Contacts of the helix formed by residues 235 - 249 (chain D) in PDB entry 2QB0
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 235 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198D GLN* 3.2 28.8 + - - +
231D TRP* 3.3 16.0 + - - -
232D TYR 3.5 2.7 - - - -
234D GLN* 1.3 88.1 - - + +
236D PRO* 1.4 65.4 - - - +
237D ASN* 3.5 2.4 + - - -
238D ARG* 3.5 14.8 + - + +
239D ALA* 3.0 19.8 + - - +
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Residues in contact with PRO 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D TYR* 3.1 27.3 - - + +
233D ASN* 3.6 13.0 - - - +
234D GLN 3.6 4.0 - - - +
235D THR* 1.4 85.8 - - - +
237D ASN* 1.3 68.3 + - - +
239D ALA* 3.2 2.4 + - + +
240D LYS* 2.9 51.0 + - - +
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Residues in contact with ASN 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D THR 3.5 0.6 - - - -
236D PRO* 1.3 85.1 - - - +
238D ARG* 1.3 62.9 + - - +
240D LYS* 3.7 20.3 + - - +
241D ARG* 3.4 42.7 + - - +
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Residues in contact with ARG 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LEU* 3.4 13.3 - - - +
103D ASP* 3.4 37.7 + - - +
104D GLU* 2.8 34.8 + - - -
194D ASN* 2.8 28.3 + - - -
198D GLN* 3.2 50.8 + - - +
231D TRP* 5.7 0.2 - - + -
235D THR* 3.5 16.1 + - - +
236D PRO 3.3 0.6 - - - -
237D ASN* 1.3 76.6 - - - +
239D ALA* 1.3 65.5 + - - +
241D ARG* 3.2 20.2 + - - +
242D VAL* 3.0 25.4 + - + +
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Residues in contact with ALA 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D TRP* 3.7 32.3 - - + +
232D TYR* 3.6 35.2 - - + -
235D THR* 3.0 19.4 + - - +
236D PRO 3.7 0.4 - - - +
238D ARG* 1.3 75.7 - - - +
240D LYS* 1.3 56.9 + - - +
242D VAL* 3.3 1.9 + - - +
243D ILE* 2.8 36.7 + - - +
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Residues in contact with LYS 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D TYR* 3.1 37.9 - - + +
236D PRO* 2.9 36.3 + - - +
237D ASN* 3.7 18.1 + - - +
239D ALA* 1.3 75.6 - - - +
241D ARG* 1.3 58.1 + - + +
243D ILE* 3.4 5.3 + - - +
244D THR* 2.8 36.4 + - - +
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Residues in contact with ARG 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE* 4.5 14.4 + - - +
103D ASP* 3.0 35.1 + - - +
237D ASN* 3.4 29.3 + - - +
238D ARG* 3.2 22.8 + - - +
240D LYS* 1.3 78.3 - - + +
242D VAL* 1.3 62.9 + - - +
244D THR* 3.4 2.6 + - - -
245D THR* 2.8 28.2 + - - -
253D ALA* 3.6 36.3 - - + +
254D TYR* 3.4 30.0 - - + +
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Residues in contact with VAL 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D MET* 4.4 1.6 - - + -
103D ASP* 4.4 1.6 - - - +
191D ALA* 3.5 26.9 - - + +
194D ASN* 3.8 24.2 - - - +
195D MET* 3.9 4.0 - - + -
231D TRP* 3.8 26.2 - - + -
238D ARG* 3.0 18.1 + - + +
239D ALA 3.7 6.1 - - - +
241D ARG* 1.3 74.6 - - - +
243D ILE* 1.3 63.7 + - - +
245D THR* 3.2 10.0 + - - -
246D PHE* 3.1 35.0 + - + -
254D TYR* 3.7 14.1 - - - +
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Residues in contact with ILE 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D ALA* 3.7 34.0 - - + +
226D LEU* 3.9 21.5 - - + +
227D ALA* 3.7 35.9 - - + +
231D TRP* 4.1 13.2 - - + -
232D TYR* 3.9 15.5 - - + -
239D ALA 2.8 21.5 + - - +
240D LYS* 3.7 4.9 - - - +
242D VAL* 1.3 73.3 - - - +
244D THR* 1.3 60.8 + - - +
246D PHE* 3.0 10.2 + - + +
247D ARG* 2.8 28.4 + - + +
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Residues in contact with THR 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D LYS* 2.8 27.2 + - - +
241D ARG 3.7 5.2 - - - -
243D ILE* 1.3 74.4 - - - +
245D THR* 1.3 57.8 + - - +
247D ARG* 3.7 29.6 + - - +
248D THR* 2.8 44.6 + - + +
250D THR 6.1 0.2 - - - +
252D ASP* 5.0 5.6 - - + +
253D ALA* 3.9 26.4 - - + +
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Residues in contact with THR 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D MET* 4.0 2.1 - - + +
187D VAL* 3.8 22.7 - - + +
188D ARG* 3.9 4.1 - - - +
191D ALA* 3.8 20.9 - - + -
241D ARG 2.8 19.1 + - - -
242D VAL* 3.3 9.9 - - - -
243D ILE 3.2 0.2 - - - -
244D THR* 1.3 77.6 - - - +
246D PHE* 1.3 56.1 + - - +
249D GLY* 2.9 27.5 + - - -
250D THR 3.8 22.0 + - - +
251D TRP* 4.2 10.8 - - + -
253D ALA* 5.0 1.6 - - - +
254D TYR* 3.5 19.8 - - - -
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Residues in contact with PHE 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D LEU* 4.2 9.0 - - + -
188D ARG* 2.8 54.2 + - + +
191D ALA* 3.5 12.6 - - + -
192D LEU* 3.4 28.9 - - + -
195D MET* 3.6 27.1 - - - -
214D LEU* 3.7 43.3 - - + -
219D TRP* 3.6 13.6 - - - +
222D ALA* 6.0 0.7 - - + -
223D ALA* 6.1 2.2 - - - -
226D LEU* 4.2 18.2 - - + -
242D VAL* 3.1 26.5 + - + -
243D ILE* 3.0 10.1 + - + +
245D THR* 1.3 75.7 - - - +
247D ARG* 1.3 58.4 + - - +
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Residues in contact with ARG 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D ARG* 3.5 10.2 + - - -
219D TRP* 3.5 21.8 - - - +
220D ASP* 3.6 25.4 + - - +
223D ALA* 4.0 25.3 - - + +
243D ILE* 2.8 15.7 + - - +
244D THR* 3.7 26.1 + - - +
246D PHE* 1.3 78.5 - - - +
248D THR* 1.3 82.0 + - + +
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Residues in contact with THR 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D ARG* 3.6 7.1 + - - -
244D THR* 2.8 31.2 + - + +
247D ARG* 1.3 107.9 - - - +
249D GLY* 1.3 63.8 + - - +
250D THR* 2.9 34.0 + - - +
252D ASP* 4.6 8.4 + - + +
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Residues in contact with GLY 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D ASP* 4.6 3.4 - - - +
187D VAL* 3.7 25.9 - - - +
188D ARG* 3.6 23.6 - - - +
245D THR 2.9 17.8 + - - -
248D THR* 1.3 78.4 - - - +
250D THR* 1.3 63.2 + - - +
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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