Contacts of the helix formed by residues 207 - 216 (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 PHE 207 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B ARG* 6.4 0.2 - - - +
146B ASN* 4.7 19.7 - - + +
195D MET* 4.2 12.6 - - + -
199D MET* 3.8 18.8 - - - -
203D GLY 3.4 17.5 - - - -
204D VAL* 3.1 22.0 + - + +
206D GLY* 1.3 74.9 - - - +
208D THR* 1.3 64.2 + - - +
209D ASN 3.4 2.2 - - - -
210D SER* 3.4 15.9 + - - -
211D LEU* 3.0 31.3 + - + +
226D LEU* 3.7 26.5 - - + -
229D SER* 3.9 27.4 - - - -
231D TRP* 4.1 22.7 - + + -
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Residues in contact with THR 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ASN* 5.5 0.8 - - - +
176D LYS* 3.6 37.7 + - + +
205D ALA 3.7 7.1 + - - -
206D GLY* 3.0 9.2 + - - -
207D PHE* 1.3 74.9 - - - +
209D ASN* 1.3 72.0 + - - +
211D LEU* 3.5 6.0 + - - +
212D ARG* 3.4 32.9 + - - +
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Residues in contact with ASN 209 (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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140B ASP* 3.7 15.7 + - - +
141B LYS* 5.0 6.1 + - - +
144B GLY* 3.2 42.7 - - - +
145B ARG* 3.7 14.2 + - - +
207D PHE 3.4 0.6 - - - -
208D THR* 1.3 82.7 + - - +
210D SER* 1.3 61.7 + - - +
212D ARG* 3.3 37.1 + - - +
213D MET* 3.3 29.7 + - + +
225D ASN* 4.4 0.7 - - - -
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Residues in contact with SER 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ARG* 4.8 4.4 - - - +
207D PHE* 3.4 16.5 + - - +
209D ASN* 1.3 75.0 - - - +
211D LEU* 1.3 63.4 + - - +
213D MET* 3.2 18.5 + - - +
214D LEU* 3.2 20.3 + - - +
222D ALA* 4.3 2.6 - - - +
225D ASN* 2.8 31.0 + - - +
226D LEU* 3.7 35.7 + - - +
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Residues in contact with LEU 211 (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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176D LYS* 3.8 29.8 - - + +
177D LEU* 3.8 26.9 - - + -
180D VAL* 3.4 38.1 - - + +
192D LEU* 4.0 18.4 - - + -
204D VAL* 3.5 24.0 - - + +
205D ALA* 4.2 2.2 - - - -
207D PHE* 3.0 29.4 + - + +
208D THR 3.8 4.5 - - - +
210D SER* 1.3 76.2 - - - +
212D ARG* 1.3 61.0 + - - +
214D LEU* 3.6 9.9 + - + +
215D GLN* 3.3 16.6 + - - +
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Residues in contact with ARG 212 (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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208D THR* 3.4 21.1 + - - +
209D ASN* 3.3 47.8 + - - +
210D SER 3.2 0.2 - - - -
211D LEU* 1.3 78.0 - - - +
213D MET* 1.3 65.6 + - + +
214D LEU 3.4 0.2 - - - -
215D GLN* 3.6 13.3 + - - +
216D GLN* 3.2 48.3 + - + +
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Residues in contact with MET 213 (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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144B GLY* 4.3 7.6 - - - +
209D ASN* 3.4 17.3 - - + +
210D SER* 3.2 9.3 + - - +
212D ARG* 1.3 78.4 - - + +
214D LEU* 1.3 62.2 + - - +
216D GLN* 3.3 8.6 + - - +
217D LYS 3.2 4.2 + - - -
218D ARG* 2.9 40.2 + - + +
221D GLU* 3.7 41.3 - - + +
222D ALA* 3.8 16.4 - - + -
225D ASN* 3.9 29.4 - - + +
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Residues in contact with LEU 214 (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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180D VAL* 4.4 10.3 - - + -
183D SER* 4.8 0.5 + - - -
184D LEU* 4.0 16.8 - - + +
192D LEU* 5.3 1.3 - - + -
195D MET* 6.2 0.4 - - - -
210D SER* 3.2 16.7 + - - +
211D LEU* 4.0 18.6 - - + +
212D ARG 3.4 0.2 - - - -
213D MET* 1.3 76.4 - - - +
215D GLN* 1.3 64.2 + - - +
217D LYS* 3.2 9.4 + - - +
219D TRP* 3.3 38.5 - - + +
222D ALA* 3.8 20.0 - - + -
226D LEU* 5.0 8.5 - - + -
246D PHE* 3.7 54.1 - - + -
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Residues in contact with GLN 215 (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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179D PRO* 3.1 42.4 + - - +
180D VAL* 3.9 11.7 - - + +
183D SER* 3.7 30.9 + - - +
211D LEU 3.3 15.1 + - - +
212D ARG* 3.8 13.6 - - - +
213D MET 3.3 0.6 - - - -
214D LEU* 1.3 79.3 - - - +
216D GLN* 1.3 63.3 + - + +
217D LYS* 3.2 8.2 + - - +
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Residues in contact with GLN 216 (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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212D ARG* 3.2 40.6 + - + +
213D MET* 3.3 7.7 + - - +
214D LEU 3.2 0.4 - - - -
215D GLN* 1.3 81.6 - - + +
217D LYS* 1.3 69.1 + - - +
218D ARG* 3.1 39.8 + - + +
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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