Contacts of the helix formed by residues 237 - 256 (chain C) in PDB entry 1L9X
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 ALA 237 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C GLU* 5.5 1.3 - - - +
166C LEU* 3.8 19.1 - - + -
235C SER* 3.3 16.0 + - - +
236C HIS* 1.3 80.9 - - - +
238C PRO* 1.3 77.5 - - + +
239C ASN* 3.2 1.8 - - + +
240C ALA 2.8 12.5 + - - -
241C VAL* 3.1 9.9 + - - +
7D ALA* 6.0 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C HIS 3.6 3.1 - - - +
237C ALA* 1.3 86.0 - - + +
239C ASN* 1.3 61.4 + - - +
241C VAL* 3.2 8.6 + - + +
242C LYS* 2.9 29.0 + - - +
7D ALA 6.3 0.4 - - - +
249D GLU* 4.3 14.6 - - + +
253D ASN* 4.3 16.6 - - - +
256D ARG* 4.0 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C LEU* 3.7 21.3 - - + +
160C SER* 3.3 18.1 + - - -
164C GLU* 3.3 21.2 + - - +
166C LEU* 3.5 21.3 - - + -
237C ALA* 3.2 1.6 - - + +
238C PRO* 1.3 80.2 - - - +
240C ALA* 1.3 60.3 + - - +
242C LYS* 3.8 12.3 + - - +
243C THR* 2.8 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C LEU* 3.4 33.0 - - + +
219C TRP* 6.2 0.2 - - - -
221C PRO* 4.8 0.7 - - - +
224C ALA* 3.4 13.2 - - + +
235C SER* 3.4 37.0 - - - +
237C ALA 2.8 11.1 + - - +
239C ASN* 1.3 77.5 - - - +
241C VAL* 1.3 63.4 + - - +
243C THR* 3.5 5.7 + - - -
244C ALA* 3.2 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ALA* 3.7 29.2 - - - +
225C PRO* 4.0 11.1 - - + +
236C HIS* 4.0 11.7 - - + +
237C ALA 3.1 12.1 + - - +
238C PRO* 3.5 8.7 - - + +
240C ALA* 1.3 76.7 - - - +
242C LYS* 1.3 62.6 + - - +
244C ALA* 3.3 5.7 + - - +
245C PHE* 3.1 19.8 + - - +
42D SER 3.3 25.1 - - - +
43D ALA* 3.6 19.1 - - - +
44D GLY* 3.9 10.3 - - - +
245D PHE* 4.1 8.6 - - + -
249D GLU* 6.4 0.4 - - + -
256D ARG* 4.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C PRO* 4.2 16.7 - - - +
157C LEU* 3.9 17.3 - - + +
238C PRO 2.9 16.6 + - - +
239C ASN* 3.9 13.0 + - - +
240C ALA 3.3 0.2 - - - -
241C VAL* 1.3 74.6 - - - +
243C THR* 1.3 66.4 + - - +
245C PHE* 3.2 1.7 + - - +
246C TYR* 3.0 47.3 + - + -
152D ASN* 4.6 6.1 + - - +
154D PRO* 5.6 0.4 - - - +
245D PHE* 3.7 16.8 - - + -
246D TYR* 2.9 41.2 + - - -
249D GLU* 3.7 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C PHE* 5.7 0.4 - - + -
153C PHE* 4.2 6.3 - - + -
157C LEU* 3.7 13.9 - - - +
161C LEU* 3.5 40.7 - - + +
166C LEU 6.0 0.7 - - - -
167C THR* 5.5 0.2 - - + -
219C TRP* 3.8 33.0 - - + -
239C ASN 2.8 23.1 + - - -
240C ALA* 3.7 7.9 - - - +
242C LYS* 1.3 75.8 - - - +
244C ALA* 1.3 63.4 + - - +
246C TYR* 3.3 2.1 + - - +
247C LEU* 3.0 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TYR* 3.2 21.4 - - + -
221C PRO* 3.2 37.2 - - - +
225C PRO* 3.7 18.4 - - + -
240C ALA 3.2 7.7 + - - +
241C VAL 3.4 9.9 - - - +
242C LYS 3.2 0.4 - - - -
243C THR* 1.3 79.9 - - - +
245C PHE* 1.3 62.7 + - - +
247C LEU 3.3 1.2 + - - -
248C ALA* 2.9 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C SER* 3.5 38.8 - - - +
43C ALA* 4.3 4.0 - - - -
225C PRO* 5.5 0.2 - - - +
241C VAL 3.1 4.0 + - - +
242C LYS 3.2 5.6 + - - +
244C ALA* 1.3 80.2 - - - +
246C TYR* 1.3 69.6 + + - +
248C ALA* 3.2 4.3 + - - +
249C GLU* 2.8 59.1 + - + +
42D SER 5.6 0.2 - - - +
241D VAL* 4.0 10.5 - - + -
242D LYS* 3.7 39.3 - - + -
245D PHE* 3.6 52.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ASN* 3.3 27.6 - - + -
153C PHE* 3.5 32.4 - + + -
154C PRO* 3.6 17.6 - - + +
157C LEU* 4.1 5.8 - - + -
242C LYS* 3.0 46.5 + - + +
243C THR 3.8 0.2 - - - +
245C PHE* 1.3 87.9 - + - +
247C LEU* 1.3 58.1 + - - +
249C GLU* 3.5 15.0 + - - +
250C PHE* 3.0 27.5 + - - +
154D PRO* 4.3 4.5 - - - +
242D LYS* 4.0 24.3 + - - +
246D TYR* 2.5 43.1 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TYR* 3.3 14.4 + - - +
