Contacts of the helix formed by residues 272 - 285 (chain M) in PDB entry 6FF7
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 PHE 272 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270M GLY* 3.3 4.7 - - - +
271M HIS* 1.3 82.8 - - - +
273M GLU* 1.3 59.9 + - - +
274M LYS* 3.0 14.8 - - + +
275M ALA* 2.9 24.0 + - - +
276M ARG* 3.8 1.9 + - - +
305M SER* 5.6 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 273 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271M HIS 3.9 0.2 + - - -
272M PHE* 1.3 73.6 - - - +
274M LYS* 1.3 57.0 + - - +
275M ALA 3.2 0.2 - - - -
276M ARG* 2.9 15.4 + - + +
277M ASP* 2.9 26.9 + - - +
305M SER* 5.2 15.6 + - - +
331U TYR* 5.3 9.2 - - + -
355U ASN* 6.0 0.9 - - + -
356U VAL* 3.4 37.9 - - + +
357U ALA* 5.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 274 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272M PHE* 3.0 10.5 - - + +
273M GLU* 1.3 78.0 - - - +
275M ALA* 1.3 55.7 + - - +
277M ASP* 3.3 7.8 + - - +
278M VAL* 2.9 29.6 + - - +
327U THR* 4.9 18.6 - - - -
328U THR* 6.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 275 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266M TYR* 4.5 13.4 - - + +
269M SER* 4.2 17.3 - - - -
270M GLY 3.3 26.0 - - - +
271M HIS* 5.0 0.7 - - - -
272M PHE* 2.9 9.5 + - - +
274M LYS* 1.3 78.3 - - - +
276M ARG* 1.3 57.7 + - - +
278M VAL* 3.9 6.3 - - - +
279M TYR* 2.9 29.3 + - - +
298M SER* 5.7 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 276 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272M PHE 3.8 0.6 + - - -
273M GLU* 2.9 20.9 + - + +
275M ALA* 1.3 77.7 - - - +
277M ASP* 1.3 59.1 + - - +
279M TYR* 3.5 7.2 + - - +
280M GLU* 2.9 26.5 + - - +
305M SER* 6.5 0.7 - - - -
313M THR* 5.4 12.8 - - - -
355U ASN* 5.8 6.3 - - + -
357U ALA* 4.9 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 277 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273M GLU 2.9 12.2 + - - +
274M LYS* 3.8 10.1 - - - +
276M ARG* 1.3 75.4 - - - +
278M VAL* 1.3 59.4 + - - +
280M GLU* 3.0 8.5 + - - +
281M GLU* 2.9 28.6 + - - +
327U THR* 6.3 2.5 - - - -
357U ALA* 5.3 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 278 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265M TYR* 5.5 6.1 - - + +
266M TYR* 5.4 11.4 - - - +
274M LYS 2.9 17.1 + - - +
275M ALA* 4.1 7.0 - - - +
277M ASP* 1.3 76.0 - - - +
279M TYR* 1.3 56.4 + - - +
281M GLU* 4.1 5.6 - - - +
282M ALA* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 279 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266M TYR* 5.3 11.1 - - + +
275M ALA 2.9 20.8 + - - +
276M ARG* 3.7 8.5 - - - +
277M ASP 3.2 0.2 - - - -
278M VAL* 1.3 75.6 - - - +
280M GLU* 1.3 59.0 + - - +
282M ALA* 4.3 5.5 - - - +
283M ILE* 2.9 29.2 + - - +
295M VAL* 4.0 29.4 - - + +
298M SER* 5.8 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 280 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276M ARG 2.9 15.4 + - - +
277M ASP* 3.0 11.6 + - - +
279M TYR* 1.3 76.1 - - - +
281M GLU* 1.3 59.8 + - - +
283M ILE* 3.2 7.0 + - - +
284M ARG* 2.9 27.7 + - - +
357U ALA* 5.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 281 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277M ASP 2.9 13.8 + - - +
278M VAL* 4.1 5.8 - - - +
280M GLU* 1.3 72.5 - - - +
282M ALA* 1.3 60.2 + - - +
284M ARG* 3.1 9.0 + - - +
285M THR* 2.9 27.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 282 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262M LEU* 3.8 31.5 - - + +
266M TYR* 6.2 1.8 - - + -
278M VAL 2.9 20.3 + - - +
279M TYR* 4.3 5.6 - - - +
281M GLU* 1.3 76.5 - - - +
283M ILE* 1.3 52.2 + - - +
285M THR* 3.3 7.9 - - - +
286M VAL* 2.7 33.1 + - - +
291M ASP* 5.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 283 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279M TYR 2.9 22.1 + - - +
280M GLU* 3.4 9.2 - - - +
281M GLU 3.1 0.4 - - - -
282M ALA* 1.3 75.6 - - - +
284M ARG* 1.3 64.0 + - - +
286M VAL* 3.3 21.1 + - - +
291M ASP* 5.8 1.8 - - - -
292M PHE* 6.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 284 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280M GLU 2.9 13.5 + - - +
281M GLU* 3.1 10.5 + - - +
283M ILE* 1.3 78.0 - - - +
285M THR* 1.3 56.6 + - - +
286M VAL 3.3 3.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 285 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258M LEU* 5.3 8.8 - - - +
281M GLU 2.9 16.0 + - - -
282M ALA* 3.3 8.3 - - - -
284M ARG* 1.3 73.7 - - - +
286M VAL* 1.3 66.2 + - - +
287M MET* 3.7 1.6 + - - +
----------------------------------------------------------
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