Contacts of the helix formed by residues 248 - 267 (chain C) in PDB entry 4WLU
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 248 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLY* 3.4 38.6 - - - -
36C ILE* 3.9 9.3 - - - +
241C LYS* 3.1 16.5 + - - +
245C GLY* 6.1 0.9 - - - -
246C SER 3.2 14.3 + - - +
247C ALA* 1.3 72.5 - - - +
249C LEU* 1.3 75.1 + - - +
250C SER 3.5 1.1 - - - -
251C MET* 3.3 2.9 + - - +
252C ALA* 2.9 29.9 + - - +
402C NAD 3.5 17.9 - - - +
38D GLN* 4.3 5.9 + - - -
67D ASP* 3.0 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PRO* 4.1 24.2 - - + -
248C THR* 1.3 90.0 + - - +
250C SER* 1.3 58.4 + - - +
252C ALA* 3.2 5.8 + - - +
253C TYR 3.0 22.0 + - - -
38D GLN* 3.6 56.3 - - + +
39D PRO* 4.3 2.7 - - + -
42D LEU* 3.6 22.0 - - + +
64D VAL* 4.1 8.7 - - + -
67D ASP* 3.0 9.7 + - - +
68D LEU* 3.7 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C LEU* 3.6 22.3 - - - +
176C ARG* 4.9 1.0 + - - -
247C ALA* 3.8 12.0 - - - +
249C LEU* 1.3 75.6 - - - +
251C MET* 1.3 60.3 + - - +
253C TYR* 3.4 4.0 + - - +
254C ALA* 2.9 27.4 + - - +
67D ASP* 2.7 42.6 + - - -
70D HIS* 4.6 7.4 + - - +
71D ILE* 3.7 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 3.6 18.9 - - + +
140C ILE* 3.9 15.5 - - + -
169C VAL* 3.6 31.9 - - + +
172C LEU* 3.9 21.1 - - + +
247C ALA 3.8 7.6 - - - +
248C THR 3.3 8.8 + - - +
249C LEU 3.2 0.6 - - - -
250C SER* 1.3 80.4 + - - +
252C ALA* 1.3 56.0 + - - +
254C ALA* 4.3 2.7 - - + +
255C GLY* 2.7 35.6 + - - +
402C NAD 2.9 62.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 4.1 5.8 - - - +
39C PRO* 3.7 17.5 - - + +
40C LEU* 3.4 39.4 - - - +
43C LEU* 3.6 3.4 - - + +
248C THR 2.9 13.3 + - - +
249C LEU 3.4 9.4 - - - +
251C MET* 1.3 74.5 - - - +
253C TYR* 1.3 58.4 + - - +
256C ALA* 2.8 33.4 + - - +
42D LEU* 4.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 3.8 11.4 - - + +
175C VAL* 3.9 17.9 - - + -
249C LEU 3.0 12.2 + - - +
250C SER 3.4 9.9 - - - +
252C ALA* 1.3 78.0 - - - +
254C ALA* 1.3 62.1 + - - +
256C ALA* 3.5 2.0 - - + +
257C ARG* 2.9 38.3 + - + +
42D LEU* 4.4 3.8 - - + -
46D ASN* 3.5 31.6 - - + -
71D ILE* 3.9 26.7 - - + -
72D GLU* 2.7 46.7 + - + +
73D THR* 5.1 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C VAL* 4.9 0.7 - - - -
171C THR* 3.5 23.1 - - + +
172C LEU* 3.5 42.0 - - + +
175C VAL* 4.3 3.1 - - + -
250C SER 2.9 16.9 + - - +
251C MET* 3.8 7.6 - - + +
253C TYR* 1.3 80.9 - - - +
255C GLY* 1.3 57.6 - - - +
257C ARG* 3.4 2.3 + - - -
258C PHE* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 3.9 11.9 - - - -
97C VAL* 5.5 1.1 - - - +
140C ILE* 4.5 12.3 - - - -
169C VAL* 4.5 14.4 - - - -
251C MET* 2.7 22.4 + - - +
252C ALA 3.8 0.7 - - - -
254C ALA* 1.3 70.0 - - - +
256C ALA* 1.3 63.6 + - - +
258C PHE* 3.4 2.8 + - - +
259C VAL* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 3.5 11.2 - - + +
43C LEU* 3.7 30.1 - - + -
44C LEU* 4.9 3.4 - - + -
252C ALA 2.8 21.5 + - - +
253C TYR* 3.5 3.6 - - + +
255C GLY* 1.3 69.0 - - - +
257C ARG* 1.3 65.7 + - - +
259C VAL* 3.2 7.1 + - - +
260C PHE* 2.9 45.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C THR* 3.8 14.7 - - + +
174C ILE* 3.9 20.1 - - - +
175C VAL* 4.1 8.1 - - - +
178C ASN* 3.9 6.7 - - - +
193C ASN* 4.6 9.9 - - - +
253C TYR* 2.9 26.2 + - + +
254C ALA* 3.6 5.6 - - - +
256C ALA* 1.3 76.9 - - - +
258C PHE* 1.3 62.3 + - - +
260C PHE* 3.3 10.5 + - - +
261C SER* 3.0 23.9 + - - +
273C VAL 5.2 1.6 + - - -
274C GLU* 3.0 36.3 + - - +
