Contacts of the helix formed by residues 275 - 284 (chain F) 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 TYR 275 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F SER 5.0 5.0 + - - -
238F GLN* 5.5 3.3 - - - -
241F TYR* 3.4 59.8 - + + +
271F GLN* 3.7 15.8 + - + -
272F GLU* 3.3 55.6 + - + +
273F CYS 3.8 0.6 - - - -
274F TYR* 1.3 115.3 + + - +
276F GLN* 1.3 59.3 + - - +
277F ASP 3.5 1.8 - - - -
278F ASP* 3.4 3.4 + - - -
279F LEU* 2.8 40.8 + - + +
649F ARG* 4.1 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 276 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F GLU 5.1 1.6 + - - -
273F CYS* 4.3 24.9 + - - +
274F TYR* 3.4 7.8 + - - -
275F TYR* 1.3 79.6 - - - +
277F ASP* 1.3 58.3 + - - +
279F LEU* 3.2 19.0 + - - +
280F ARG* 2.9 57.1 + - - +
649F ARG* 4.2 0.4 - - - +
6H LYS* 6.3 1.0 - - - +
7H LEU* 4.5 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 277 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276F GLN* 1.3 75.9 - - - +
278F ASP* 1.3 75.9 + - - -
280F ARG* 3.2 18.2 + - - +
281F VAL* 3.0 35.6 + - + +
647F ALA 4.9 6.4 - - - +
649F ARG* 2.4 40.9 + - - -
671F PRO* 4.3 16.9 - - - +
52H GLN* 4.3 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 278 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F TYR* 3.3 26.1 + - - +
275F TYR 3.4 4.7 + - - +
276F GLN 3.4 0.4 - - - -
277F ASP* 1.3 88.4 + - - +
279F LEU* 1.3 60.1 + - - +
281F VAL* 4.0 9.3 - - - +
282F LEU* 2.8 33.2 + - - +
296F THR* 4.9 12.2 - - - +
300F PHE* 5.0 17.2 - - - -
301F ARG* 5.6 9.3 + - - +
649F ARG* 4.1 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 279 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F TYR* 5.0 11.0 - - + -
244F PHE* 5.6 2.7 - - + -
264F PHE* 4.0 27.4 - - + -
268F HIS* 4.5 22.4 - - + +
271F GLN* 6.4 2.9 - - + -
272F GLU 5.7 2.7 - - - +
275F TYR* 2.8 38.6 + - + +
276F GLN* 3.4 22.0 - - - +
278F ASP* 1.3 76.8 - - - +
280F ARG* 1.3 58.4 + - + +
282F LEU* 3.8 9.3 - - + +
283F SER* 2.9 30.5 + - - -
7H LEU* 5.6 9.6 - - + +
9H LEU* 5.4 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 280 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276F GLN* 2.9 61.2 + - - +
277F ASP* 3.2 16.9 + - - +
279F LEU* 1.3 74.2 - - + +
281F VAL* 1.3 64.5 + - - +
283F SER* 2.6 23.2 + - - -
284F SER* 3.0 12.8 + - - -
9H LEU* 5.4 7.2 - - + -
52H GLN* 3.7 16.4 - - - +
25L ASP 2.9 26.3 + - - +
26L MET* 3.0 40.5 + - - +
27L GLY* 3.5 16.0 - - - +
28L ILE* 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 281 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F ASP* 3.0 22.4 + - + +
278F ASP* 4.0 11.9 - - - +
280F ARG* 1.3 74.5 - - - +
282F LEU* 1.3 58.9 + - - +
284F SER* 2.7 27.8 + - - +
285F LEU* 3.2 21.0 - - + +
294F ASN* 3.6 33.4 - - + +
296F THR* 6.2 4.0 - - + -
297F MET* 5.4 4.5 - - + -
301F ARG* 5.9 5.4 - - - +
52H GLN* 3.4 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 282 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F TYR* 5.5 2.9 - - + +
244F PHE* 4.0 21.5 - - + -
245F VAL* 4.6 18.6 - - + +
248F TYR* 3.2 59.5 + - + -
249F LEU* 5.5 1.1 - - - +
264F PHE* 3.7 24.1 - - + -
278F ASP 2.8 20.0 + - - +
279F LEU* 3.8 11.4 - - + +
281F VAL* 1.3 76.7 - - - +
283F SER* 1.3 60.8 + - - +
284F SER 3.5 0.2 + - - -
285F LEU* 3.6 13.9 - - + +
301F ARG* 3.7 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 283 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F TYR* 5.0 1.9 + - - -
264F PHE* 3.6 27.3 - - - -
279F LEU 2.9 16.5 + - - -
280F ARG* 2.6 24.9 + - - -
282F LEU* 1.3 75.9 - - - +
284F SER* 1.3 57.2 + - - +
285F LEU 3.4 5.1 + - - +
9H LEU* 3.8 25.4 + - - +
11H ASN* 3.3 23.4 + - - +
45H TYR* 4.2 2.8 + - - -
48H LYS* 6.0 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 284 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280F ARG 3.0 13.2 + - - -
281F VAL* 2.7 27.5 + - - +
283F SER* 1.3 77.2 - - - +
285F LEU* 1.3 58.2 + - - +
290F HIS* 3.3 22.9 + - - -
294F ASN* 5.3 1.0 + - - -
11H ASN* 5.0 0.4 - - - -
45H TYR* 3.6 31.0 - - - -
48H LYS* 5.4 15.0 - - - -
49H GLU* 4.6 11.4 + - - +
52H GLN* 5.0 2.9 + - - -
----------------------------------------------------------
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