2 3.8 - - + -
323H VAL* 3.9 28.5 - - + -
326H HIS* 4.5 30.1 - - + +
330H ARG* 3.4 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H ASN* 3.1 13.1 + - - +
276H LEU* 1.3 89.0 - - + +
278H LEU* 1.3 59.4 + - + +
280H ILE* 3.2 11.8 - - - +
281H TYR* 2.9 50.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 278 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231H CYS 5.0 0.2 - - - +
232H VAL* 4.0 31.6 - - + +
270H ASN* 3.3 36.8 - - - +
275H ASN* 3.0 37.7 + - + +
277H ALA* 1.3 76.7 - - + +
279H LEU* 1.3 58.7 - - - +
281H TYR* 3.3 23.3 + - + +
282H LEU* 2.9 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 279 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267H VAL* 5.0 4.9 - - + +
270H ASN* 3.7 35.4 - - + +
271H VAL* 5.0 3.8 - - + +
274H ASN* 5.0 3.1 - - - +
275H ASN 3.2 18.6 - - - +
276H LEU* 3.1 18.2 + - - +
278H LEU* 1.3 78.9 - - - +
280H ILE* 1.3 57.1 + - - +
282H LEU* 3.2 12.9 + - + +
283H MET* 2.9 34.9 + - + +
311H CYS* 4.6 22.9 - - + -
318H CYS* 5.7 1.3 - - - -
330H ARG* 4.3 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 280 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H LEU* 2.9 15.0 + - + +
277H ALA* 3.2 19.5 - - - +
279H LEU* 1.3 76.1 - - - +
281H TYR* 1.3 67.0 + - + +
283H MET* 3.8 8.7 - - + -
284H ARG* 2.9 61.1 + - + +
329H LEU* 5.1 24.5 - - + +
332H PHE* 5.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 281 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231H CYS* 3.5 15.3 - - - +
232H VAL 3.8 9.0 - - - -
233H GLY 4.7 0.2 - - - -
234H SER* 3.4 25.4 - - - -
236H GLU* 4.4 9.5 + - - -
239H ARG* 3.2 59.9 + - + +
243H LEU* 5.1 1.7 - - - +
277H ALA* 2.9 34.7 + - + +
278H LEU* 3.3 25.1 - - + +
279H LEU 3.2 0.2 - - - -
280H ILE* 1.3 86.2 - - + +
282H LEU* 1.3 58.0 + - + +
284H ARG* 3.2 15.8 + - - +
285H MET* 2.9 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 282 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231H CYS* 4.6 4.9 - - - -
262H PHE* 4.3 17.7 - - + +
263H ILE* 4.3 16.8 - - + -
266H GLY* 4.1 2.2 - - - -
267H VAL* 3.9 29.8 - - + +
270H ASN* 3.8 23.1 - - - +
278H LEU* 2.9 21.6 + - + +
279H LEU* 3.7 9.0 - - + +
281H TYR* 1.3 75.3 - - + +
283H MET* 1.3 67.9 + - + +
285H MET* 3.2 28.1 + - - +
286H VAL* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 283 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263H ILE* 5.7 1.1 - - + -
267H VAL* 4.6 4.3 - - + -
279H LEU* 2.9 23.5 + - + +
280H ILE* 3.8 7.9 - - + +
281H TYR 3.2 0.2 - - - -
282H LEU* 1.3 87.5 - - + +
284H ARG* 1.3 61.6 + - - +
286H VAL* 3.2 15.0 + - + +
287H LYS* 2.9 26.7 + - - +
307H ALA 3.9 11.4 - - - +
308H VAL* 4.9 9.4 - - - -
311H CYS* 3.6 33.4 - - + -
330H ARG* 6.1 2.7 - - + -
332H PHE* 4.7 12.3 - - + -
333H ALA* 3.7 31.0 - - + -
336H LEU* 3.7 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 284 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H GLU* 4.0 18.4 + - - -
239H ARG* 4.7 11.8 - - - +
240H ALA* 6.3 0.8 - - - +
243H LEU* 3.7 31.4 - - + +
280H ILE* 2.9 48.6 + - + +
281H TYR* 3.7 14.3 - - - +
283H MET* 1.3 75.3 - - - +
