Contacts of the helix formed by residues 234 - 250 (chain C) in PDB entry 6Q3W
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 SER 234 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230C SER 4.3 2.5 + - - -
231C LEU 2.4 30.8 + - - -
232C ALA 3.0 0.4 - - - +
233C SER* 1.3 81.4 - - - +
235C GLU* 1.3 63.0 + - - +
237C PRO* 3.2 17.6 - - - +
238C VAL* 3.8 10.0 + - - +
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Residues in contact with GLU 235 (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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231C LEU* 3.8 20.6 - - + +
232C ALA 3.4 4.0 - - - +
234C SER* 1.3 83.4 + - - +
236C TYR* 1.3 65.8 + - - +
238C VAL* 3.0 22.3 + - - +
239C ARG* 2.8 53.7 + - - +
348C PHE* 3.4 32.5 - - + -
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Residues in contact with TYR 236 (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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44C HIS* 3.6 31.9 - + - -
46C ASP* 4.3 2.4 + - - -
47C TYR* 3.3 24.7 + + - -
180C MET* 3.9 25.4 - - + -
181C PRO* 3.3 28.0 - - + -
182C CYS* 3.6 6.8 - - + +
183C GLY 3.4 16.8 + - - -
232C ALA 3.4 13.9 + - - +
233C SER 4.6 1.6 - - - +
235C GLU* 1.3 77.4 - - - +
237C PRO* 1.4 71.3 - - + +
239C ARG* 3.3 17.4 + - - +
240C ARG* 3.3 20.7 + - + +
346C GLY* 4.9 13.7 - - - -
348C PHE* 4.5 6.3 - + + -
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Residues in contact with PRO 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C MET* 5.6 0.4 - - + -
181C PRO* 4.2 27.4 - - + -
233C SER 3.4 18.6 - - - +
234C SER* 3.2 17.9 - - - +
236C TYR* 1.4 94.8 - - + +
238C VAL* 1.3 60.3 + - - +
240C ARG* 3.1 8.6 + - + +
241C ARG* 3.1 23.4 + - - +
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Residues in contact with VAL 238 (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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234C SER 3.8 7.7 + - - +
235C GLU* 3.0 23.1 + - - +
237C PRO* 1.3 78.4 - - - +
239C ARG* 1.3 73.6 + - - +
241C ARG* 3.5 6.2 + - - +
242C GLN* 3.2 32.7 + - - +
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Residues in contact with ARG 239 (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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44C HIS* 5.0 1.1 - - + +
47C TYR* 3.8 4.7 - - - +
235C GLU* 2.8 48.9 + - - +
236C TYR* 3.6 10.3 - - - +
237C PRO 3.2 0.2 - - - -
238C VAL* 1.3 82.0 - - - +
240C ARG* 1.3 62.2 + - - +
242C GLN* 3.4 36.4 + - - +
243C CYS* 3.3 19.8 + - - -
277C ARG* 5.4 3.4 - - - +
318C TYR* 2.8 61.2 + - + +
319C GLU* 3.1 33.9 + - - +
320C VAL* 3.9 11.6 - - + +
348C PHE* 4.8 1.8 - - - -
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Residues in contact with ARG 240 (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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47C TYR* 3.5 63.1 + - + +
171C GLN* 5.1 1.2 - - - +
175C HIS* 4.1 9.3 - - - -
181C PRO* 2.9 40.9 + - - +
182C CYS 3.6 13.7 + - - -
183C GLY* 4.7 0.6 - - - -
236C TYR* 3.3 15.8 + - + +
237C PRO* 3.1 10.2 + - + +
239C ARG* 1.3 78.8 - - - +
241C ARG* 1.3 62.1 + - - +
243C CYS* 3.1 15.1 + - - +
244C GLU* 3.2 12.5 + - - +
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Residues in contact with ARG 241 (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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237C PRO 3.1 14.6 + - - +
238C VAL* 3.9 7.9 - - - +
239C ARG 3.4 0.4 - - - -
240C ARG* 1.3 76.8 - - - +
242C GLN* 1.3 63.6 + - + +
244C GLU* 3.3 9.1 + - - +
245C GLU* 3.1 22.4 + - - +
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Residues in contact with GLN 242 (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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238C VAL* 3.2 20.8 + - - +
239C ARG* 3.7 34.5 - - - +
240C ARG 3.2 0.4 - - - -
241C ARG* 1.3 78.8 - - - +
