Contacts of the helix formed by residues 245 - 265 (chain B) in PDB entry 2QFZ
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 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240B PRO* 4.2 14.6 - - + -
242B ASN* 3.1 38.5 + - - +
243B VAL 3.0 1.6 - - - -
244B ASP* 1.3 80.5 - - + +
246B ARG* 1.3 61.4 + - - +
247B PRO* 3.5 2.4 - - - -
248B ALA* 3.8 7.3 + - - +
249B THR* 2.9 27.2 + - - +
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Residues in contact with ARG 246 (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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205B LEU* 3.0 20.4 + - - +
210B THR* 3.0 19.6 + - - -
230B MET* 4.3 15.4 - - - +
234B LEU* 3.7 23.8 - - - +
239B LEU* 4.2 18.6 - - + +
240B PRO* 2.8 38.6 + - + +
241B ALA 3.0 25.1 + - - -
242B ASN 3.8 4.7 - - - +
243B VAL* 3.1 31.6 + - + +
245B ARG* 1.3 76.3 - - - +
247B PRO* 1.4 70.7 - - + +
249B THR* 3.4 1.0 + - - -
250B LEU* 3.0 29.1 + - + +
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Residues in contact with PRO 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B VAL 3.5 12.8 - - - +
244B ASP 3.6 10.8 - - - +
245B ARG 3.5 4.7 - - - -
246B ARG* 1.4 91.8 - - + +
248B ALA* 1.3 56.8 + - - +
250B LEU* 3.8 7.1 - - + +
251B GLN* 2.9 31.7 + - - +
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Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ASP 5.9 0.4 - - - +
245B ARG* 4.3 7.9 - - - +
246B ARG 3.4 0.4 - - - -
247B PRO* 1.3 79.8 - - - +
249B THR* 1.3 57.6 + - - +
251B GLN* 3.9 4.7 - - - +
252B ARG* 2.9 32.5 + - - +
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Residues in contact with THR 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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238B TYR 3.6 24.2 - - - +
239B LEU* 4.2 4.0 - - + -
240B PRO* 3.6 20.7 - - + +
245B ARG* 2.9 15.9 + - - +
246B ARG 3.4 6.7 + - - -
247B PRO 3.3 0.4 - - - -
248B ALA* 1.3 74.3 - - - +
250B LEU* 1.3 67.2 + - - +
252B ARG* 3.1 21.8 + - - +
253B LYS* 2.8 46.7 + - + +
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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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230B MET* 6.0 2.9 - - + -
233B LYS* 5.2 2.2 - - + +
238B TYR* 3.7 19.3 - - + +
239B LEU* 4.0 23.0 - - + +
246B ARG* 3.0 17.7 + - + +
247B PRO* 3.8 6.5 - - + +
249B THR* 1.3 75.1 - - - +
251B GLN* 1.3 58.3 + - - +
253B LYS* 4.1 0.8 - - - +
254B GLN* 2.9 66.4 + - - +
362B ASP* 3.5 17.5 - - - +
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Residues in contact with GLN 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 PRO 2.9 18.6 + - - +
248B ALA* 4.0 5.2 - - - +
250B LEU* 1.3 76.4 - - - +
252B ARG* 1.3 64.7 + - - +
254B GLN* 3.8 8.6 - - - +
255B LYS* 3.0 47.2 + - + +
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Residues in contact with ARG 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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248B ALA 2.9 19.1 + - - +
249B THR* 3.1 28.7 + - - +
251B GLN* 1.3 78.6 - - - +
253B LYS* 1.3 72.6 + - - +
255B LYS* 3.9 6.3 - - - +
256B GLU* 3.0 44.3 + - + +
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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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237B GLY 3.8 7.1 + - - -
238B TYR* 2.5 71.8 + - + +
249B THR* 2.8 37.7 + - + +
250B LEU 4.1 0.2 - - - +
252B ARG* 1.3 87.3 - - - +
254B GLN* 1.3 66.6 + - - +
256B GLU* 3.4 17.4 - - - +
257B TYR 3.1 12.5 + - - -
365B TRP* 2.8 32.8 + - + +
369B LYS* 4.6 7.9 - - - +
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Residues in contact with GLN 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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238B TYR* 4.0 1.8 - - - +
250B LEU* 2.9 43.1 + - - +
251B GLN* 3.8 6.2 - - - +
253B LYS* 1.3 77.8 - - - +
255B LYS* 1.3 56.3 + - + +
257B TYR* 3.3 4.5 + - - +
258B PHE* 3.0 46.0 + - + -
358B ASN* 3.6 35.1 + - - +
361B ALA* 3.9 17.3 - - + -
362B ASP* 3.1 33.1 + - - +
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Residues in contact with LYS 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 GLN* 3.0 46.5 + - + +
252B ARG* 3.9 6.1 - - - +
254B GLN* 1.3 75.3 - - + +
256B GLU* 1.3 57.8 + - - +
258B PHE* 3.1 17.6 + - + +
259B ALA* 2.9 27.7 + - - +