72D GLU* 2.8 48.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C CYS* 4.0 19.7 - - + -
167C PHE* 3.6 46.7 - + + -
169C VAL* 4.3 19.1 - - + -
171C THR* 3.3 26.7 - - - +
254C ALA 3.0 12.4 + - - +
255C GLY 3.8 3.8 - - - +
256C ALA 3.3 0.2 - - - -
257C ARG* 1.3 78.4 - - - +
259C VAL* 1.3 65.2 + - + +
261C SER* 3.3 3.6 + - - -
262C LEU* 3.0 28.2 + - + +
274C GLU* 3.8 34.8 - - + -
275C CYS 4.0 1.1 - - - -
276C SER* 3.7 21.3 - - - -
294C LEU* 4.9 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 4.6 9.0 - - + -
40C LEU* 5.5 0.7 - - + -
44C LEU* 3.9 26.0 - - + -
95C VAL* 4.4 16.8 - - + -
97C VAL* 3.6 32.1 - - + -
138C CYS* 4.8 7.2 - - + -
255C GLY 3.1 15.6 + - - +
256C ALA 3.6 6.5 - - - +
258C PHE* 1.3 77.9 - - + +
260C PHE* 1.3 60.5 + - + +
262C LEU* 3.2 8.2 + - - +
263C VAL* 2.9 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 3.6 24.9 - - + -
44C LEU* 4.0 18.2 - - + -
47C SER* 3.4 25.6 - - - -
49C LEU* 3.8 26.4 - - + +
50C VAL* 4.9 3.1 - - + -
256C ALA* 2.9 38.9 + - + +
257C ARG* 3.7 8.3 - - - +
259C VAL* 1.3 76.8 - - + +
261C SER* 1.3 60.4 + - - +
263C VAL* 3.8 1.5 - - + -
264C ASP* 2.9 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C ARG* 3.0 11.2 + - - +
258C PHE 3.5 8.5 - - - -
260C PHE* 1.3 74.8 - - - +
262C LEU* 1.3 57.8 + - - +
264C ASP* 3.8 4.6 - - - +
265C ALA* 3.0 29.6 + - - +
272C VAL* 3.4 20.7 - - - +
274C GLU* 2.7 42.3 + - - +
294C LEU* 4.3 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C VAL* 4.7 6.3 - - + -
136C MET* 3.7 34.1 - - + -
138C CYS* 3.6 31.4 - - - -
167C PHE* 4.0 29.2 - - + -
258C PHE* 3.0 20.0 + - + +
259C VAL* 3.5 9.2 - - - +
261C SER* 1.3 77.8 - - - +
263C VAL* 1.3 56.4 + - + +
265C ALA* 3.4 4.2 + - + +
266C MET* 2.9 36.4 + - + +
294C LEU* 4.2 23.1 - - + +
295C GLY 5.5 0.4 - - - +
298C GLY* 4.7 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ALA* 4.0 28.5 - - + -
27C VAL* 5.0 3.1 - - + -
49C LEU* 3.8 31.0 - - + +
50C VAL* 5.8 1.8 - - + -
95C VAL* 4.3 14.1 - - + -
259C VAL* 2.9 33.9 + - + +
260C PHE* 3.9 3.6 - - + +
262C LEU* 1.3 72.2 - - - +
264C ASP* 1.3 56.7 + - - +
266C MET* 3.1 10.6 + - + +
267C ASN* 2.8 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 3.4 28.9 - - - +
260C PHE* 2.9 22.2 + - - +
261C SER* 3.8 7.1 - - - +
263C VAL* 1.3 76.0 - - - +
265C ALA* 1.3 59.3 + - - +
267C ASN* 3.1 14.4 + - - +
268C GLY 3.3 0.5 + - - -
269C LYS* 3.0 56.5 + - + +
272C VAL* 4.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C SER 3.0 17.9 + - - +
262C LEU* 3.6 5.4 - - + +
264C ASP* 1.3 75.3 - - - +
266C MET* 1.3 57.6 + - - +
268C GLY* 3.0 19.1 + - - -
269C LYS 3.9 12.1 - - - +
272C VAL* 4.3 6.8 - - + +
294C LEU* 3.6 35.7 - - + +
295C GLY* 3.5 24.7 - - - +
296C LYS* 3.6 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ALA* 6.0 1.8 - - + -
94C ASP* 3.9 37.9 - - + +
95C VAL* 4.1 13.0 - - - -
136C MET* 3.8 40.2 - - + -
262C LEU* 2.9 22.3 + - + +
263C VAL* 3.1 13.2 + - + +
265C ALA* 1.3 76.2 - - - +
267C ASN* 1.3 62.2 + - - +
268C GLY 3.2 3.6 + - - -
295C GLY 4.3 2.9 - - - +
296C LYS* 3.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ASN* 3.0 37.0 + - - +
25C ALA* 6.4 0.2 - - - +
49C LEU* 4.3 8.3 - - - +
263C VAL* 2.8 33.8 + - - +
264C ASP* 3.1 8.2 + - - +
266C MET* 1.3 75.6 + - - +
268C GLY* 1.3 58.3 + - - +
269C LYS* 3.5 2.7 + - + -
296C LYS* 4.3 5.6 + - - +
----------------------------------------------------------
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