Contacts of the helix formed by residues 203 - 218 (chain D) in PDB entry 2WQT
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 HIS 203 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ASP* 3.6 27.5 + - + +
168A GLY* 5.6 4.6 - - - -
123D PHE* 3.8 12.8 - + - -
127D TYR* 4.5 6.7 + - - -
178D LEU* 3.6 25.3 + - + +
179D LYS* 3.6 35.4 + - + +
197D GLY 3.8 2.0 + - - -
200D CYS 3.0 11.5 + - - +
201D LEU 3.1 2.0 + - - -
202D GLY* 1.3 78.7 - - - +
204D PRO* 1.3 68.7 - - + +
205D LEU* 3.1 43.4 + - + +
206D ASN* 2.8 38.8 + - - +
207D ALA 3.7 0.3 + - - -
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Residues in contact with PRO 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ILE* 3.9 25.8 - - + -
178D LEU* 3.4 28.7 - - + +
197D GLY* 3.3 20.2 - - - +
200D CYS* 3.7 17.7 - - + +
203D HIS* 1.3 90.3 - - + +
205D LEU* 1.3 65.4 + - + +
207D ALA* 3.2 15.4 + - - +
208D ALA 3.2 8.3 + - - -
230D THR* 3.7 28.0 - - + +
233D LEU* 4.9 1.8 - - + -
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Residues in contact with LEU 205 (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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110D LEU* 3.7 21.5 - - + -
123D PHE* 3.5 25.1 - - + +
126D LEU* 3.8 12.3 - - + +
127D TYR* 3.6 52.9 - - + +
130D ILE* 3.6 24.9 - - + -
178D LEU* 4.2 11.2 - - + -
203D HIS* 3.1 13.8 + - + +
204D PRO* 1.3 76.5 - - + +
206D ASN* 1.3 60.0 + - - +
208D ALA* 3.6 4.6 - - - +
209D VAL* 2.8 31.9 + - - +
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Residues in contact with ASN 206 (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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89A GLY* 3.5 5.2 - - - -
90A ASP 3.0 24.6 + - - -
91A ASN 4.6 0.2 - - - -
92A GLU* 3.5 31.2 + - + +
123D PHE* 3.4 21.4 - - - -
201D LEU* 3.0 34.9 + - + +
202D GLY* 4.1 1.0 - - - -
203D HIS* 2.8 19.1 + - - +
205D LEU* 1.3 75.4 - - - +
207D ALA* 1.3 59.7 + - - +
209D VAL* 3.3 5.6 + - - +
210D TRP* 2.9 30.7 + - - +
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Residues in contact with ALA 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D VAL* 3.9 22.0 - - + +
64D THR* 4.5 3.8 - - + -
200D CYS* 4.6 4.0 - - - -
201D LEU* 3.9 18.0 - - + +
203D HIS 3.7 1.6 + - - -
204D PRO 3.2 10.1 + - - +
206D ASN* 1.3 78.3 - - - +
208D ALA* 1.3 57.1 + - - +
210D TRP* 3.4 3.1 + - - +
211D LEU* 2.9 30.1 + - - +
230D THR* 3.2 30.1 - - - +
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Residues in contact with ALA 208 (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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110D LEU* 3.8 22.4 - - + -
126D LEU* 3.4 31.5 - - + +
204D PRO 3.2 7.4 + - - +
205D LEU* 3.6 2.9 - - - +
207D ALA* 1.3 80.6 - - - +
209D VAL* 1.3 56.3 + - - +
211D LEU* 3.3 5.2 + - - +
212D ALA* 2.8 31.2 + - - +
228D ILE* 4.5 17.4 - - + +
230D THR* 4.6 3.1 - - + +
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Residues in contact with VAL 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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92A GLU* 6.1 0.7 - - - +
121D ILE* 3.7 13.2 - - + +
122D THR 4.3 1.1 - - - -
123D PHE* 3.8 34.3 - - + +
126D LEU* 4.1 18.4 - - + -
205D LEU 2.8 23.3 + - - +
206D ASN* 3.3 6.9 + - - +
208D ALA* 1.3 75.2 - - - +
210D TRP* 1.3 63.8 + - - +
212D ALA* 3.2 4.5 + - - +
213D ARG* 3.0 58.2 + - - +
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Residues in contact with TRP 210 (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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39D TYR* 4.4 6.1 - - - -
