Contacts of the helix formed by residues 237 - 255 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLY 4.6 0.2 - - - +
236B GLN* 1.3 76.5 - - - +
238B PRO* 1.3 65.3 - - - +
239B TYR* 3.2 3.8 - - + +
240B MET* 3.2 30.7 + - + +
241B MET* 3.3 20.2 + - - +
279B THR* 3.0 33.4 + - - +
280B GLY* 3.9 10.2 + - - +
281B VAL 3.3 28.7 + - - +
282B ASP* 3.1 41.2 + - - +
295B LYS* 4.5 8.1 - - - +
296B MET* 6.0 3.1 - - + -
262C MET* 5.8 7.9 - - - +
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Residues in contact with PRO 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 3.2 48.0 - - + +
17B GLN* 3.8 20.6 - - + +
18B VAL* 3.4 26.7 - - + +
236B GLN* 3.1 11.7 - - + +
237B ARG* 1.3 86.3 - - - +
239B TYR* 1.3 67.8 + - - +
241B MET* 2.8 29.6 + - + +
242B GLY 3.4 3.8 + - - -
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Residues in contact with TYR 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLN* 3.0 19.7 + - - +
20B GLN* 3.5 16.8 - - + -
21B GLY* 3.3 40.5 - - - -
24B ALA* 2.9 24.7 - - + +
237B ARG* 3.2 2.8 - - + -
238B PRO* 1.3 80.8 - - - +
240B MET* 1.3 82.3 + - + +
241B MET 3.0 1.4 + - - -
242B GLY 3.4 0.7 + - - -
243B TYR* 3.1 38.0 + + - +
296B MET* 6.3 0.9 - - + -
299B LEU* 3.9 50.1 + - + +
301B ILE* 4.3 23.3 - - + -
259C ASN* 5.5 2.0 - - - -
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Residues in contact with MET 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ARG* 3.2 32.9 + - + +
238B PRO 3.2 0.6 - - - -
239B TYR* 1.3 98.8 - - + +
241B MET* 1.3 61.1 + - - +
243B TYR* 3.9 7.2 - - + -
244B LEU* 3.1 62.7 + - + +
279B THR* 4.1 12.5 - - + +
299B LEU* 6.2 1.1 - - + -
259C ASN* 3.8 28.7 - - - +
262C MET* 4.4 17.0 - - + -
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Residues in contact with MET 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 3.2 28.5 - - - +
18B VAL* 4.7 3.1 - - + -
88B LEU* 4.0 14.8 - - + -
89B ASP* 3.8 29.4 - - - +
101B ILE* 4.1 6.2 - - - +
102B GLY* 4.0 5.4 - - - -
103B THR* 3.3 30.7 - - - +
236B GLN* 4.5 1.6 - - + +
237B ARG 3.3 20.4 - - - +
238B PRO* 2.8 14.9 + - + +
240B MET* 1.3 76.8 - - - +
242B GLY* 1.3 58.3 + - - +
245B SER* 2.6 38.4 + - - -
279B THR* 3.8 24.9 - - + +
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Residues in contact with GLY 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 4.1 5.5 - - - +
22B VAL* 3.7 27.8 - - - +
88B LEU* 3.9 13.9 - - - +
238B PRO 3.4 4.2 + - - -
239B TYR 3.4 4.7 + - - -
241B MET* 1.3 76.5 - - - +
243B TYR* 1.3 66.2 + - - +
245B SER* 3.1 3.1 + - - -
246B VAL* 2.9 28.4 + - - +
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Residues in contact with TYR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY 3.4 26.5 - - - +
24B ALA* 3.5 21.7 + - + -
25B ALA* 3.5 16.5 - - + +
28B ALA* 4.1 10.7 - - - +
239B TYR* 3.1 41.3 + + + +
240B MET* 3.8 11.2 - - + +
242B GLY* 1.3 77.1 - - - +
244B LEU* 1.3 68.5 + - + +
246B VAL 3.2 0.5 + - - -
247B THR* 3.0 35.5 + - - -
255C ILE* 3.6 38.6 + - + +
259C ASN* 3.3 33.3 + - + -
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ILE* 3.9 14.1 - - + -
240B MET* 3.1 43.0 + - + +
241B MET 4.2 1.1 - - - +
243B TYR* 1.3 85.8 - - + +
245B SER* 1.3 61.1 + - - +
247B THR* 4.1 7.6 - - - +
248B VAL* 2.8 35.5 + - + +
277B ILE* 4.3 20.9 - - + -
279B THR* 4.6 7.2 - - + -
255C ILE* 4.9 0.9 - - + -
259C ASN 3.9 13.2 - - - +
262C MET* 4.2 15.3 - - + -
263C MET* 3.7 29.8 - - + -
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Residues in contact with SER 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 5.7 0.2 - - - -
6B VAL* 5.4 1.8 - - - -
62B ALA* 3.8 22.9 - - - +
86B VAL* 4.2 5.1 - - - +
88B LEU* 3.4 23.4 - - - +
101B ILE* 3.8 15.8 - - - +
241B MET 2.6 23.6 + - - -
242B GLY* 3.1 9.8 + - - -
244B LEU* 1.3 78.5 - - - +
246B VAL* 1.3 60.3 + - - +
248B VAL* 4.4 0.2 - - - +
249B LEU* 3.2 32.8 + - - +
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 3.8 23.6 - - + +
6B VAL* 4.5 9.9 - - + -
22B VAL* 3.8 34.5 - - + +
25B ALA* 3.6 18.4 - - + -
26B GLY 4.4 0.7 - - - +
29B LEU* 4.5 3.1 - - + -
31B VAL* 4.0 18.6 - - + -
33B THR* 4.4 6.7 - - + -
