Contacts of the helix formed by residues 237 - 255 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B MET* 5.7 5.1 - - - -
236C GLN* 1.3 81.1 - - - +
238C PRO* 1.3 67.1 - - - +
239C TYR* 3.2 2.7 - - - -
240C MET* 3.0 24.4 + - + +
241C MET* 3.2 18.8 + - - +
279C THR* 3.0 45.0 + - - +
280C GLY* 3.7 16.4 + - - +
281C VAL 4.6 4.4 + - - +
282C ASP* 3.0 37.2 + - - +
295C LYS* 4.2 13.9 - - - +
296C MET* 3.9 12.0 - - - +
299C LEU* 4.1 18.7 - - - +
301C ILE* 3.5 28.7 - - + +
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Residues in contact with PRO 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C TYR* 3.3 26.5 - - + +
17C GLN* 3.1 34.8 - - + +
18C VAL* 3.5 33.4 - - + +
216C ASP* 5.5 0.4 - - + +
217C THR* 6.0 1.3 - - - +
236C GLN* 3.5 8.1 - - + +
237C ARG* 1.3 87.5 - - - +
239C TYR* 1.3 66.7 + - + +
241C MET* 3.1 15.7 + - + +
242C GLY 3.1 18.5 + - - -
301C ILE* 5.9 2.5 - - + -
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Residues in contact with TYR 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ASN* 5.1 4.6 + - - -
17C GLN* 3.5 20.2 + - + +
20C GLN* 3.8 22.2 - - + -
21C GLY* 3.4 15.6 - - - -
24C ALA* 3.5 18.4 - - + +
238C PRO* 1.3 82.6 - - + +
240C MET* 1.3 75.1 + - - +
242C GLY 3.4 0.5 + - - -
243C TYR* 2.9 50.5 + + - +
300C GLY 4.2 15.0 + - - -
301C ILE* 3.9 23.6 - - + -
302C PRO* 3.3 37.9 - - + +
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Residues in contact with MET 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ASN* 4.1 21.8 - - - +
262B MET* 4.1 20.9 - - + -
237C ARG* 3.0 20.3 + - + +
239C TYR* 1.3 90.4 - - + +
241C MET* 1.3 67.5 + - - +
243C TYR* 4.3 6.5 - - + +
244C LEU* 2.9 66.8 + - + +
279C THR* 4.4 13.5 - - + +
299C LEU* 5.4 4.0 - - + +
301C ILE* 4.2 26.0 - - + -
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Residues in contact with MET 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C TYR* 3.5 26.2 - - - +
18C VAL* 5.2 3.1 - - + -
88C LEU* 4.0 14.4 - - + -
89C ASP* 3.7 26.9 - - - -
101C ILE* 4.1 17.7 - - - +
102C GLY* 4.2 2.9 - - - -
103C THR* 3.5 27.6 - - - +
236C GLN* 3.5 20.6 - - + +
237C ARG 3.2 16.0 + - - +
238C PRO* 3.1 8.9 + - + +
240C MET* 1.3 76.5 - - - +
242C GLY* 1.3 61.1 + - - +
245C SER* 2.9 32.3 + - - -
279C THR* 3.8 19.7 - - + +
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Residues in contact with GLY 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C VAL* 3.7 28.0 - - - +
22C VAL* 3.7 16.7 - - - +
88C LEU* 4.5 3.6 - - - -
238C PRO 3.1 10.1 + - - -
239C TYR 3.7 0.7 - - - -
241C MET* 1.3 78.4 - - - +
243C TYR* 1.3 64.5 + - - +
244C LEU 3.3 0.2 + - - -
245C SER* 3.5 2.8 - - - -
246C VAL* 3.4 23.2 + - - +
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Residues in contact with TYR 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B ILE* 3.1 52.0 + - + +
259B ASN* 3.3 26.6 + - + -
21C GLY 3.7 4.7 - - - +
24C ALA* 3.9 5.2 - - + -
25C ALA* 3.4 38.7 - - + +