107C TRP* 4.2 15.9 - - + -
149C MET* 3.6 36.3 - - + +
150C PHE* 4.3 4.3 - - + -
153C PHE* 3.7 22.0 - - + -
217C VAL* 4.7 1.8 - - + -
219C TRP* 3.4 38.4 - - + -
221C PRO* 3.8 13.9 - - + -
243C THR* 3.0 21.2 + - + +
244C ALA 3.9 1.3 - - - +
246C TYR* 1.3 74.8 - - - +
248C ALA* 1.3 66.3 + - - +
250C PHE* 3.4 6.1 + - + +
251C PHE* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TYR* 3.4 45.7 + - + +
40C LEU* 5.0 3.1 - - - -
42C SER* 4.2 5.4 - - - +
43C ALA* 3.5 11.4 - - + -
244C ALA 2.9 17.9 + - - +
245C PHE 3.5 3.4 - - - +
247C LEU* 1.3 75.8 - - - +
249C GLU* 1.3 58.6 + - - +
251C PHE* 3.3 4.7 + - - +
252C VAL* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ALA* 3.6 12.9 - - + +
152C ASN* 4.8 9.1 + - - +
245C PHE* 2.8 34.8 + - + +
246C TYR* 3.6 19.9 - - - +
248C ALA* 1.3 77.9 - - - +
250C PHE* 1.3 63.8 + - - +
252C VAL* 3.8 1.9 - - - +
253C ASN* 2.9 26.9 + - + +
256C ARG* 4.5 3.9 + - - +
238D PRO* 4.2 16.0 - - + +
241D VAL* 6.0 0.6 - - + +
242D LYS* 2.7 48.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C TRP* 4.1 13.5 - + - -
148C ARG* 3.2 34.8 - - + -
149C MET* 3.7 29.6 - - + +
152C ASN* 6.0 4.7 - - - +
153C PHE* 5.8 0.2 - - + -
215C TYR* 3.4 54.5 - + - -
246C TYR 3.0 17.8 + - - +
247C LEU* 3.6 5.4 - - - +
248C ALA 3.3 0.2 - - - -
249C GLU* 1.3 77.4 - - - +
251C PHE* 1.3 67.1 + - - +
253C ASN* 3.2 10.9 + - + +
254C GLU* 3.0 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 3.7 29.2 - - + -
39C TYR* 5.7 2.0 - + + +
40C LEU* 3.7 23.8 - - + -
68C GLY 4.6 1.1 - - - -
69C ILE 3.4 31.6 - - - -
70C LEU* 4.3 5.8 - - + -
105C PRO* 3.7 36.3 - - + -
106C VAL 4.2 0.7 - - - -
107C TRP* 3.6 43.7 - + + -
215C TYR* 4.8 4.3 - + - -
247C LEU 3.1 14.6 + - - +
248C ALA* 3.7 4.3 - - - +
250C PHE* 1.3 85.1 - - - +
252C VAL* 1.3 61.4 + - - +
254C GLU* 3.0 17.0 + - + +
255C ALA* 3.1 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PRO* 3.7 25.1 - - + -
12C ILE* 4.0 14.4 - - + -
40C LEU* 4.0 9.6 - - + +
43C ALA* 3.4 35.7 - - + +
44C GLY 4.2 0.2 - - - +
45C ALA* 3.7 22.7 - - + -
248C ALA 2.9 20.7 + - - +
249C GLU 3.9 2.2 - - - +
251C PHE* 1.3 76.3 - - - +
253C ASN* 1.3 62.2 + - - +
255C ALA* 3.1 11.6 + - - +
256C ARG* 3.2 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ASN* 5.4 5.6 + - - -
249C GLU* 2.9 21.9 + - + +
250C PHE* 3.4 10.6 - - + +
252C VAL* 1.3 76.9 - - - +
254C GLU* 1.3 65.1 + - - +
256C ARG* 3.1 40.1 + - - +
257C LYS* 3.7 20.9 + - - +
238D PRO* 4.7 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C TYR* 2.6 32.7 + - + -
105C PRO* 3.7 20.5 - - + +
148C ARG* 4.9 2.0 - - - +
215C TYR* 2.5 32.1 + - + +
250C PHE* 3.0 46.0 + - + +
251C PHE* 3.0 11.1 + - - +
253C ASN* 1.3 80.4 - - - +
255C ALA* 1.3 56.3 + - - +
256C ARG 3.1 0.4 - - - -
257C LYS* 2.8 56.3 + - - +
258C ASN* 4.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PRO* 4.2 7.6 - - + +
12C ILE* 4.1 20.9 - - + -
67C ASN* 3.4 51.2 + - + +
68C GLY 4.6 0.2 - - - +
105C PRO* 3.7 7.3 - - + +
251C PHE 3.1 11.5 + - - +
252C VAL 3.1 10.0 + - - +
254C GLU* 1.3 73.8 - - - +
256C ARG* 1.3 59.1 + - - +
257C LYS 3.1 4.7 + - - -
258C ASN* 3.5 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LYS* 3.0 52.6 + - + +
10C PRO* 4.2 18.7 - - + +
43C ALA 3.5 21.8 + - - -
44C GLY* 4.2 9.3 + - - -
249C GLU* 4.5 4.8 + - - +
252C VAL* 3.2 21.0 + - - +
253C ASN* 3.1 52.0 + - - +
254C GLU 3.1 1.4 - - - -
255C ALA* 1.3 76.3 - - - +
257C LYS* 1.3 57.8 + - - +
258C ASN 3.3 3.6 - - - -
236D HIS 4.0 17.0 + - - -
238D PRO* 4.0 31.7 - - - +
241D VAL* 4.7 1.8 - - - +
----------------------------------------------------------
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