Contacts of the helix formed by residues 206 - 223 (chain L) in PDB entry 2O5J
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 THR 206 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L THR* 4.8 3.2 + - + +
17L GLY 4.0 3.8 + - - -
18L ARG* 3.3 27.5 + - - +
201L THR* 3.7 3.3 + - - -
205L VAL* 1.3 75.4 - - - +
207L PRO* 1.3 78.7 - - + +
208L LEU* 3.2 26.5 - - + +
209L GLU* 2.6 42.9 + - - +
210L ALA* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 207 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L THR* 4.5 4.9 - - - +
18L ARG* 3.2 14.4 - - - +
19L GLU 3.6 12.3 - - - +
20L TYR 3.4 29.8 - - - +
21L GLY* 3.5 10.1 - - - +
23L PHE* 3.3 27.9 - - + -
199L ILE* 3.7 14.7 - - + +
201L THR* 3.6 9.6 - - - +
206L THR* 1.3 96.1 - - + +
208L LEU* 1.3 59.4 + - - +
210L ALA* 3.5 3.3 - - + +
211L LEU* 3.1 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228K PRO* 5.7 8.7 - - + -
11L PHE* 5.5 11.0 - - + -
13L VAL* 5.7 9.0 - - + -
15L THR* 5.8 6.2 + - + -
23L PHE* 3.5 19.8 - - + -
206L THR* 3.2 13.6 - - + +
207L PRO* 1.3 75.4 - - - +
209L GLU* 1.3 72.8 + - + +
211L LEU* 3.4 5.3 + - + +
212L ASN* 3.1 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 209 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L ARG* 3.1 15.4 + - - -
205L VAL* 3.5 9.5 - - + +
206L THR* 2.6 52.0 + - + +
208L LEU* 1.3 87.5 - - + +
210L ALA* 1.3 57.8 + - - +
212L ASN* 3.4 6.5 + - - +
213L GLN* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44L LEU* 3.7 10.3 - - + -
48L ILE* 3.5 26.9 - - + +
174L VAL* 3.9 14.8 - - + -
199L ILE* 4.7 0.7 - - + -
205L VAL* 4.6 9.1 - - + +
206L THR 3.0 17.7 + - - +
207L PRO* 3.5 7.6 - - + +
209L GLU* 1.3 76.3 - - - +
211L LEU* 1.3 57.9 + - - +
213L GLN* 3.2 7.4 + - - +
214L ALA* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225K PHE* 4.3 12.3 - - + -
11L PHE* 4.1 17.5 - - + -
23L PHE* 3.8 34.5 - - + -
40L LEU* 3.9 25.6 - - + -
44L LEU* 3.7 28.7 - - + +
197L LEU* 4.6 6.3 - - + -
199L ILE* 4.0 4.0 - - + -
207L PRO 3.1 13.9 + - - +
208L LEU* 3.8 7.4 - - + +
210L ALA* 1.3 78.5 - - - +
212L ASN* 1.3 57.5 + - - +
214L ALA* 3.2 4.5 + - + +
215L VAL* 2.9 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 212 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225K PHE* 5.3 8.4 + - - +
11L PHE* 5.8 1.9 - - - -
208L LEU* 3.1 42.8 + - - +
209L GLU* 3.7 6.3 - - - +
211L LEU* 1.3 73.4 - - - +
213L GLN* 1.3 67.0 + - - +
215L VAL* 3.4 16.6 - - - +
216L GLU* 3.1 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 213 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L SER* 4.9 4.7 + - - +
48L ILE* 4.6 19.7 - - + -
49L PRO* 5.4 10.0 - - + +
209L GLU 3.0 14.6 + - - +
210L ALA* 3.4 10.5 - - - +
212L ASN* 1.3 76.7 - - - +
214L ALA* 1.3 57.5 + - - +
216L GLU* 3.3 11.5 - - - +
217L ILE* 3.1 27.3 + - + +
220L GLU* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 214 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L LEU* 4.5 5.8 - - + +
43L ILE* 3.3 31.5 - - + +
44L LEU* 3.9 20.4 - - + -
47L SER* 4.8 0.7 - - - -
48L ILE* 5.0 1.3 - - + +
210L ALA 2.8 13.1 + - - +
211L LEU* 3.2 15.9 - - + +
213L GLN* 1.3 73.5 - - - +
215L VAL* 1.3 66.0 - - + +
216L GLU 3.1 1.3 - - - -
