Contacts of the helix formed by residues 214 - 228 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G PHE* 3.6 20.9 - - + -
11G ILE* 4.5 10.3 - - + -
14G ASN* 3.5 44.4 - - + +
170G VAL* 3.8 14.1 - - + -
171G TYR 2.9 22.1 + - - +
172G GLY* 3.8 15.0 - - - -
173G PRO* 3.9 10.8 - - + -
212G VAL 3.6 0.6 + - - -
213G TYR* 1.3 75.0 - - + +
215G GLY* 1.3 64.8 + - - +
217G VAL* 3.1 6.0 + - + +
218G ALA* 2.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 215 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ASN* 5.6 1.8 - - - -
213G TYR* 3.1 19.7 + - - -
214G VAL* 1.3 83.5 - - - +
216G ASP* 1.3 58.7 + - - +
218G ALA* 3.4 7.7 + - - +
219G ASP* 3.1 33.9 + - - +
293G LYS* 5.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 216 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212G VAL* 4.4 2.7 - - + -
213G TYR* 2.9 17.2 + - - +
215G GLY* 1.3 75.6 - - - +
217G VAL* 1.3 67.2 + - - +
219G ASP* 3.0 13.5 + - - +
220G VAL* 2.9 28.8 + - - +
288G TYR* 4.4 2.9 + - - +
291G PRO 4.7 4.5 - - - +
292G PHE* 3.4 30.5 - - + +
293G LYS* 2.8 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ILE* 4.0 19.7 - - + -
167G TYR* 3.5 31.2 - - + -
170G VAL* 3.9 28.5 - - + -
212G VAL* 4.2 8.5 - - + -
213G TYR 3.2 10.7 + - - +
214G VAL* 3.1 10.3 + - + +
216G ASP* 1.3 77.9 - - - +
218G ALA* 1.3 62.5 + - - +
220G VAL* 3.3 3.5 + - - +
221G ASN* 3.0 32.7 + - - +
235G LEU* 4.1 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ASN* 3.9 30.5 - - + +
15G ILE* 4.6 6.7 - - + +
18G ALA* 4.0 13.5 - - + -
214G VAL 2.9 11.8 + - - +
215G GLY* 3.5 12.3 - - - +
217G VAL* 1.3 79.1 - - - +
219G ASP* 1.3 63.9 + - - +
221G ASN* 3.1 9.6 + - - +
222G LEU* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 219 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ALA* 5.3 5.0 - - - +
215G GLY 3.1 20.3 + - - +
216G ASP* 3.0 15.9 + - - +
218G ALA* 1.3 78.5 - - - +
220G VAL* 1.3 64.2 + - - +
222G LEU* 3.2 7.7 + - - +
223G TRP* 2.9 24.4 + - - +
288G TYR* 4.0 15.1 + - + +
290G LYS* 5.7 4.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G PHE* 3.6 26.5 - - + -
216G ASP 2.9 17.5 + - - +
217G VAL 3.6 7.4 - - - +
219G ASP* 1.3 75.5 - - - +
221G ASN* 1.3 63.8 + - - +
223G TRP* 3.1 1.7 + - - +
224G PHE* 3.0 36.0 + - + -
235G LEU* 3.7 31.2 - - + -
283G LEU* 4.6 6.3 - - + -
288G TYR* 3.6 35.7 - - + +
292G PHE* 4.1 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 221 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G ILE* 3.5 24.0 - - + +
73G PHE* 3.4 30.5 - - + -
75G GLU* 3.8 3.5 - - - +
112G LEU* 4.0 1.7 - - - +
165G PHE* 3.3 28.9 - - - -
167G TYR* 3.1 24.6 + - - -
217G VAL* 3.0 30.9 + - - +
218G ALA* 3.1 8.9 + - - +
220G VAL* 1.3 77.9 - - - +
222G LEU* 1.3 65.8 + - + +
224G PHE* 3.3 3.3 + - - +
225G LEU* 3.1 19.9 + - - +
235G LEU* 4.7 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G ILE* 4.5 11.0 - - + -
18G ALA* 3.8 35.0 - - + +
19G LEU* 3.9 29.6 - - + +
22G LYS* 3.8 29.6 - - + -
73G PHE* 4.1 14.1 - - + -
218G ALA 3.0 17.5 + - - +
219G ASP* 3.9 7.2 - - - +
221G ASN* 1.3 78.1 - - + +
223G TRP* 1.3 63.1 + - - +
225G LEU* 3.2 7.8 + - + +
226G GLU* 3.0 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 223 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G ASP 2.9 17.5 + - - +
220G VAL 3.5 4.5 - - - +
222G LEU* 1.3 76.8 - - - +
224G PHE* 1.3 92.7 + + - +
226G GLU* 3.2 7.6 + - - -
227G ASN* 2.7 73.4 + - + +
229G VAL* 4.5 3.4 - - + -
286G ALA 3.6 15.3 - - - -
287G GLY* 3.5 32.5 + - - -
288G TYR* 3.5 35.8 - + + +
289G ASP* 5.8 1.0 + - - +
290G LYS* 4.1 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 224 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G LEU* 4.0 7.4 - - + -
161G GLN* 2.9 20.4 + - - +
163G VAL* 4.0 8.1 - - + -
165G PHE* 3.5 32.8 - + + -
220G VAL* 3.0 25.6 + - + +
221G ASN 3.8 2.2 - - - +
223G TRP* 1.3 97.4 - + - +
225G LEU* 1.3 65.6 + - - +
227G ASN* 4.4 0.4 - - - +
228G GLY 2.9 12.5 + - - -
229G VAL* 3.8 35.1 + - + -
233G PHE* 3.6 37.7 - + - -
283G LEU* 3.7 26.7 - - + -
286G ALA* 4.2 12.1 - - + -
288G TYR* 4.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G ILE* 4.2 15.5 - - + -
19G LEU* 5.1 5.2 - - + -
24G ILE* 6.2 1.1 - - + -
70G GLU* 4.5 14.1 - - + +
71G ALA* 3.6 25.6 - - + -
73G PHE* 3.7 29.6 - - + -
110G PRO* 4.4 16.8 - - + -
112G LEU* 3.9 7.9 - - + +
161G GLN* 4.2 7.4 - - - +
221G ASN 3.1 13.5 + - - +
222G LEU* 3.2 11.0 + - + +
224G PHE* 1.3 77.4 - - - +
226G GLU* 1.3 66.1 + - + +
228G GLY* 3.8 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 226 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LYS* 3.1 37.0 + - - +
222G LEU* 3.0 22.6 + - - +
223G TRP* 3.7 9.4 - - - +
225G LEU* 1.3 80.5 - - + +
227G ASN* 1.3 67.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 227 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G TRP* 2.7 81.5 + - + +
224G PHE 4.3 0.7 - - - +
226G GLU* 1.3 90.4 + - - +
228G GLY* 1.3 57.1 + - - +
229G VAL* 3.2 16.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 228 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161G GLN* 3.2 31.2 + - - +
224G PHE 2.9 8.5 + - - -
225G LEU 3.8 3.5 + - - -
226G GLU 3.6 2.0 - - - -
227G ASN* 1.3 75.8 - - - +
229G VAL* 1.3 62.2 + - - +
230G SER* 3.7 3.1 + - - -
----------------------------------------------------------
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