Contacts of the helix formed by residues 251 - 264 (chain X) in PDB entry 2QW0
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 THR 251 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203X MET* 3.7 24.7 - - + -
204X PRO* 5.7 2.7 - - + -
250X ALA* 1.3 77.9 - - - +
252X PRO* 1.3 75.6 - - - +
253X THR* 3.4 10.0 + - - -
254X HIS* 3.1 35.8 + - + +
255X LEU* 3.0 23.1 + - - +
280X ALA 5.8 0.2 - - - +
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Residues in contact with PRO 252 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250X ALA 4.2 2.5 - - - +
251X THR* 1.3 87.4 - - - +
253X THR* 1.3 62.1 + - - +
255X LEU* 3.4 1.2 + - - +
256X ASP* 3.2 23.0 + - - +
279X PHE* 5.1 0.7 - - + -
280X ALA* 3.3 28.7 - - + +
281X GLY* 4.2 2.5 - - - -
283X THR* 4.5 11.7 - - - +
284X MET* 3.7 43.0 - - + -
285X PRO* 5.5 2.9 - - + -
288X VAL* 3.9 8.3 - - + +
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Residues in contact with THR 253 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231X PHE* 6.4 0.7 - - + -
251X THR* 3.1 8.8 + - - -
252X PRO* 1.3 75.6 - - - +
254X HIS* 1.3 70.8 + - + +
256X ASP* 3.5 6.7 + - - +
257X ALA* 3.2 22.0 + - + +
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Residues in contact with HIS 254 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202X LEU* 3.7 32.6 - - + +
203X MET* 5.3 1.8 - - - -
204X PRO* 5.6 2.9 - - + -
231X PHE* 3.4 51.9 - + + +
250X ALA* 3.8 17.4 - - + +
251X THR* 3.1 40.3 + - + +
253X THR* 1.3 80.8 - - + +
255X LEU* 1.3 57.4 + - - +
257X ALA* 3.2 4.0 + - - +
258X LEU* 2.8 37.2 + - + +
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Residues in contact with LEU 255 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248X LEU* 4.4 3.6 - - + -
250X ALA* 4.1 12.8 - - + +
251X THR 3.0 17.6 + - - +
252X PRO 3.4 3.8 + - - +
253X THR 3.3 0.2 - - - -
254X HIS* 1.3 73.8 - - - +
256X ASP* 1.3 57.0 + - - +
258X LEU* 3.6 14.4 - - + +
259X ALA* 2.7 37.7 + - - +
277X VAL* 3.6 25.1 - - + -
278X THR 4.5 1.8 - - - +
279X PHE* 3.4 48.7 - - + -
284X MET* 4.2 9.0 - - + -
292X VAL* 3.9 15.9 - - + +
296X LEU* 3.7 18.2 - - + +
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Residues in contact with ASP 256 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252X PRO 3.2 13.2 + - - +
253X THR* 3.7 11.0 - - - +
255X LEU* 1.3 75.6 - - - +
257X ALA* 1.3 65.2 + - - +
259X ALA* 3.5 3.7 + - - +
260X ALA* 3.3 23.2 + - - +
288X VAL* 3.9 33.5 - - + +
291X THR* 4.1 11.8 + - - +
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Residues in contact with ALA 257 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231X PHE* 3.8 23.6 - - + -
233X PRO* 4.0 15.0 - - + +
253X THR* 3.2 10.5 + - + +
254X HIS 3.2 9.5 + - - +
256X ASP* 1.3 80.9 - - - +
258X LEU* 1.3 64.0 + - - +
260X ALA* 3.3 3.8 + - - +
261X ALA* 3.0 23.7 + - - +
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Residues in contact with LEU 258 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200X LEU* 6.4 0.2 - - + -
202X LEU* 4.1 23.3 - - + -
231X PHE* 4.1 9.4 - - + -
233X PRO* 3.5 24.9 - - + +
236X ALA* 3.9 16.4 - - + -
237X LEU* 3.8 21.7 - - + +
248X LEU* 4.2 19.5 - - + -
254X HIS* 2.8 29.7 + - + +
255X LEU* 3.8 11.7 - - + +
257X ALA* 1.3 75.0 - - - +
259X ALA* 1.3 52.0 + - - +
261X ALA* 3.3 5.1 + - - +
262X ALA* 2.8 35.0 + - - +
296X LEU* 4.3 15.0 - - + -
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Residues in contact with ALA 259 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255X LEU 2.7 21.9 + - - +
256X ASP 3.9 2.0 - - - +
258X LEU* 1.3 73.4 - - - +
260X ALA* 1.3 57.8 + - - +
262X ALA* 3.4 1.6 + - - +
263X ALA* 2.9 28.6 + - - +
291X THR* 3.8 42.2 - - - +
292X VAL* 4.3 3.1 - - + +
295X HIS* 3.4 9.1 - - + +
296X LEU* 4.1 18.1 - - + +
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Residues in contact with ALA 260 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256X ASP* 3.3 17.4 + - - +
257X ALA* 3.8 3.4 - - - +
259X ALA* 1.3 76.4 - - - +
261X ALA* 1.3 57.3 + - - +
263X ALA* 3.2 6.7 + - - +
264X HIS* 2.8 37.9 + - - +
291X THR* 6.2 0.4 - - - -
295X HIS* 5.6 0.7 - - - -
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Residues in contact with ALA 261 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233X PRO* 4.0 20.4 - - + -
234X VAL* 4.0 22.2 - - + +
237X LEU* 4.0 10.8 - - + -
257X ALA 3.0 16.5 + - - +
258X LEU 3.8 3.4 - - - +
260X ALA* 1.3 76.8 - - - +
262X ALA* 1.3 57.4 + - - +
264X HIS* 3.4 5.7 + - - -
265X ALA* 3.0 30.8 + - - +
269X LEU* 5.1 0.2 - - - +
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Residues in contact with ALA 262 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237X LEU* 3.5 17.8 - - + +
258X LEU 2.8 17.4 + - - +
259X ALA 3.6 4.0 - - - +
261X ALA* 1.3 76.8 - - - +
263X ALA* 1.3 57.6 + - - +
265X ALA* 3.3 3.8 + - - +
266X GLY* 2.8 29.5 + - - +
271X LEU* 4.3 9.4 - - + -
295X HIS* 3.3 25.6 - - - +
296X LEU* 4.0 9.2 - - + -
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Residues in contact with ALA 263 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259X ALA 2.9 18.1 + - - +
260X ALA* 3.5 8.3 - - - +
262X ALA* 1.3 73.9 - - - +
264X HIS* 1.3 56.9 + - - +
265X ALA 3.0 9.9 + - - -
266X GLY* 3.5 8.9 + - - +
295X HIS* 3.7 35.8 - - + +
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Residues in contact with HIS 264 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260X ALA 2.8 21.1 + - - +
261X ALA* 3.5 7.0 - - - +
263X ALA* 1.3 70.2 - - - +
265X ALA* 1.3 55.2 + - - +
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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