217L ILE* 3.0 22.5 - - - +
218L LEU* 3.2 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222K LEU* 4.2 27.4 - - + +
225K PHE* 4.6 18.6 - - + -
40L LEU* 3.8 24.2 - - + -
211L LEU* 2.9 25.7 + - + +
212L ASN* 3.4 21.3 - - - +
214L ALA* 1.3 72.9 - - - +
216L GLU* 1.3 63.2 + - + +
218L LEU* 3.4 8.0 + - - +
219L ARG* 3.0 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 216 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212L ASN 3.1 15.2 + - - +
213L GLN* 3.3 13.2 - - - +
214L ALA 3.1 0.2 - - - -
215L VAL* 1.3 80.4 - - + +
217L ILE* 1.3 57.3 + - - +
218L LEU 3.1 1.6 - - - -
219L ARG* 2.8 40.9 + - - +
220L GLU* 2.7 69.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 217 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K PHE* 4.8 6.7 - - + -
43L ILE* 3.3 34.1 - - + -
47L SER* 3.3 29.8 - - - +
49L PRO* 6.3 0.9 - - + -
213L GLN* 3.1 13.3 + - + +
214L ALA 3.0 19.0 + - - +
216L GLU* 1.3 75.7 - - - +
218L LEU* 1.3 58.8 + - - +
220L GLU* 3.0 13.9 + - - +
221L HIS* 2.9 54.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K THR* 5.9 0.7 - - + -
36K LEU* 3.8 28.7 - - + -
218K LEU* 5.1 9.4 - - + -
222K LEU* 3.6 33.2 - - + -
39L PRO* 4.5 23.8 - - + -
40L LEU* 5.7 7.4 - - + +
43L ILE* 5.1 9.4 - - + -
214L ALA 3.2 7.8 + - - +
215L VAL* 3.6 10.5 - - - +
216L GLU 3.1 0.6 - - - -
217L ILE* 1.3 84.1 - - + +
219L ARG* 1.3 59.7 + - - +
221L HIS* 3.0 9.2 + - + +
222L LEU* 2.9 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 219 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219K ARG* 3.9 43.8 - - + +
222K LEU* 4.1 7.8 - - + +
215L VAL* 3.0 18.7 + - + +
216L GLU* 2.8 43.1 + - - +
218L LEU* 1.3 74.7 - - - +
220L GLU* 1.3 69.5 + - - +
222L LEU* 2.8 29.2 + - - +
223L THR* 2.9 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216L GLU* 2.7 65.6 + - - +
217L ILE* 3.0 16.6 + - - +
219L ARG* 1.3 81.1 - - - +
221L HIS* 1.3 65.5 + - + +
223L THR* 3.5 16.8 + - - -
224L TYR* 3.8 15.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 221 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K LYS* 5.9 4.7 - - - -
9K PRO* 5.9 0.6 - - - +
28K LEU* 6.3 3.8 - - + -
32K PHE* 4.1 26.3 - + - -
36K LEU* 5.1 17.7 - - + -
43L ILE* 5.1 3.6 - - + -
217L ILE* 2.9 43.5 + - + +
218L LEU* 3.0 17.3 + - + +
220L GLU* 1.3 81.7 - - + +
222L LEU* 1.3 62.8 - - + +
223L THR 3.2 0.7 - - - -
224L TYR* 3.3 28.3 + + + +
225L PHE* 2.9 31.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K LEU* 5.5 4.5 - - + -
40K LEU* 6.4 0.2 - - + -
215K VAL* 3.7 25.4 - - + +
218K LEU* 3.9 19.5 - - + -
219K ARG* 3.3 40.3 - - + +
222K LEU* 3.5 27.1 - - + -
218L LEU* 2.9 33.6 + - + +
219L ARG* 2.8 10.0 + - - +
221L HIS* 1.3 78.9 - - + +
223L THR* 1.3 56.4 + - - +
224L TYR 3.4 0.2 - - - -
225L PHE* 3.2 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 223 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219K ARG* 5.7 7.2 + - - +
219L ARG* 2.9 23.4 + - - +
220L GLU* 3.5 12.4 + - - -
221L HIS 3.2 0.6 - - - -
222L LEU* 1.3 75.7 - - - +
224L TYR* 1.3 56.7 + - - +
225L PHE 2.9 12.2 + - - -
226L SER* 3.3 26.0 + - - +
----------------------------------------------------------
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