28C ALA* 3.5 12.5 - - - +
239C TYR* 2.9 49.0 + + + +
240C MET* 3.4 10.7 + - + +
242C GLY* 1.3 75.5 - - - +
244C LEU* 1.3 64.6 + - + +
247C THR* 2.6 39.1 + - - -
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Residues in contact with LEU 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B ILE* 5.2 1.3 - - + -
259B ASN* 3.5 24.5 - - + +
262B MET* 3.8 25.1 - - + +
263B MET* 4.4 12.8 - - + -
101C ILE* 3.8 16.8 - - + -
240C MET* 2.9 46.4 + - + +
243C TYR* 1.3 83.2 - - + +
245C SER* 1.3 58.0 + - - +
247C THR* 3.0 8.6 + - - +
248C VAL* 2.6 39.5 + - + +
277C ILE* 4.1 21.5 - - + -
279C THR* 4.9 2.7 - - + -
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Residues in contact with SER 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 5.6 0.2 - - - -
6C VAL* 5.7 2.5 - - - -
62C ALA* 3.7 21.9 - - - +
86C VAL* 4.2 2.9 - - - +
88C LEU* 3.5 24.1 - - - +
101C ILE* 3.4 21.6 - - - +
241C MET 2.9 22.9 + - - -
242C GLY* 3.5 5.6 - - - -
244C LEU* 1.3 76.3 - - - +
246C VAL* 1.3 63.1 + - - -
248C VAL* 3.4 1.4 + - - +
249C LEU* 3.1 31.2 + - - +
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Residues in contact with VAL 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 3.9 30.0 - - + +
6C VAL* 4.6 4.3 - - + -
22C VAL* 3.8 34.5 - - + +
25C ALA* 3.7 19.1 - - + -
26C GLY* 4.0 10.5 - - - +
29C LEU* 4.4 5.2 - - + -
31C VAL* 4.1 13.7 - - + -
33C THR* 4.3 7.4 - - + -
242C GLY 3.4 13.8 + - - +
244C LEU 3.3 0.4 - - - -
245C SER* 1.3 74.1 - - - +
247C THR* 1.3 56.7 + - - +
249C LEU* 3.1 3.1 + - - +
250C TYR* 2.7 35.6 + - - +
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Residues in contact with THR 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU* 3.9 19.5 - - + -
255B ILE* 3.9 24.1 - - + +
263B MET* 4.4 9.4 - - - -
25C ALA* 4.4 0.3 - - - +
29C LEU* 3.9 20.2 - - + +
243C TYR* 2.6 37.6 + - - -
244C LEU* 3.0 11.4 + - + -
246C VAL* 1.3 79.6 - - - +
248C VAL* 1.3 61.7 + - - +
250C TYR* 3.5 1.4 + - + +
251C LEU* 3.1 34.5 + - + +
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Residues in contact with VAL 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B MET* 4.4 15.7 - - + -
86C VAL* 4.4 8.1 - - + -
99C VAL* 4.4 11.9 - - + -
101C ILE* 4.1 9.2 - - + -
244C LEU 2.6 22.5 + - - +
245C SER 3.9 2.9 - - - +
247C THR* 1.3 72.7 - - - +
249C LEU* 1.3 58.0 + - - +
251C LEU* 3.2 10.2 + - - +
252C MET* 2.9 53.6 + - + +
260C THR* 3.8 9.3 - - + +
264C LEU* 4.5 7.0 - - + -
277C ILE* 4.1 26.2 - - + -
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Residues in contact with LEU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ILE* 3.9 28.5 - - + -
60C GLY* 4.0 3.4 - - - -
61C ILE 3.6 31.0 - - - +
62C ALA* 3.7 13.0 - - + +
84C PRO* 3.1 39.0 - - + +
86C VAL* 3.7 25.6 - - + -
245C SER 3.1 20.3 + - - +
246C VAL 3.7 2.5 - - - +
248C VAL* 1.3 73.1 - - - +
250C TYR* 1.3 67.7 + - - +
252C MET* 3.2 15.7 + - - +
253C ASN* 3.2 17.2 + - - -
