Contacts of the helix formed by residues 237 - 255 (chain D) in PDB entry 3C6Q
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 ARG 237 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D GLN* 1.3 80.7 - - - +
238D PRO* 1.3 66.8 - - - +
239D TYR* 3.3 2.5 - - - -
240D MET* 3.0 23.8 + - + +
241D MET* 3.2 18.6 + - - +
279D THR* 3.0 44.8 + - - +
280D GLY* 3.7 16.8 + - - +
281D VAL 4.6 4.0 + - - +
282D ASP* 3.0 37.6 + - - +
295D LYS* 4.2 13.7 - - - +
296D MET* 3.8 12.0 - - - +
299D LEU* 4.0 18.5 - - - +
301D ILE* 3.5 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D TYR* 3.3 26.5 - - + +
17D GLN* 3.2 34.8 - - + +
18D VAL* 3.5 32.6 - - + +
216D ASP* 5.5 0.4 - - + +
217D THR* 5.9 1.6 - - - +
236D GLN* 3.5 7.9 - - + +
237D ARG* 1.3 87.6 - - - +
239D TYR* 1.3 66.3 + - + +
241D MET* 3.1 16.3 + - + +
242D GLY 3.1 18.2 + - - -
301D ILE* 5.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLN* 3.4 21.1 + - + +
20D GLN* 3.8 21.3 - - + -
21D GLY* 3.4 16.2 - - - -
24D ALA* 3.5 18.3 - - + +
237D ARG 4.9 0.2 - - - -
238D PRO* 1.3 82.3 - - + +
240D MET* 1.3 74.6 + - - +
242D GLY 3.4 0.5 + - - -
243D TYR* 3.0 50.5 + + - +
300D GLY 4.2 15.3 + - - -
301D ILE* 3.9 22.2 - - + -
302D PRO* 3.2 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D ARG* 3.0 20.2 + - + +
239D TYR* 1.3 92.4 - - + +
241D MET* 1.3 68.2 + - - +
243D TYR* 4.3 7.4 - - + +
244D LEU* 2.9 67.2 + - + +
279D THR* 4.4 14.6 - - + +
299D LEU* 5.5 5.6 - - + +
301D ILE* 4.1 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D TYR* 3.5 26.2 - - - +
18D VAL* 5.2 3.4 - - + -
88D LEU* 4.0 14.4 - - + -
89D ASP* 3.7 26.7 - - - -
101D ILE* 4.1 18.4 - - - +
102D GLY* 4.3 2.5 - - - -
103D THR* 3.4 27.4 - - - +
236D GLN* 3.5 20.0 - - + +
237D ARG 3.2 16.7 + - - +
238D PRO* 3.1 8.7 + - + +
240D MET* 1.3 75.9 - - - +
242D GLY* 1.3 61.6 + - - +
245D SER* 2.9 32.2 + - - -
279D THR* 3.8 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D VAL* 3.7 27.6 - - - +
22D VAL* 3.7 17.1 - - - +
88D LEU* 4.3 4.2 - - - +
238D PRO 3.1 7.7 + - - -
239D TYR 3.8 0.7 - - - -
241D MET* 1.3 82.3 - - - +
243D TYR* 1.3 61.5 + - - +
244D LEU 3.4 0.2 + - - -
245D SER* 3.5 2.6 - - - -
246D VAL* 3.4 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D GLY 3.7 4.9 - - - +
24D ALA* 3.9 5.2 - - + -
25D ALA* 3.4 41.2 - - + +
28D ALA* 3.5 23.4 - - + +
29D LEU* 6.0 2.7 - - + -
239D TYR* 3.0 50.2 + + + +
240D MET* 3.4 13.4 + - + +
242D GLY* 1.3 75.8 - - - +
244D LEU* 1.3 65.0 + - + +
247D THR* 2.6 45.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D ILE* 3.8 17.5 - - + -
240D MET* 2.9 50.8 + - + +
243D TYR* 1.3 84.0 - - + +
245D SER* 1.3 57.6 + - - +
247D THR* 2.9 10.0 + - + +
248D VAL* 2.6 39.5 + - + +
277D ILE* 4.1 31.4 - - + -
279D THR* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 5.6 0.2 - - - -
6D VAL* 5.7 2.5 - - - -
62D ALA* 3.7 22.0 - - - +
86D VAL* 4.2 2.4 - - - +
88D LEU* 3.5 23.3 - - - +
101D ILE* 3.4 21.2 - - - +
241D MET 2.9 23.4 + - - -
242D GLY* 3.5 6.3 - - - -
244D LEU* 1.3 76.1 - - - +
246D VAL* 1.3 63.1 + - - -
248D VAL* 3.5 1.2 + - - +
249D LEU* 3.1 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 3.8 29.3 - - + +