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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 ARG* 3.0 30.6 + - + +
253B LYS* 3.4 30.1 - - - +
255B LYS* 1.3 72.8 - - - +
257B TYR* 1.3 63.7 + - - +
259B ALA* 3.5 9.4 - - + +
260B PHE* 3.2 38.3 + - + -
365B TRP* 3.5 27.3 - - + -
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Residues in contact with TYR 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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253B LYS 3.1 7.2 + - - +
254B GLN 3.7 6.5 - - - +
256B GLU* 1.3 74.6 - - - +
258B PHE* 1.3 70.0 + + - +
260B PHE* 2.9 30.6 + + - +
261B ILE* 3.1 21.8 + - + +
304B ARG* 4.0 0.2 - - - +
305B ILE* 3.7 13.2 + - - -
308B ILE* 3.6 30.1 - - + +
360B GLU* 2.5 46.0 + - + +
361B ALA* 3.7 22.7 - - + -
364B TYR* 3.6 42.4 - + + -
365B TRP* 3.8 17.9 - - + +
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Residues in contact with PHE 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 GLN* 3.0 33.2 + - + -
255B LYS* 3.1 17.0 + - + +
257B TYR* 1.3 84.5 - + - +
259B ALA* 1.3 60.5 + - - +
261B ILE* 3.4 17.4 + - + +
262B GLU* 3.2 24.3 + - - +
357B CYS* 3.3 39.0 - - + -
358B ASN* 3.5 25.4 - - - -
361B ALA* 4.1 5.6 - - + -
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Residues in contact with ALA 259 (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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255B LYS 2.9 12.7 + - - +
256B GLU* 3.5 15.3 - - + +
257B TYR 3.2 0.2 - - - -
258B PHE* 1.3 74.1 - - - +
260B PHE* 1.3 61.6 + - + +
262B GLU* 3.5 6.0 + - - +
263B HIS* 3.0 31.2 + - - +
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Residues in contact with PHE 260 (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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256B GLU* 3.2 26.9 + - + -
257B TYR* 2.9 19.7 + + - +
259B ALA* 1.3 74.6 - - + +
261B ILE* 1.3 67.5 + - - +
263B HIS* 3.2 2.1 + - + -
264B TYR* 3.1 38.3 + + + +
308B ILE* 3.8 32.7 - - + +
312B ARG* 3.3 49.8 - - - -
364B TYR* 3.9 7.6 - + - -
365B TRP* 3.6 36.3 - + - -
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Residues in contact with ILE 261 (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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257B TYR* 3.1 32.4 + - + +
258B PHE* 3.4 20.6 + - + +
260B PHE* 1.3 74.8 - - - +
262B GLU* 1.3 67.3 + - - +
265B TYR* 3.0 40.0 + - + +
304B ARG* 3.9 33.0 - - - +
308B ILE* 3.9 18.4 - - + -
357B CYS* 6.2 4.5 - - - -
360B GLU* 4.1 3.6 - - - +
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Residues in contact with GLU 262 (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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258B PHE 3.2 14.7 + - - +
259B ALA* 3.8 7.9 - - - +
260B PHE 3.2 0.2 - - - -
261B ILE* 1.3 86.2 - - - +
263B HIS* 1.3 64.0 + - - +
265B TYR 4.4 5.2 + - - +
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Residues in contact with HIS 263 (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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259B ALA 3.0 18.8 + - - +
260B PHE* 3.2 4.0 + - + +
262B GLU* 1.3 80.4 - - - +
264B TYR* 1.3 96.5 + + + +
265B TYR 4.3 1.7 - - - +
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Residues in contact with TYR 264 (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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260B PHE* 3.1 31.9 + + + +
263B HIS* 1.3 104.3 - + + +
265B TYR* 1.3 66.3 + - + +
273B HIS* 5.8 5.8 - + - -
307B PHE* 4.7 7.6 - - + -
308B ILE* 5.0 4.0 - - + -
311B ILE* 3.1 41.3 - - + -
312B ARG* 2.9 52.2 + - + +
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Residues in contact with TYR 265 (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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260B PHE 4.7 0.2 - - - +
261B ILE* 3.0 34.7 + - + +
262B GLU 4.5 4.0 - - - +
263B HIS 3.4 3.9 - - - +
264B TYR* 1.3 82.9 - - + +
277B TYR* 4.4 16.2 - + - -
300B GLU 5.1 0.9 + - - -
303B GLU* 4.4 7.1 + - - +
304B ARG* 4.0 50.1 + - + +
307B PHE* 3.5 44.9 - + + -
308B ILE* 4.4 6.3 - - + -
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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
------------------------------------------------------------
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