243C CYS* 1.3 56.6 + - - +
245C GLU* 3.2 7.3 + - - +
246C VAL* 2.9 36.0 + - + +
273C GLU* 3.9 32.5 + - - +
277C ARG* 3.6 28.0 - - + +
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Residues in contact with CYS 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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47C TYR* 4.3 2.9 - - + -
48C ASN* 3.2 35.9 - - - +
239C ARG 3.3 16.6 - - - -
240C ARG 3.1 7.5 + - - +
242C GLN* 1.3 75.3 - - - +
244C GLU* 1.3 58.9 + - - +
246C VAL* 3.2 7.2 + - - +
247C ALA* 2.9 33.4 + - - +
255C LEU* 4.3 19.3 - - + +
277C ARG* 5.4 6.5 - - - -
281C VAL* 5.4 1.1 - - - -
318C TYR* 3.9 18.8 - - - -
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Residues in contact with GLU 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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240C ARG 3.2 8.9 + - - +
241C ARG* 3.3 12.5 + - - +
243C CYS* 1.3 77.9 - - - +
245C GLU* 1.3 57.1 + - - +
247C ALA* 3.8 5.1 + - - +
248C ARG* 3.1 28.1 + - - +
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Residues in contact with GLU 245 (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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241C ARG 3.1 11.6 + - - +
242C GLN* 3.5 11.0 - - - +
243C CYS 3.1 0.4 - - - -
244C GLU* 1.3 76.9 - - - +
246C VAL* 1.3 65.5 + - + +
248C ARG* 3.3 7.2 + - - +
249C ALA* 3.1 23.0 + - - +
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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
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242C GLN* 2.9 25.2 + - + +
243C CYS* 3.7 6.7 - - - +
245C GLU* 1.3 77.2 - - + +
247C ALA* 1.3 63.5 + - - +
249C ALA* 3.0 14.5 + - - +
250C LEU* 3.1 37.4 + - + +
255C LEU* 4.1 11.2 - - + -
270C VAL* 4.8 17.9 - - + -
273C GLU 5.4 6.7 - - - +
275C PHE* 5.6 5.8 - - + -
277C ARG* 5.9 1.6 - - + -
278C ALA* 3.7 34.3 - - + +
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Residues in contact with ALA 247 (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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243C CYS 2.9 16.6 + - - +
244C GLU* 4.0 5.4 - - - +
246C VAL* 1.3 78.8 - - - +
248C ARG* 1.3 61.3 + - - +
250C LEU* 3.3 3.1 + - - +
251C GLY 3.2 3.1 + - - -
252C ALA* 2.8 44.6 + - - +
253C ALA 4.5 2.5 - - - +
254C SER* 4.1 28.5 - - - +
255C LEU* 4.6 7.6 - - + +
258C VAL* 5.5 0.2 - - - -
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Residues in contact with ARG 248 (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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244C GLU 3.1 20.0 + - - +
245C GLU* 3.6 8.3 - - - +
246C VAL 3.2 0.2 - - - -
247C ALA* 1.3 77.2 - - - +
249C ALA* 1.3 61.2 + - - +
250C LEU 3.5 0.3 + - - -
251C GLY* 3.8 7.7 + - - -
252C ALA 4.5 3.4 - - - -
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Residues in contact with ALA 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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245C GLU 3.1 12.1 + - - +
246C VAL* 3.0 11.5 + - - +
248C ARG* 1.3 77.6 - - - +
250C LEU* 1.3 70.8 + - + +
251C GLY 3.5 0.2 - - - -
269C LEU* 4.2 26.5 - - - +
270C VAL* 5.0 4.0 - - + -
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Residues in contact with LEU 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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246C VAL* 3.1 38.5 + - + +
247C ALA* 3.3 4.5 + - - +
248C ARG 3.3 0.4 - - - -
249C ALA* 1.3 88.3 - - + +
251C GLY* 1.3 57.7 + - - +
252C ALA* 3.1 7.7 + - - +
258C VAL* 3.8 40.6 - - + -
262C GLU* 5.3 1.8 - - + +
263C LEU* 4.9 12.6 - - + -
266C ALA* 4.9 15.9 - - + +
269C LEU* 4.9 12.8 - - + -
270C VAL* 4.9 6.7 - - + -
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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
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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