242B GLY 2.9 17.9 + - - +
243B TYR 3.5 6.3 - - - +
245B SER* 1.3 75.6 - - - +
247B THR* 1.3 56.0 + - - +
249B LEU* 2.9 4.9 + - - +
250B TYR* 2.7 32.9 + - - +
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Residues in contact with THR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 4.4 0.7 - - - +
29B LEU* 3.7 20.9 - - + +
243B TYR* 3.0 34.8 + - - -
244B LEU* 3.9 8.1 - - - -
246B VAL* 1.3 74.5 - - - +
248B VAL* 1.3 65.3 + - - +
250B TYR* 2.9 4.4 + - + +
251B LEU* 2.9 33.2 + - + +
251C LEU* 4.1 13.7 - - + -
255C ILE* 4.2 7.2 - - + +
263C MET* 3.7 30.7 - - + -
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL* 4.1 15.7 - - + -
99B VAL* 4.4 9.6 - - + -
101B ILE* 4.2 5.8 - - + -
244B LEU 2.8 24.9 + - - +
245B SER 4.4 0.7 - - - +
247B THR* 1.3 73.6 - - - +
249B LEU* 1.3 61.2 + - - +
251B LEU* 3.6 7.2 + - + -
252B MET* 3.3 46.4 + - + +
260B THR* 3.8 5.9 - - + +
264B LEU* 4.3 12.1 - - + -
277B ILE* 4.0 26.2 - - + -
263C MET* 4.2 17.3 - - + -
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 3.7 27.8 - - + -
60B GLY* 3.8 3.8 - - - -
61B ILE 3.5 36.1 - - - +
62B ALA* 3.7 9.2 - - + +
84B PRO* 3.2 44.8 - - + +
86B VAL* 4.0 17.7 - - + -
245B SER 3.2 22.6 + - - +
246B VAL 2.9 4.5 + - - +
248B VAL* 1.3 77.1 - - - +
250B TYR* 1.3 64.5 + - - +
252B MET* 3.5 10.9 + - - +
253B ASN* 3.0 24.5 + - - -
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Residues in contact with TYR 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 3.9 17.7 - - + -
4B ILE* 4.1 10.3 - - + +
29B LEU* 3.6 60.4 + - + -
30B GLY 5.6 0.7 - - - -
31B VAL* 4.7 10.5 - - + -
246B VAL 2.7 12.0 + - - +
247B THR* 3.2 9.2 - - + +
249B LEU* 1.3 74.6 - - - +
251B LEU* 1.3 76.1 - - + +
253B ASN* 3.0 18.5 + - - +
254B LYS* 3.0 52.3 + - + +
29C LEU* 5.3 1.8 + - + +
250C TYR* 3.3 32.5 + + - -
251C LEU* 5.7 0.7 - - + -
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B THR* 2.9 32.5 + - + +
248B VAL* 3.9 1.8 - - + +
250B TYR* 1.3 84.9 - - + +
252B MET* 1.3 58.2 + - - +
254B LYS* 4.2 4.0 - - - +
255B ILE* 2.7 42.3 + - + +
260B THR* 3.4 24.2 - - + +
263B MET* 4.0 17.7 - - + -
29C LEU* 4.8 12.6 - - + -
247C THR* 3.9 26.5 - - + -
250C TYR* 5.4 0.9 - - + -
251C LEU* 3.8 31.9 - - + -
263C MET* 4.4 2.2 - - - -
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Residues in contact with MET 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PRO* 4.3 17.4 - - + +
86B VAL* 4.4 8.1 - - + -
98B TYR* 3.9 23.1 - - + -
99B VAL* 3.6 31.2 - - + -
248B VAL* 3.3 27.2 + - + +
249B LEU* 3.8 10.1 - - - +
250B TYR 3.1 1.0 - - - -
251B LEU* 1.3 76.8 - - - +
253B ASN* 1.3 57.9 + - - +
256B GLY* 3.3 23.5 - - - -
257B VAL* 3.6 30.7 + - + +
260B THR* 3.5 24.5 - - + +
261B LEU* 4.2 9.9 - - + -
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Residues in contact with ASN 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 4.0 23.6 - - + +
4B ILE* 5.2 3.2 - - - +
59B ASN* 3.2 48.3 + - - +
60B GLY* 4.5 1.2 - - - +
84B PRO* 4.4 7.1 - - - +
249B LEU 3.0 22.8 + - - -
250B TYR* 3.0 9.7 + - - +
252B MET* 1.3 81.4 - - - +
254B LYS* 1.3 64.7 + - + +
255B ILE 3.7 0.2 - - - -
256B GLY* 4.2 2.3 + - - -
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Residues in contact with LYS 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 4.3 14.3 - - + +
250B TYR* 3.0 61.3 + - + +
251B LEU* 3.0 6.0 + - - +
253B ASN* 1.3 81.9 - - - +
255B ILE* 1.3 61.1 + - + +
256B GLY 3.5 0.2 - - - -
28C ALA* 3.6 30.9 + - - +
29C LEU* 4.2 23.5 + - + -
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Residues in contact with ILE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B LEU* 2.7 31.5 + - + +
254B LYS* 1.3 76.6 - - + +
256B GLY* 1.3 54.2 + - - +
259B ASN* 2.9 43.6 + - + +
260B THR* 3.4 22.2 - - - +
263B MET* 5.7 1.8 - - - -
28C ALA* 4.2 3.6 - - + -
29C LEU* 4.0 28.7 - - + -
243C TYR* 3.1 36.9 + - + +
244C LEU* 5.2 1.8 - - + -
247C THR* 3.9 23.8 - - + +
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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
------------------------------------------------------------
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