Contacts of the helix formed by residues 246 - 257 (chain B) in PDB entry 2QUH
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 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B SER* 3.0 3.0 + - - -
245B SER* 1.3 84.4 + - - +
247B PHE* 1.3 68.1 + - - +
248B TYR 3.6 1.3 - - - -
249B LYS* 3.5 11.1 + - - +
250B ASN* 3.2 24.8 + - - -
291B ASN* 3.7 16.1 - - - +
292B SER* 4.0 6.5 - - - -
294B PRO* 3.9 4.3 - - - +
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Residues in contact with PHE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLN* 4.0 11.7 - - - -
235B PHE* 4.3 12.1 - + - -
237B ASP* 4.2 10.8 - - - -
240B TYR* 4.1 12.8 - + + +
241B MET* 3.3 50.5 - - + +
244B SER* 2.8 29.6 + - - +
246B GLY* 1.3 75.7 - - - +
248B TYR* 1.3 63.2 + - - +
250B ASN* 3.1 15.4 + - - +
251B VAL* 3.1 16.5 + - + +
283B ILE* 3.8 20.9 - - + -
286B ALA* 3.9 15.0 - - + +
287B PRO* 4.0 18.4 - - + -
292B SER* 3.7 24.5 + - - +
293B PHE* 4.8 0.9 - + - -
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Residues in contact with TYR 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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198A ASP* 3.3 10.0 + - - -
237A ASP 4.5 2.5 - - - -
238A LEU* 4.1 25.8 - - + +
241A MET* 3.4 47.3 - - + -
242A GLY* 4.9 5.6 - - - +
248A TYR* 5.4 4.9 - + - -
283A ILE* 3.0 30.6 - - + +
241B MET* 3.8 32.0 + - + +
244B SER 4.8 3.2 + - - +
246B GLY 3.6 0.2 - - - -
247B PHE* 1.3 76.4 - - - +
249B LYS* 1.3 69.3 + - - +
251B VAL* 3.1 17.8 + - + +
252B VAL* 2.9 47.4 + - + +
255B GLN* 5.0 5.6 + - - -
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Residues in contact with LYS 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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208A LEU* 3.6 32.7 - - + +
209A ASP* 5.8 2.6 + - - -
212A TYR* 6.0 7.3 - - - -
238A LEU* 4.5 35.0 - - + +
239A ASP* 4.8 11.7 + - - -
245B SER 3.6 24.5 + - - +
246B GLY* 3.5 11.8 + - - +
247B PHE 3.2 0.8 - - - -
248B TYR* 1.3 81.4 - - - +
250B ASN* 1.3 63.1 + - - +
252B VAL* 3.3 7.2 + - - +
253B LYS* 3.1 18.8 + - - +
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Residues in contact with ASN 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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246B GLY 3.2 6.3 + - - -
247B PHE 3.1 8.9 + - - +
249B LYS* 1.3 76.9 - - - +
251B VAL* 1.3 67.6 + - - +
253B LYS* 3.0 11.1 + - - +
254B ILE* 2.9 34.4 + - + +
286B ALA* 4.4 7.9 - - + +
289B PHE* 4.0 5.4 - - + +
291B ASN* 2.7 26.9 - - - +
292B SER* 2.6 30.3 + - - +
329B TYR* 2.7 35.6 + - + -
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Residues in contact with VAL 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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241B MET* 4.1 10.5 - - + -
247B PHE* 3.1 20.5 + - + +
248B TYR* 3.1 22.2 + - + +
250B ASN* 1.3 76.6 - - - +
252B VAL* 1.3 58.7 + - - +
254B ILE* 3.2 5.8 + - - +
255B GLN* 2.8 58.4 + - + +
282B ALA* 3.9 4.7 - - + +
283B ILE* 3.6 35.0 - - + -
286B ALA* 3.7 21.5 - - + +
