Contacts of the helix formed by residues 215 - 228 (chain M) 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 M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119M TYR* 4.8 2.0 - - - +
120M GLU* 3.2 40.1 + - - +
213M GLU* 2.8 13.2 + - + +
214M LYS* 1.3 77.9 - - + +
216M LYS* 1.3 59.4 + - - +
218M LYS* 3.4 46.7 + - + +
219M HIS* 2.9 27.0 + - - +
6Q LEU* 5.3 6.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120M GLU* 3.2 1.4 + - - -
206M ILE* 3.4 29.7 + - + +
207M PRO* 3.2 41.5 - - + +
210M ASP* 5.1 2.8 - - + +
212M GLU* 3.3 38.5 + - - +
213M GLU 3.3 6.1 - - - +
214M LYS* 2.7 14.9 + - - +
215M GLN* 1.3 68.4 - - - +
217M VAL* 1.3 69.2 + - - +
219M HIS* 3.0 5.4 + - - +
220M ASN* 2.8 21.5 + - - +
14P ASP* 5.8 2.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
120M GLU* 2.6 15.1 + - - +
123M ASP* 3.1 28.0 - - + +
124M LEU* 3.8 2.7 - - - +
125M ALA 3.5 14.4 - - - +
202M LEU* 3.0 60.0 - - + +
203M ILE 4.2 0.4 - - - +
204M GLY* 3.6 14.8 - - - +
206M ILE* 3.6 34.1 - - + +
216M LYS* 1.3 73.2 - - - +
218M LYS* 1.3 59.9 + - - +
220M ASN* 3.5 2.1 + - - +
221M ILE 3.2 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 218 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118M LEU* 3.4 47.9 + - + -
119M TYR* 4.3 7.2 - - - +
120M GLU* 2.7 26.1 + - + -
125M ALA* 4.1 8.7 - - + -
215M GLN* 3.4 45.2 + - + +
217M VAL* 1.3 71.5 - - - +
219M HIS* 1.3 67.4 + - - +
221M ILE* 2.8 18.8 + - - +
222M MET* 3.0 12.2 + - + +
233M GLU* 3.3 31.7 + - - -
6Q LEU* 5.2 10.0 - - + +
358Q ARG* 6.1 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 219 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207M PRO* 5.1 2.0 - - + -
208M LEU* 3.6 49.4 + - + +
211M GLY 6.1 1.8 - - - -
212M GLU 5.3 5.2 - - - -
213M GLU* 2.9 30.1 + - + +
215M GLN 2.9 19.1 + - - +
216M LYS* 3.4 7.4 - - - +
218M LYS* 1.3 76.6 - - - +
220M ASN* 1.3 63.1 + - - +
222M MET* 3.4 6.8 + - - +
223M LYS* 3.1 22.6 + - + +
6Q LEU* 3.9 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 220 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202M LEU* 3.7 10.5 - - - +
205M SER* 2.7 38.0 + - - +
207M PRO* 3.4 28.8 - - + +
208M LEU* 4.0 10.2 + - - +
216M LYS 2.8 9.6 + - - +
217M VAL 3.6 2.7 - - - +
219M HIS* 1.3 77.3 - - - +
221M ILE* 1.3 59.0 + - - +
223M LYS* 3.1 17.2 + - - +
224M ILE* 2.9 59.2 + - - +
255P ASP* 4.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118M LEU* 3.6 32.8 - - + -
201M ILE* 4.0 9.0 - - + -
202M LEU* 3.1 45.1 - - + -
217M VAL 3.2 1.8 + - - -
218M LYS* 2.8 18.8 + - - +
220M ASN* 1.3 73.8 - - - +
222M MET* 1.3 59.5 + - - +
224M ILE* 3.0 18.8 + - + +
225M LEU* 2.6 42.3 + - + +
254P PHE* 3.2 37.7 - - + -
255P ASP 4.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 222 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118M LEU* 3.6 22.0 - - + -
218M LYS 3.0 6.5 + - - +
219M HIS* 3.7 9.0 - - - +
221M ILE* 1.3 81.9 - - - +
223M LYS* 1.3 52.5 + - - +
225M LEU* 3.2 20.8 + - + -
226M ASN* 2.7 34.5 + - + +
231M ILE* 4.0 19.3 - - + +
232M SER* 3.6 25.4 - - - +
233M GLU* 3.6 23.3 - - - +
236M PHE* 4.2 4.7 - - + -
5Q LEU 4.5 2.5 - - - +
6Q LEU* 3.5 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208M LEU* 3.3 52.8 - - + +
219M HIS* 3.1 7.1 + - + +
220M ASN* 3.1 22.0 + - - +
222M MET* 1.3 76.4 - - - +
224M ILE* 1.3 71.1 + - + +
226M ASN* 2.8 25.9 + - + +
227M GLU* 3.0 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 224 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220M ASN* 2.9 48.1 + - - +
221M ILE* 3.3 17.0 - - + +
223M LYS* 1.3 90.7 - - + +
225M LEU* 1.3 64.9 + - + +
226M ASN 3.2 0.5 + - - -
227M GLU* 3.4 19.4 + - - +
228M LYS* 3.5 25.8 + - + +
254P PHE* 4.2 19.5 - - + +
255P ASP* 3.8 22.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
118M LEU* 5.8 1.6 - - + -
201M ILE* 5.6 5.4 - - + -
221M ILE* 2.6 25.0 + - + +
222M MET* 3.4 17.3 - - + +
224M ILE* 1.3 76.1 - - + +
226M ASN* 1.3 53.7 + - - +
228M LYS* 2.6 23.1 - - + +
229M TYR* 3.6 23.4 - - + -
231M ILE* 3.8 22.2 - - + +
236M PHE* 3.7 30.7 - - + -
254P PHE* 3.5 53.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 226 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222M MET* 2.7 14.6 + - + +
223M LYS* 2.8 18.9 + - - +
225M LEU* 1.3 75.5 - - - +
227M GLU* 1.3 71.2 + - - +
228M LYS 2.9 8.8 - - - +
229M TYR 3.6 7.4 - - - +
230M ASP* 3.8 17.0 - - - +
231M ILE 3.3 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223M LYS* 3.0 48.4 + - + +
224M ILE* 3.4 13.7 + - - +
226M ASN* 1.3 81.2 - - - +
228M LYS* 1.3 62.6 + - + +
229M TYR 3.6 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 228 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163M VAL* 6.0 4.2 - - - +
170M PRO* 5.7 5.9 - - - +
224M ILE* 3.5 21.4 + - + +
225M LEU* 2.6 23.9 - - + +
226M ASN 2.9 3.8 - - - +
227M GLU* 1.3 76.1 - - + +
229M TYR* 1.3 92.6 + - + +
254P PHE* 4.9 21.8 + - + -
256P ARG* 4.8 14.5 - - - +
----------------------------------------------------------
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