Contacts of the helix formed by residues 253 - 266 (chain C) in PDB entry 2QMR
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 HIS 253 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217C ILE* 4.9 4.5 - - + +
221C PHE* 3.5 44.9 - + + -
249C ARG 3.6 20.4 + - - -
250C LEU* 2.8 12.6 + - - +
252C PRO* 1.3 82.7 - - + +
254C MET* 1.3 64.8 + - - +
255C HIS 3.3 2.5 - - - -
256C ASN* 2.9 29.3 + - + +
257C ILE* 3.3 13.0 + - + +
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Residues in contact with MET 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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243C LEU* 4.0 12.8 - - + -
247C MET* 3.8 29.6 - - - -
250C LEU* 3.0 24.7 + - + +
251C LEU* 3.2 19.6 + - + +
252C PRO 3.4 1.2 + - - -
253C HIS* 1.3 76.2 - - - +
255C HIS* 1.3 59.8 + - + +
256C ASN 3.2 0.2 + - - -
257C ILE* 3.2 10.2 + - - +
258C VAL* 2.9 37.1 + - - +
279C PHE* 4.3 21.8 - - - -
283C LEU* 5.3 2.9 - - + -
288C ILE* 4.8 6.3 - - + -
292C VAL* 3.5 34.3 - - + -
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Residues in contact with HIS 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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253C HIS 3.1 1.4 + - - -
254C MET* 1.3 80.1 - - + +
256C ASN* 1.3 67.8 + - - +
258C VAL* 3.8 4.9 + - - +
259C GLU* 3.3 36.7 + - - +
291C ASP 5.5 1.7 + - - -
292C VAL* 3.8 20.6 - - + +
295C ARG* 3.6 51.5 + - + -
296C HIS* 3.2 16.4 + - - -
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Residues in contact with ASN 256 (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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221C PHE* 6.4 1.3 - - + -
252C PRO 5.6 1.0 + - - -
253C HIS* 2.9 22.2 + - + +
255C HIS* 1.3 82.2 - - - +
257C ILE* 1.3 60.4 - - + +
259C GLU* 3.5 8.7 + - - +
260C TYR* 3.0 29.5 + - - +
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Residues in contact with ILE 257 (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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221C PHE* 4.1 19.1 - - + -
239C LEU* 4.4 17.9 - - + -
250C LEU* 3.7 47.3 - - + +
253C HIS* 3.7 21.3 - - + +
254C MET* 3.2 10.7 + - - +
256C ASN* 1.3 77.9 - - + +
258C VAL* 1.3 52.2 + - - +
260C TYR* 2.9 9.0 + - - +
261C MET* 2.7 40.2 + - + +
279C PHE* 3.5 35.9 - - + -
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Residues in contact with VAL 258 (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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254C MET* 2.9 28.4 + - + +
255C HIS* 3.9 6.5 - - - +
257C ILE* 1.3 75.7 - - - +
259C GLU* 1.3 53.0 + - - +
261C MET* 4.5 1.8 - - - +
262C LEU* 2.8 39.2 + - + +
279C PHE* 4.4 11.9 - - + -
280C TRP* 3.6 20.5 - - + -
283C LEU* 4.8 0.4 - - + -
292C VAL* 3.8 26.9 - - + -
293C LEU* 4.3 6.1 - - + -
296C HIS* 3.6 41.1 - - + +
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Residues in contact with GLU 259 (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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255C HIS* 3.3 26.1 + - - +
256C ASN* 3.9 8.7 - - - +
257C ILE 3.3 0.4 - - - -
258C VAL* 1.3 78.9 - - - +
260C TYR* 1.3 61.5 + - - +
262C LEU* 3.7 12.7 - - + +
263C GLN* 3.3 26.5 + - - +
296C HIS* 3.8 22.9 - - + -
299C LYS* 6.0 2.5 - - - +
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Residues in contact with TYR 260 (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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224C ALA* 3.3 47.7 + - + -