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASP* 4.5 9.9 - - + -
201A TYR* 3.4 26.9 - - + -
202A LEU* 3.4 14.8 - - + -
208A LEU* 4.4 9.0 - - + -
238A LEU* 4.3 6.7 - - + -
248B TYR* 2.9 55.7 + - + +
249B LYS* 3.5 8.1 - - - +
251B VAL* 1.3 73.0 - - - +
253B LYS* 1.3 66.9 + - - +
255B GLN* 3.0 22.3 + - - +
256B LYS* 3.0 13.3 + - - +
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Residues in contact with LYS 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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201A TYR* 3.5 22.2 - - - +
208A LEU* 3.7 31.2 - - + +
249B LYS* 3.1 14.2 + - - +
250B ASN* 3.0 23.8 + - - +
252B VAL* 1.3 77.5 - - - +
254B ILE* 1.3 59.0 + - - +
256B LYS* 3.3 2.4 + - - +
257B HIS* 2.7 32.5 - - - -
291B ASN* 5.0 0.4 + - - -
327B ILE* 4.5 24.8 + - + +
329B TYR* 3.1 31.2 + - + +
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Residues in contact with ILE 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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250B ASN* 2.9 16.7 + - + +
251B VAL 3.6 5.2 - - - +
253B LYS* 1.3 76.1 - - - +
255B GLN* 1.3 57.1 + - - +
257B HIS* 2.9 22.9 + - - +
258B VAL* 3.4 25.2 + - + +
282B ALA* 3.9 24.2 - - + +
285B ALA* 4.1 8.1 - - + -
286B ALA* 3.6 37.0 - - + +
289B PHE* 3.7 17.3 - - + -
319B MET* 5.3 2.9 - - - -
323B VAL* 4.3 16.2 - - + -
327B ILE* 4.2 18.6 - - + -
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Residues in contact with GLN 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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202A LEU* 5.0 5.3 - - + +
255A GLN* 5.7 1.0 - - - +
274A CYS* 3.2 17.0 - - - +
275A ILE* 3.5 17.7 + - + +
276A GLY* 3.3 33.8 + - - +
279A SER* 4.4 3.8 + - - -
283A ILE* 6.0 1.2 - - - +
248B TYR* 5.0 6.2 + - - -
251B VAL* 2.8 47.3 + - - +
252B VAL* 3.0 17.2 + - - +
254B ILE* 1.3 72.9 - - - +
256B LYS* 1.3 61.3 + - - +
257B HIS 3.5 0.3 + - - -
258B VAL 3.6 1.7 - - - +
279B SER* 3.6 33.1 + - - -
282B ALA* 3.6 11.2 - - + -
283B ILE* 5.1 3.0 - - - +
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Residues in contact with LYS 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TYR* 2.9 58.8 + - + +
202A LEU* 4.1 20.8 - - + +
204A LYS 3.0 17.7 + - - -
205A ASP* 4.5 3.4 + - - +
206A LEU 3.5 16.6 + - - +
274A CYS* 3.4 22.2 - - - +
252B VAL 3.0 5.0 + - - +
253B LYS 3.6 9.9 - - - +
254B ILE 3.1 0.2 - - - -
255B GLN* 1.3 78.2 - - - +
257B HIS* 1.3 71.0 + - + +
258B VAL 3.5 0.2 - - - -
259B THR* 6.0 0.2 - - - +
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Residues in contact with HIS 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TYR* 3.7 14.1 + - - -
253B LYS 2.7 26.5 - - - -
254B ILE 2.9 7.6 + - - +
256B LYS* 1.3 94.8 - - + +
258B VAL* 1.3 62.3 + - - +
259B THR* 4.2 1.3 - - - -
262B GLN* 4.0 5.6 + - - -
323B VAL* 4.1 11.0 - - + -
326B ARG* 2.7 72.0 + - + +
327B ILE* 3.6 18.5 - - + +
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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