Contacts of the helix formed by residues 214 - 228 (chain M) in PDB entry 2X86
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 VAL 214 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M PHE* 3.6 21.1 - - + -
11M ILE* 4.5 10.1 - - + -
14M ASN* 3.5 43.7 - - + +
170M VAL* 3.8 15.0 - - + -
171M TYR 2.9 21.2 + - - +
172M GLY* 3.8 15.0 - - - -
173M PRO* 3.9 11.0 - - + -
212M VAL 3.6 0.4 + - - -
213M TYR* 1.3 74.8 - - + +
215M GLY* 1.3 65.5 + - - +
217M VAL* 3.1 6.6 + - + +
218M ALA* 2.9 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 215 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M ASN* 5.6 2.0 - - - -
213M TYR* 3.1 19.5 + - - -
214M VAL* 1.3 84.2 - - - +
216M ASP* 1.3 59.2 + - - +
218M ALA* 3.4 7.5 + - - +
219M ASP* 3.1 33.5 + - - +
293M LYS* 5.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 216 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212M VAL* 4.4 3.1 - - + +
213M TYR* 2.9 17.0 + - - +
215M GLY* 1.3 75.2 - - - +
217M VAL* 1.3 67.0 + - - +
219M ASP* 3.0 13.8 + - - +
220M VAL* 2.9 29.1 + - - +
288M TYR* 4.4 2.6 + - - +
291M PRO 4.7 4.2 - - - +
292M PHE* 3.4 30.4 - - + +
293M LYS* 2.8 53.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M ILE* 4.1 19.7 - - + -
167M TYR* 3.6 31.0 - - + -
170M VAL* 3.9 28.3 - - + -
212M VAL* 4.2 7.6 - - + -
213M TYR 3.8 11.2 - - - +
214M VAL* 3.1 10.7 + - + +
216M ASP* 1.3 78.0 - - - +
218M ALA* 1.3 64.4 + - - +
220M VAL* 3.3 3.1 + - - +
221M ASN* 3.0 33.0 + - - +
235M LEU* 4.1 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M ASN* 3.9 30.7 - - + +
15M ILE* 4.7 7.2 - - - +
18M ALA* 4.0 13.0 - - + -
214M VAL 2.9 11.8 + - - +
215M GLY* 3.5 11.9 - - - +
217M VAL* 1.3 78.6 - - - +
219M ASP* 1.3 64.4 + - - +
221M ASN* 3.1 9.6 + - - +
222M LEU* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 219 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M ALA* 5.3 4.3 - - - +
215M GLY 3.1 19.1 + - - +
216M ASP* 3.0 16.3 + - - +
218M ALA* 1.3 78.2 - - - +
220M VAL* 1.3 64.2 + - - +
222M LEU* 3.2 7.3 + - - +
223M TRP* 2.9 24.5 + - - +
288M TYR* 4.0 13.8 + - + +
290M LYS* 5.7 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165M PHE* 3.6 25.8 - - + -
216M ASP 2.9 17.4 + - - +
217M VAL 3.6 7.2 - - - +
218M ALA 3.2 0.2 - - - -
219M ASP* 1.3 74.9 - - - +
221M ASN* 1.3 65.3 + - - +
223M TRP* 3.1 1.9 + - - +
224M PHE* 3.0 35.7 + - + -
235M LEU* 3.6 31.2 - - + -
283M LEU* 4.6 6.5 - - + -
288M TYR* 3.6 35.9 - - + +
292M PHE* 4.1 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 221 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M ILE* 3.5 23.6 - - + +
73M PHE* 3.4 31.8 - - + -
75M GLU* 3.8 3.3 - - - +
112M LEU* 4.1 1.7 - - - +
165M PHE* 3.3 31.1 - - - -
167M TYR* 3.1 24.6 + - - -
217M VAL* 3.0 29.9 + - - +
218M ALA 3.1 8.7 + - - +
220M VAL* 1.3 78.2 - - - +
222M LEU* 1.3 66.2 + - + +
224M PHE* 3.3 3.6 + - - +
225M LEU* 3.1 19.9 + - - +
235M LEU* 4.7 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M ILE* 4.5 10.5 - - + -
18M ALA* 3.8 37.2 - - + +
19M LEU* 3.9 30.1 - - + +
22M LYS* 3.8 27.8 - - + -
73M PHE* 4.1 13.2 - - + -
218M ALA 3.0 16.9 + - - +
219M ASP* 3.9 8.3 - - - +
221M ASN* 1.3 79.6 - - + +
223M TRP* 1.3 63.6 + - - +
225M LEU* 3.2 7.9 + - + +
226M GLU* 3.0 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 223 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219M ASP 2.9 17.0 + - - +
220M VAL 3.1 4.0 + - - +
222M LEU* 1.3 77.4 - - - +
224M PHE* 1.3 91.8 + + - +
226M GLU* 3.2 7.8 + - - -
227M ASN* 2.7 74.8 + - + +
229M VAL* 4.5 3.6 - - + -
286M ALA 3.6 15.9 - - - -
287M GLY* 3.5 32.6 + - - -
288M TYR* 3.5 36.0 - + + +
289M ASP* 5.8 1.2 + - - +
290M LYS* 4.1 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 224 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112M LEU* 4.0 7.4 - - + -
161M GLN* 2.9 11.7 + - - +
163M VAL* 4.1 7.2 - - + -
165M PHE* 3.5 32.3 - + + -
220M VAL* 3.0 25.7 + - + +
221M ASN 3.8 2.2 - - - +
223M TRP* 1.3 98.7 - + + +
225M LEU* 1.3 65.1 + - - +
227M ASN* 4.4 0.4 - - - +
228M GLY 2.9 21.5 + - - -
229M VAL* 3.8 34.5 + - + -
233M PHE* 3.6 37.7 - + - -
283M LEU* 3.7 26.5 - - + -
286M ALA* 4.2 12.6 - - + -
288M TYR* 4.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M ILE* 4.2 18.8 - - + -
19M LEU* 4.9 5.6 - - + -
24M ILE* 6.0 1.6 - - + -
70M GLU* 4.6 13.9 - - + +
71M ALA* 3.6 23.3 - - + -
73M PHE* 3.7 30.5 - - + -
110M PRO* 4.4 7.6 - - + -
112M LEU* 3.9 7.5 - - + +
161M GLN* 4.2 16.3 - - - +
221M ASN 3.1 12.5 + - - +
222M LEU* 3.5 11.2 - - + +
224M PHE* 1.3 78.5 - - - +
226M GLU* 1.3 66.1 + - + +
227M ASN 3.3 0.2 + - - -
228M GLY* 3.8 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 226 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M LYS* 3.1 37.4 + - - +
222M LEU* 3.0 22.7 + - - +
223M TRP* 3.7 10.2 + - - +
225M LEU* 1.3 80.5 - - + +
227M ASN* 1.3 68.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 227 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223M TRP* 2.7 79.1 + - + +
224M PHE 4.3 0.9 - - - +
225M LEU 3.2 0.2 - - - -
226M GLU* 1.3 90.6 - - - +
228M GLY* 1.3 57.2 + - - +
229M VAL* 3.2 16.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 228 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161M GLN* 3.2 31.4 + - - +
224M PHE 2.9 7.9 + - - -
225M LEU 3.8 3.2 + - - -
226M GLU 3.6 1.8 - - - -
227M ASN* 1.3 76.1 - - - +
229M VAL* 1.3 62.5 + - - +
230M SER* 3.7 2.8 + - - -
----------------------------------------------------------
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