6D VAL* 4.7 4.7 - - + -
22D VAL* 3.8 34.8 - - + +
25D ALA* 3.7 19.1 - - + -
26D GLY* 4.0 10.8 - - - +
29D LEU* 4.4 5.4 - - + -
31D VAL* 4.2 13.5 - - + -
33D THR* 4.3 7.6 - - + -
242D GLY 3.4 13.4 + - - +
244D LEU 3.3 0.4 - - - -
245D SER* 1.3 73.5 - - - +
247D THR* 1.3 55.2 + - - +
249D LEU* 3.1 3.1 + - - +
250D TYR* 2.7 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ALA* 4.4 0.5 - - - +
29D LEU* 3.9 26.8 - - + +
243D TYR* 2.6 39.7 + - + -
244D LEU* 2.9 16.3 + - + +
246D VAL* 1.3 79.2 - - - +
248D VAL* 1.3 63.0 + - - +
250D TYR* 3.5 1.7 + - + +
251D LEU* 3.1 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D VAL* 4.4 7.9 - - + -
99D VAL* 4.4 11.9 - - + -
101D ILE* 4.1 8.7 - - + -
244D LEU* 2.6 23.8 + - + +
245D SER 4.0 3.1 - - - +
247D THR* 1.3 73.4 - - - +
249D LEU* 1.3 58.4 + - - +
251D LEU* 3.2 12.5 + - + +
252D MET* 2.9 54.3 + - + +
260D THR* 3.8 9.0 - - + +
264D LEU* 4.5 12.3 - - + -
277D ILE* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 3.9 28.3 - - + -
60D GLY* 4.0 3.1 - - - -
61D ILE 3.6 31.2 - - - +
62D ALA* 3.7 13.0 - - + +
84D PRO* 3.1 39.3 - - + +
86D VAL* 3.7 25.8 - - + -
245D SER 3.1 21.2 + - - +
246D VAL 3.7 2.5 - - - +
248D VAL* 1.3 72.7 - - - +
250D TYR* 1.3 68.0 + - - +
252D MET* 3.1 15.2 + - - +
253D ASN* 3.2 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU* 4.6 10.1 - - + -
4D ILE* 3.7 10.8 - - + +
29D LEU* 3.5 65.0 + - + +
30D GLY 4.8 2.9 - - - -
31D VAL* 4.3 16.6 - - + -
246D VAL* 2.7 22.0 + - + +
247D THR* 3.6 3.8 - - + +
249D LEU* 1.3 72.0 - - - +
251D LEU* 1.3 75.9 + - + +
253D ASN* 3.0 16.5 + - - +
254D LYS* 3.1 52.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D THR* 3.1 30.8 + - + +
248D VAL* 3.3 12.6 - - + +
250D TYR* 1.3 89.8 - - + +
252D MET* 1.3 60.4 + - - +
253D ASN 3.1 0.2 + - - -
254D LYS* 4.4 4.9 - - + +
255D ILE* 2.8 56.1 + - + +
260D THR* 3.2 14.8 - - + +
263D MET* 3.7 24.2 - - + -
264D LEU* 6.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D PRO* 4.2 24.8 - - + +
86D VAL* 4.4 7.4 - - + -
98D TYR* 3.5 44.6 - - + -
99D VAL* 4.1 2.5 - - + -
248D VAL* 2.9 37.1 + - + +
249D LEU* 3.1 11.4 + - - +
251D LEU* 1.3 75.7 - - - +
253D ASN* 1.3 59.2 + - - +
256D GLY* 3.0 25.3 + - - -
257D VAL* 3.6 24.7 + - + +
260D THR* 3.2 12.7 + - + -
261D LEU* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU* 3.5 32.0 - - + +
4D ILE* 5.7 1.8 - - - +
59D ASN* 3.2 41.1 + - - +
60D GLY* 5.0 0.2 - - - -
84D PRO* 4.4 8.5 - - - +
249D LEU 3.2 14.3 + - - -
250D TYR* 3.0 9.2 + - - +
251D LEU 3.0 0.4 - - - -
252D MET* 1.3 79.2 - - - +
254D LYS* 1.3 65.9 + - - +
255D ILE 3.6 0.2 + - - -
256D GLY* 4.3 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU* 4.4 16.3 - - + +
250D TYR* 3.1 57.7 + - + +
251D LEU* 4.1 6.5 - - + +
253D ASN* 1.3 80.8 - - - +
255D ILE* 1.3 66.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D LEU* 2.8 31.7 + - + +
254D LYS* 1.3 83.7 - - + +
256D GLY* 1.3 59.5 + - - +
259D ASN* 3.5 34.6 + - + +
260D THR* 3.4 28.3 - - - +
263D MET* 3.9 21.8 - - + -
----------------------------------------------------------
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