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Residues in contact with TYR 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 5.6 1.2 + - - +
250B TYR* 3.3 32.1 + + - -
251B LEU* 5.4 1.3 - - + -
2C LEU* 4.6 9.9 - - + -
4C ILE* 3.8 10.6 - - + +
29C LEU* 3.5 61.7 + - + -
30C GLY 4.8 2.9 - - - -
31C VAL* 4.4 15.9 - - + -
246C VAL* 2.7 22.0 + - + +
247C THR 3.6 4.9 - - - +
249C LEU* 1.3 71.6 - - - +
251C LEU* 1.3 74.7 + - + +
253C ASN* 3.0 16.7 + - - +
254C LYS* 3.1 52.7 + - + +
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Residues in contact with LEU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 4.6 13.0 - - + -
247B THR* 4.1 22.4 - - + -
250B TYR* 5.7 0.4 - - + -
251B LEU* 3.8 23.6 - - + -
263B MET* 3.8 23.3 - - + -
247C THR* 3.1 18.1 + - + +
248C VAL* 3.3 9.2 - - - +
250C TYR* 1.3 85.1 - - + +
252C MET* 1.3 60.2 + - - +
253C ASN 3.1 0.2 + - - -
254C LYS* 4.4 2.2 - - - +
255C ILE* 2.8 44.0 + - + +
260C THR* 3.2 14.1 - - + +
263C MET* 3.7 20.9 - - + -
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Residues in contact with MET 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C PRO* 4.1 23.9 - - + +
86C VAL* 4.4 8.1 - - + -
98C TYR* 3.5 44.0 - - + -
99C VAL* 4.1 2.2 - - + -
248C VAL* 2.9 37.1 + - + +
249C LEU* 3.2 12.1 + - - +
251C LEU* 1.3 75.3 - - - +
253C ASN* 1.3 58.9 + - - +
256C GLY* 3.0 25.3 + - - -
257C VAL* 3.6 25.2 + - + +
260C THR* 3.2 12.7 + - + -
261C LEU* 3.8 21.5 - - + -
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Residues in contact with ASN 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C LEU* 3.5 32.3 - - + +
4C ILE* 5.7 1.8 - - - +
59C ASN* 3.2 40.7 + - - +
84C PRO* 4.4 8.3 - - - +
249C LEU 3.2 15.3 + - - +
250C TYR* 3.0 9.0 + - - +
251C LEU 3.0 0.6 - - - -
252C MET* 1.3 79.6 - - - +
254C LYS* 1.3 65.8 + - + +
255C ILE 3.6 0.2 + - - -
256C GLY* 4.3 1.9 + - - -
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Residues in contact with LYS 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ALA* 3.2 41.3 + - - +
29B LEU* 4.0 19.9 + - + +
2C LEU* 4.4 16.5 - - + +
250C TYR* 3.1 55.7 + - + +
251C LEU* 4.1 3.8 - - - +
253C ASN* 1.3 80.4 - - - +
255C ILE* 1.3 58.8 + - - +
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Residues in contact with ILE 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ALA 5.5 0.2 - - - +
28B ALA* 4.5 2.5 - - + -
29B LEU* 3.7 29.4 - - + -
243B TYR* 3.6 31.7 + - + +
244B LEU* 4.9 2.0 - - + -
247B THR* 4.2 16.2 - - + +
251C LEU* 2.8 23.4 + - + +
254C LYS* 1.3 79.0 - - + +
256C GLY* 1.3 59.5 + - - +
259C ASN* 3.5 29.9 + - + +
260C THR* 3.4 29.8 - - - +
263C MET* 3.9 20.2 - - + -
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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
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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) + - + + + + + -
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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