285H MET* 1.3 56.7 + - - +
287H LYS* 3.2 10.2 + - + +
288H ALA* 2.9 29.6 + - - +
332H PHE* 4.8 13.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 285 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227H ILE* 5.9 0.7 - - + +
228H THR* 5.2 3.4 - - + -
231H CYS* 3.5 28.5 - - + -
243H LEU* 4.2 10.7 - - + +
246H ILE* 4.9 6.5 - - + +
259H PHE* 3.5 44.8 - - + -
262H PHE* 3.6 31.4 - - + -
263H ILE* 3.7 20.4 - - + -
281H TYR 2.9 12.3 + - - +
282H LEU* 3.2 19.5 - - - +
283H MET 3.2 0.2 - - - -
284H ARG* 1.3 76.7 - - - +
286H VAL* 1.3 57.0 + - + +
288H ALA* 3.2 5.3 + - - +
289H LEU* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 286 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263H ILE* 4.2 27.6 - - + -
282H LEU 2.9 19.0 + - - +
283H MET* 3.2 18.4 + - + +
285H MET* 1.3 73.2 - - - +
287H LYS* 1.3 60.6 + - - +
289H LEU* 3.2 11.9 + - + +
290H MET* 2.9 38.5 + - + +
304H LEU* 4.8 18.4 - - + -
307H ALA* 6.1 2.0 - - + -
308H VAL* 4.7 18.2 - - + -
336H LEU* 4.5 16.8 - - + -
340H ILE* 5.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 287 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H MET 2.9 14.5 + - - +
284H ARG* 3.2 14.6 + - + +
286H VAL* 1.3 77.4 - - - +
288H ALA* 1.3 60.6 + - - +
290H MET* 3.3 7.1 + - + +
291H ASP* 3.1 50.4 + - - +
332H PHE* 4.5 25.3 - - + -
335H ARG* 5.2 9.1 - - - +
336H LEU* 3.7 26.7 - - + +
339H GLN* 3.9 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 288 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243H LEU* 3.8 27.6 - - + +
246H ILE* 3.8 23.9 - - + +
247H ALA* 4.1 11.9 - - + +
284H ARG 2.9 13.4 + - - +
285H MET* 3.5 10.5 - - - +
286H VAL 3.2 0.2 - - - -
287H LYS* 1.3 75.4 - - - +
289H LEU* 1.3 65.7 + - - +
291H ASP* 3.1 17.6 + - - +
292H ASN* 3.7 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H ILE* 4.4 10.1 - - + -
252H LEU* 6.1 2.2 - - + -
256H LEU* 3.8 26.7 - - + -
259H PHE* 3.6 33.2 - - + -
260H SER* 5.9 0.2 - - - -
263H ILE* 3.7 19.7 - - + -
285H MET 2.9 15.9 + - - +
286H VAL* 3.4 16.4 - - + +
288H ALA* 1.3 75.7 - - - +
290H MET* 1.3 62.1 + - - +
291H ASP 3.4 0.3 + - - -
292H ASN 3.5 7.3 + - - +
295H LEU* 4.0 32.1 - - + +
297H LEU* 4.5 17.2 - - + +
304H LEU* 5.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 290 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286H VAL* 2.9 23.3 + - + +
287H LYS* 3.3 14.8 - - + +
288H ALA 3.1 0.2 - - - -
289H LEU* 1.3 78.3 - - - +
291H ASP* 1.3 63.8 + - - +
292H ASN 3.2 11.0 + - - +
297H LEU* 3.9 26.0 - - + -
304H LEU* 5.7 1.8 - - + -
336H LEU* 4.9 6.3 - - + +
339H GLN* 3.6 31.9 - - + +
340H ILE* 3.7 30.5 - - + -
343H HIS* 4.8 7.9 - - + +
344H PHE* 4.5 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 291 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247H ALA* 3.3 25.5 - - + +
287H LYS* 3.1 41.6 + - - +
288H ALA* 3.1 12.4 + - - +
290H MET* 1.3 84.6 - - - +
292H ASN* 1.3 58.6 + - - -
293H PRO* 3.3 11.3 - - - +
----------------------------------------------------------
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