Contacts of the helix formed by residues 247 - 258 (chain B) in PDB entry 1QAS
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 GLY 247 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234B VAL* 3.4 25.7 - - - +
237B LEU* 4.8 2.1 - - - +
245B GLU* 3.0 13.4 + - - +
246B ALA* 1.3 77.0 - - - +
248B PRO* 1.3 71.6 - - - +
249B ALA 3.1 0.2 + - - -
250B LEU* 3.9 1.9 - - - +
251B ALA 3.3 13.5 + - - -
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Residues in contact with PRO 248 (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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230B VAL* 4.0 13.0 - - + +
234B VAL* 3.9 17.7 - - + -
246B ALA 4.2 0.4 - - - +
247B GLY* 1.3 82.0 - - - +
249B ALA* 1.3 52.4 + - + +
251B ALA* 3.4 2.5 - - + +
252B LEU* 2.7 49.4 + - + +
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Residues in contact with ALA 249 (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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246B ALA* 2.8 21.1 + - + +
248B PRO* 1.3 79.1 - - + +
250B LEU* 1.3 50.3 + - - +
252B LEU* 3.1 8.8 + - - +
253B SER* 2.5 41.1 + - - +
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Residues in contact with LEU 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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237B LEU* 4.0 9.6 - - + -
243B GLU* 4.1 20.2 - - + +
244B GLU 5.2 0.2 - - - -
245B GLU* 3.5 18.8 - - + -
246B ALA* 2.7 49.3 + - + +
247B GLY 3.9 2.0 - - - +
249B ALA* 1.3 69.6 - - - +
251B ALA* 1.3 55.9 + - - +
253B SER* 2.8 31.2 + - - +
254B LEU* 2.9 43.1 + - + +
257B ARG* 5.9 1.1 - - - +
283B ASP* 5.4 4.5 - - - +
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Residues in contact with ALA 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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230B VAL* 3.8 15.9 - - + +
233B LEU* 4.0 11.7 - - + +
234B VAL* 3.6 20.4 - - + -
237B LEU* 3.9 14.5 - - + +
247B GLY 3.3 11.4 + - - +
248B PRO 3.4 9.6 - - - +
250B LEU* 1.3 79.8 - - - +
252B LEU* 1.3 61.1 + - - +
254B LEU* 3.5 2.7 + - - +
255B ILE* 3.2 30.9 + - - +
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Residues in contact with LEU 252 (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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230B VAL* 3.5 29.2 - - + -
248B PRO* 2.7 36.9 + - + +
249B ALA* 3.6 6.1 - - - +
251B ALA* 1.3 74.2 - - - +
253B SER* 1.3 57.6 + - - +
255B ILE* 3.9 7.3 - - + +
256B GLU* 3.0 30.3 + - - +
268B ARG* 3.3 50.9 - - + +
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Residues in contact with SER 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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249B ALA* 2.5 28.7 + - - +
250B LEU* 2.8 17.1 + - - +
252B LEU* 1.3 70.7 - - - +
254B LEU* 1.3 59.9 + - - -
256B GLU* 3.4 5.1 + - - +
257B ARG* 2.9 52.7 + - - +
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Residues in contact with LEU 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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233B LEU* 4.7 4.9 - - + -
237B LEU* 4.1 21.5 - - + -
250B LEU* 2.9 52.2 + - + +
251B ALA* 4.0 3.6 - - - +
253B SER* 1.3 76.6 - - - +
255B ILE* 1.3 55.3 + - - +
257B ARG* 3.6 23.6 - - - +
258B TYR* 2.7 55.7 + - + +
270B MET* 3.9 14.7 - - + +
278B TYR* 3.7 22.9 - - + -
283B ASP* 4.0 9.4 - - - +
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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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228B LEU 5.3 0.2 - - - +
230B VAL* 3.7 21.1 - - + +
233B LEU* 4.3 8.7 - - + -
251B ALA 3.2 18.0 + - - +
252B LEU* 3.9 7.9 - - + +
253B SER 3.2 0.2 - - - -
254B LEU* 1.3 73.6 - - - +
256B GLU* 1.3 67.8 + - - +
259B GLU* 3.0 38.3 + - + +
265B LYS* 3.8 21.9 - - + +
268B ARG* 3.7 26.9 - - - +
269B GLN* 3.5 26.0 - - - +
270B MET* 4.2 18.6 - - + +
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Residues in contact with GLU 256 (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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252B LEU 3.0 18.1 + - - +
253B SER* 3.7 5.4 - - - +
255B ILE* 1.3 75.8 - - - +
257B ARG* 1.3 64.7 + - - +
259B GLU 4.6 0.5 + - - +
265B LYS* 2.9 57.5 + - - +
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Residues in contact with ARG 257 (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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250B LEU* 5.9 1.2 - - - +
253B SER* 2.9 34.8 + - - +
254B LEU* 3.6 16.9 - - - +
256B GLU* 1.3 83.0 - - + +
258B TYR* 1.3 93.8 + - + +
259B GLU 5.0 1.0 - - - +
283B ASP* 2.8 35.5 + - - -
289B LEU* 5.7 0.4 - - - +
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Residues in contact with TYR 258 (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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254B LEU* 2.7 39.7 + - + +
257B ARG* 1.3 100.5 - - + +
259B GLU* 1.3 58.1 + - - +
260B PRO* 3.0 15.5 - - - +
274B GLY* 3.8 10.1 - - - +
277B MET* 3.5 22.2 - - + +
278B TYR* 3.5 35.4 - + + +
281B SER* 3.0 37.7 + - - -
282B ALA* 4.2 4.3 + - - +
283B ASP* 2.5 32.9 + - + +
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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