225C GLY* 5.5 0.9 - - - -
232C ARG* 3.4 24.8 + - - +
235C VAL* 4.4 8.7 - - + +
236C CYS* 4.1 10.8 - - - -
239C LEU* 4.2 20.4 - - + -
256C ASN 3.0 14.6 + - - +
257C ILE* 2.9 10.4 + - - +
259C GLU* 1.3 74.8 - - - +
261C MET* 1.3 72.6 + - - +
263C GLN* 3.2 6.4 + - + +
264C ARG* 2.9 67.5 + - + +
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Residues in contact with MET 261 (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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236C CYS* 3.6 36.3 - - + +
239C LEU* 4.7 6.1 - - + -
240C VAL* 3.8 9.4 - - + -
257C ILE* 2.7 27.3 + - + +
258C VAL 3.9 1.3 - - - +
260C TYR* 1.3 81.8 - - + +
262C LEU* 1.3 54.1 + - - +
264C ARG* 2.9 2.3 + - - +
265C THR* 2.7 41.4 + - - -
276C ALA* 3.5 29.7 - - - +
279C PHE* 3.5 47.8 - - + -
280C TRP* 3.6 16.2 - - + -
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Residues in contact with LEU 262 (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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258C VAL* 2.8 23.7 + - + +
259C GLU* 3.7 13.2 - - + +
261C MET* 1.3 73.6 - - - +
263C GLN* 1.3 60.0 + - + +
265C THR* 3.8 8.2 + - - -
266C GLN* 3.4 28.6 + - - +
280C TRP* 3.4 10.4 - - + -
296C HIS* 4.2 18.2 - - + +
299C LYS* 3.8 35.2 - - + +
300C LEU* 3.8 46.0 - - + +
303C VAL* 4.5 6.6 - - + +
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Residues in contact with GLN 263 (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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259C GLU 3.3 15.8 + - - +
260C TYR* 3.2 7.0 + - + +
261C MET 3.2 0.6 - - - -
262C LEU* 1.3 80.3 - - + +
264C ARG* 1.3 85.5 + - - +
266C GLN* 3.7 26.3 + - - +
267C ASP* 3.7 8.7 + - - -
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Residues in contact with ARG 264 (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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232C ARG* 3.4 24.1 - - - +
236C CYS* 3.6 9.0 - - - -
260C TYR* 2.9 64.3 + - + +
261C MET* 2.9 3.8 + - - +
263C GLN* 1.3 102.3 + - - +
265C THR* 1.3 61.7 + - - +
266C GLN 3.1 2.2 - - - -
267C ASP* 2.4 60.2 + - - +
272C VAL* 4.1 6.6 - - + +
273C ALA* 3.4 10.7 + - - -
276C ALA* 3.4 20.8 - - + +
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Residues in contact with THR 265 (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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261C MET 2.7 24.3 + - - -
262C LEU* 4.0 7.2 - - - -
263C GLN 3.4 0.2 - - - -
264C ARG* 1.3 72.4 - - - +
266C GLN* 1.3 57.6 + - - +
267C ASP 3.4 0.2 - - - -
273C ALA* 3.5 18.3 - - - +
276C ALA* 3.8 12.2 - - - +
277C CYS* 4.0 22.7 - - + -
280C TRP* 2.6 35.9 + - + +
303C VAL* 3.8 21.7 - - + +
304C LEU* 5.1 3.1 - - + -
375C LEU* 4.6 11.5 - - + +
379C SER* 5.6 0.7 - - - +
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Residues in contact with GLN 266 (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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262C LEU* 3.4 23.8 + - - +
263C GLN* 3.7 25.4 + - - +
264C ARG 3.1 0.4 - - - -
265C THR* 1.3 77.5 - - - +
267C ASP* 1.3 63.2 + - - +
268C GLN* 3.9 3.1 + - - +
273C ALA* 5.1 0.2 - - - -
303C VAL* 3.5 34.2 - - + +
306C ASN* 6.3 1.3 - - - +
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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