Contacts of the helix formed by residues 215 - 228 (chain S) 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 S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119S TYR* 4.8 1.8 - - - +
120S GLU* 3.2 39.4 + - - +
213S GLU* 2.8 13.0 + - + +
214S LYS* 1.3 76.4 - - + +
216S LYS* 1.3 56.8 + - - +
218S LYS* 3.4 46.1 + - + +
219S HIS* 2.9 27.7 + - - +
6T LEU* 5.1 3.8 - - + +
358T ARG* 6.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120S GLU* 3.2 1.0 + - - -
206S ILE* 3.4 30.5 - - + +
207S PRO* 3.1 40.5 - - + +
210S ASP* 5.1 3.0 - - - +
212S GLU* 3.3 39.0 + - - +
213S GLU 3.3 6.3 - - - +
214S LYS* 2.7 15.7 + - - +
215S GLN* 1.3 69.4 - - - +
217S VAL* 1.3 68.3 + - - +
219S HIS* 3.1 4.4 + - - +
220S ASN* 2.8 21.7 + - - +
14V ASP* 5.8 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120S GLU* 2.6 15.1 + - - +
123S ASP* 3.2 28.7 - - + +
124S LEU* 3.8 2.0 - - - +
125S ALA 3.6 12.6 - - - +
202S LEU* 3.0 61.1 - - + +
203S ILE 4.1 0.7 - - - +
204S GLY* 3.6 14.6 - - - +
206S ILE* 3.5 34.3 - - + +
216S LYS* 1.3 73.4 - - - +
218S LYS* 1.3 59.6 + - - +
220S ASN* 3.4 2.3 + - - +
221S ILE 3.2 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 218 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118S LEU* 3.4 47.4 + - + -
119S TYR* 4.3 7.3 - - - +
120S GLU* 2.7 26.3 + - + +
125S ALA* 4.1 8.5 - - + -
215S GLN* 3.4 43.3 + - + +
217S VAL* 1.3 69.5 - - - +
219S HIS* 1.3 66.7 + - - +
221S ILE* 2.9 19.6 + - - +
222S MET* 3.0 11.6 + - - +
233S GLU* 3.3 24.0 + - - -
6T LEU* 3.6 21.2 - - + +
7T LYS 5.7 0.2 + - - -
358T ARG* 6.0 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 219 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207S PRO* 5.1 2.0 - - + -
208S LEU* 3.6 49.6 + - + +
211S GLY* 6.1 2.0 - - - -
212S GLU 5.3 4.7 - - - -
213S GLU* 2.9 28.3 + - + +
215S GLN 2.9 19.7 + - - +
216S LYS* 3.1 7.8 + - - +
218S LYS* 1.3 76.5 - - - +
220S ASN* 1.3 63.5 + - - +
222S MET* 3.5 2.3 + - - +
223S LYS* 3.2 21.9 + - + +
5T LEU* 5.0 10.1 - - - -
6T LEU* 3.5 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 220 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202S LEU* 3.7 11.1 - - - +
205S SER* 2.7 36.6 + - - +
207S PRO* 3.4 28.4 - - + +
208S LEU* 4.0 9.4 + - - +
216S LYS 2.8 12.3 + - - +
217S VAL 3.6 3.4 - - - +
219S HIS* 1.3 74.3 - - - +
221S ILE* 1.3 60.1 + - - +
223S LYS* 3.1 16.6 + - - +
224S ILE* 2.9 57.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118S LEU* 3.6 32.1 - - + -
201S ILE* 4.0 12.6 - - + -
202S LEU* 3.1 47.3 - - + -
217S VAL 3.2 1.8 + - - -
218S LYS* 2.9 18.0 + - - +
220S ASN* 1.3 75.8 - - - +
222S MET* 1.3 57.8 + - - +
224S ILE* 3.0 19.0 + - + +
225S LEU* 2.6 41.8 + - + +
254V PHE* 3.2 34.3 - - + -
255V ASP 4.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 222 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118S LEU* 3.6 24.5 - - + -
218S LYS 3.0 6.6 + - - +
219S HIS* 3.7 8.3 - - - +
221S ILE* 1.3 82.3 - - - +
223S LYS* 1.3 53.2 + - - +
225S LEU* 3.2 20.0 + - + -
226S ASN* 2.7 34.3 + - + +
231S ILE* 4.0 19.3 - - + +
232S SER* 3.6 24.7 - - - +
233S GLU* 3.6 17.7 - - - +
236S PHE* 4.2 6.5 - - + -
5T LEU 3.9 22.4 - - - +
6T LEU* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208S LEU* 3.3 52.5 - - + +
219S HIS* 3.2 7.6 + - + +
220S ASN* 3.1 23.7 + - - +
222S MET* 1.3 76.9 - - - +
224S ILE* 1.3 71.8 + - + +
226S ASN* 2.9 25.5 + - + +
227S GLU* 3.0 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 224 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205S SER* 5.7 0.2 - - - -
220S ASN* 2.9 46.9 + - - +
221S ILE* 3.0 17.2 + - + +
223S LYS* 1.3 89.2 - - + +
225S LEU* 1.3 64.4 + - + +
226S ASN 3.2 0.7 + - - -
227S GLU* 3.4 20.8 + - - +
228S LYS* 3.6 26.4 + - - +
254V PHE* 4.0 19.5 - - + +
255V ASP* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118S LEU* 5.8 1.6 - - + -
201S ILE* 5.6 5.6 - - + -
221S ILE* 2.6 24.9 + - + +
222S MET* 3.4 16.8 - - + +
224S ILE* 1.3 74.5 - - + +
226S ASN* 1.3 53.3 + - - +
228S LYS* 2.6 22.6 - - + +
229S TYR* 3.6 22.7 - - + -
231S ILE* 3.8 22.9 - - + +
236S PHE* 3.7 31.2 - - + -
254V PHE* 3.6 54.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 226 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222S MET* 2.7 13.2 + - + +
223S LYS* 2.9 17.9 + - - +
225S LEU* 1.3 75.9 - - - +
227S GLU* 1.3 66.3 + - - +
228S LYS 2.8 12.0 - - - +
229S TYR 3.6 7.3 - - - +
230S ASP* 3.8 17.5 - - - +
231S ILE 3.3 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223S LYS* 3.0 48.9 + - + +
224S ILE* 3.4 13.6 + - - +
226S ASN* 1.3 83.0 - - - +
228S LYS* 1.3 61.7 + - + +
229S TYR 3.7 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 228 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163S VAL* 6.0 4.4 - - - +
170S PRO* 5.7 5.1 - - - +
224S ILE* 3.6 22.5 + - + +
225S LEU* 2.6 23.8 - - + +
226S ASN 2.8 4.2 - - - +
227S GLU* 1.3 77.4 - - + +
229S TYR* 1.3 93.1 + - + +
254V PHE* 4.7 22.4 + - + -
256V ARG* 4.5 16.5 - - - +
----------------------------------------------------------
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