Contacts of the helix formed by residues 215 - 228 (chain O) in PDB entry 2GLJ
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 GLN 215 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119O TYR* 4.8 1.4 - - - +
120O GLU* 3.2 39.9 + - + +
213O GLU* 2.8 12.6 + - + +
214O LYS* 1.3 78.0 - - + +
216O LYS* 1.3 56.8 + - - +
218O LYS* 3.4 45.0 + - + +
219O HIS* 2.9 28.1 + - - +
6P LEU* 5.1 8.0 - - + +
8P GLU* 5.0 6.8 - - - +
358P ARG* 6.3 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120O GLU* 3.2 1.2 + - - -
206O ILE* 3.3 29.8 + - + +
207O PRO* 3.1 43.9 - - + +
210O ASP* 5.1 2.6 - - + +
212O GLU* 3.3 38.6 + - - +
213O GLU 3.3 6.5 - - - +
214O LYS* 2.7 15.4 + - - +
215O GLN* 1.3 70.0 - - - +
217O VAL* 1.3 67.6 + - - +
219O HIS* 3.1 3.9 + - - +
220O ASN 2.8 21.5 + - - -
14R ASP* 5.7 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120O GLU* 2.6 16.0 + - - +
123O ASP* 3.1 29.2 - - + +
124O LEU* 3.8 2.5 - - - +
125O ALA* 3.6 12.3 - - + +
202O LEU* 3.0 62.0 - - + +
203O ILE 4.2 0.4 - - - +
204O GLY* 3.7 15.3 - - - +
206O ILE* 3.6 32.1 - - + -
216O LYS* 1.3 73.1 - - - +
218O LYS* 1.3 60.1 + - - +
220O ASN* 3.5 3.3 + - - +
221O ILE 3.2 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 218 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118O LEU* 3.4 48.3 + - + -
119O TYR* 4.3 6.7 - - - +
120O GLU* 2.7 26.5 + - + +
125O ALA* 4.1 9.0 - - + -
215O GLN* 3.4 44.9 + - + +
217O VAL* 1.3 71.1 - - - +
219O HIS* 1.3 68.5 + - - +
221O ILE* 2.9 18.7 + - - +
222O MET* 3.0 11.3 + - - +
233O GLU* 3.3 32.6 + - - -
6P LEU* 4.4 10.6 - - + +
8P GLU* 5.6 3.0 + - - -
358P ARG* 5.8 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 219 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207O PRO* 5.2 1.8 - - + -
208O LEU* 3.6 49.0 + - + +
211O GLY 6.1 1.6 - - - -
212O GLU 5.3 5.6 - - - +
213O GLU* 2.9 28.3 + - + +
215O GLN 2.9 20.9 + - - +
216O LYS* 3.1 7.6 + - - +
218O LYS* 1.3 75.7 - - - +
220O ASN* 1.3 62.0 + - - +
222O MET* 3.4 5.1 + - - +
223O LYS* 3.1 21.9 + - + +
5P LEU* 4.7 21.1 - - + -
6P LEU* 3.6 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 220 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202O LEU* 3.7 11.1 - - - +
205O SER* 2.6 38.2 + - - +
207O PRO* 3.4 28.4 - - + +
208O LEU* 4.0 10.1 + - - +
216O LYS 2.8 12.3 + - - +
217O VAL 3.6 3.4 - - - +
219O HIS* 1.3 75.0 - - - +
221O ILE* 1.3 58.1 + - - +
223O LYS* 3.1 16.5 + - - +
224O ILE* 2.9 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118O LEU* 3.6 33.0 - - + -
201O ILE* 4.0 9.0 - - + -
202O LEU* 3.1 45.8 - - + -
217O VAL 3.2 1.2 + - - -
218O LYS* 2.9 17.8 + - - +
220O ASN* 1.3 74.1 - - - +
222O MET* 1.3 61.0 + - - +
224O ILE* 3.1 17.7 + - + +
225O LEU* 2.6 40.6 + - + +
254R PHE* 3.2 37.2 - - + -
255R ASP 4.1 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 222 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118O LEU* 3.7 21.1 - - + -
218O LYS 3.0 4.8 + - - +
219O HIS* 3.7 6.5 - - - +
221O ILE* 1.3 82.0 - - - +
223O LYS* 1.3 52.1 + - - +
225O LEU* 3.2 19.1 + - + -
226O ASN* 2.8 34.7 + - + +
231O ILE* 4.0 18.8 - - + +
232O SER* 3.6 24.7 - - - +
233O GLU* 3.6 18.8 - - - -
236O PHE* 4.2 6.3 - - + -
5P LEU* 3.4 11.2 - - - +
6P LEU* 3.3 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LEU* 5.9 3.8 - - - +
208O LEU* 3.3 53.9 - - + +
219O HIS* 3.1 6.7 + - + +
220O ASN* 3.1 22.9 + - - +
222O MET* 1.3 77.0 - - - +
224O ILE* 1.3 70.9 + - + +
226O ASN* 2.8 25.1 + - - +
227O GLU* 3.0 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 224 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220O ASN* 2.9 47.2 + - - +
221O ILE* 3.4 15.3 - - + +
223O LYS* 1.3 88.7 - - + +
225O LEU* 1.3 64.6 + - + +
226O ASN 3.2 0.5 + - - -
227O GLU* 3.4 20.4 + - - +
228O LYS* 3.5 25.8 + - + +
254R PHE* 4.0 21.1 - - + +
255R ASP* 3.5 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118O LEU* 5.8 1.6 - - + -
201O ILE* 5.6 5.6 - - + -
221O ILE* 2.6 25.6 + - + +
222O MET* 3.4 16.4 - - + +
224O ILE* 1.3 75.0 - - + +
226O ASN* 1.3 52.6 + - - +
228O LYS* 2.6 23.4 - - + +
229O TYR* 3.6 21.7 - - + -
231O ILE* 3.8 21.7 - - + +
236O PHE* 3.7 31.2 - - + -
254R PHE* 3.5 55.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 226 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H GLU* 5.9 0.8 + - - -
10H LYS* 6.2 2.4 - - - +
222O MET* 2.8 14.1 + - + +
223O LYS* 2.8 17.4 + - - +
225O LEU* 1.3 75.9 - - - +
227O GLU* 1.3 70.5 + - - +
228O LYS 2.9 9.1 - - - +
229O TYR 3.6 7.4 - - - +
230O ASP* 3.8 17.5 - - - +
231O ILE 3.3 23.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LEU* 4.1 25.1 - - + +
223O LYS* 3.0 48.4 + - + +
224O ILE* 3.8 12.9 - - - +
226O ASN* 1.3 83.5 - - - +
228O LYS* 1.3 63.9 + - + +
229O TYR 3.7 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 228 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163O VAL* 5.9 4.2 - - - +
170O PRO* 5.7 4.6 - - - +
224O ILE* 3.5 21.2 + - + +
225O LEU* 2.6 24.0 - - + +
226O ASN 2.9 3.8 - - - +
227O GLU* 1.3 77.2 - - + +
229O TYR* 1.3 92.4 + - + +
254R PHE* 4.7 21.8 + - + -
256R ARG* 4.4 18.1 - - - +
----------------------------------------------------------
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