61D VAL* 4.2 5.6 - - + -
76D GLN* 3.7 27.0 + - - +
77D PRO* 3.5 44.0 - - + +
78D ASP 3.6 38.1 - - - -
79D PHE* 4.3 13.0 - + + -
201D LEU* 4.5 7.9 - - + -
206D ASN 2.9 17.6 + - - +
207D ALA* 3.6 8.1 - - - +
209D VAL* 1.3 79.4 - - - +
211D LEU* 1.3 89.5 + - + +
213D ARG* 3.4 10.1 + - - +
214D LYS* 3.1 46.7 + - + +
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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
----------------------------------------------------------
59D ARG* 3.8 24.7 - - + -
61D VAL* 3.9 15.5 - - + -
79D PHE* 3.8 29.4 - - + -
207D ALA 2.9 17.8 + - - +
208D ALA 3.7 2.9 - - - +
210D TRP* 1.3 82.3 - - + +
212D ALA* 1.3 66.9 + - - +
213D ARG 3.2 0.3 + - - -
214D LYS* 3.2 2.2 + - - +
215D MET* 2.9 49.6 + - + +
222D LEU* 4.1 5.6 - - + -
228D ILE* 3.7 40.6 - - + -
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Residues in contact with ALA 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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116D LEU* 4.0 33.0 - - + +
118D ALA 4.6 0.8 - - - +
121D ILE* 3.8 18.4 - - + -
126D LEU* 4.4 4.5 - - + -
208D ALA 2.8 20.4 + - - +
209D VAL 3.2 5.1 + - - +
211D LEU* 1.3 73.6 - - - +
213D ARG* 1.3 62.3 + - - +
215D MET* 3.6 2.1 + - - +
216D ALA* 3.1 23.7 + - - +
222D LEU* 3.9 14.6 + - + +
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Residues in contact with ARG 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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84A ALA 5.5 2.4 + - - -
87A CYS 4.8 10.3 + - - -
92A GLU* 5.9 0.8 + - - -
118D ALA 4.6 1.8 - - - -
119D THR* 3.4 25.0 - - - +
120D ASP* 4.0 11.0 + - - +
121D ILE* 2.7 38.7 + - + -
122D THR* 4.2 7.7 - - - +
123D PHE 5.2 0.4 - - - +
209D VAL* 3.0 34.4 + - - +
210D TRP* 3.6 8.5 - - + +
212D ALA* 1.3 73.2 - - - +
214D LYS* 1.3 66.7 + - - +
216D ALA* 3.2 6.5 + - - +
217D SER* 2.9 24.8 + - - -
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Residues in contact with LYS 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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39D TYR* 4.3 24.9 + - - -
76D GLN* 4.4 20.9 - - - +
79D PHE* 4.5 7.1 - - + -
210D TRP* 3.1 37.1 + - + +
211D LEU* 3.5 9.9 - - - +
213D ARG* 1.3 77.6 - - - +
215D MET* 1.3 73.8 + - + +
217D SER* 3.0 12.3 + - - +
218D LEU* 2.9 46.6 + - + +
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Residues in contact with MET 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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59D ARG* 3.8 33.0 - - - -
79D PHE* 3.2 46.0 - - + -
211D LEU* 2.9 26.8 + - + +
212D ALA 4.0 3.8 - - - +
214D LYS* 1.3 86.4 - - + +
216D ALA* 1.3 59.8 + - - +
218D LEU* 3.3 13.5 + - + +
220D GLU* 2.9 49.9 + - - +
222D LEU* 3.8 30.7 - - + +
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Residues in contact with ALA 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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116D LEU 4.0 4.7 - - - +
117D PRO 3.4 28.9 - - - +
118D ALA 3.9 9.6 - - - +
119D THR* 3.8 14.7 - - + +
212D ALA 3.1 19.3 + - - +
213D ARG 3.5 4.0 - - - +
215D MET* 1.3 74.9 - - - +
217D SER* 1.3 63.0 + - - +
219D GLY* 3.2 13.9 + - - -
221D PRO* 4.2 13.5 - - - +
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Residues in contact with SER 217 (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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119D THR* 3.9 16.8 - - - +
213D ARG 2.9 14.4 + - - -
214D LYS* 3.0 18.9 + - - +
216D ALA* 1.3 74.3 - - - +
218D LEU* 1.3 67.9 + - - +
219D GLY 3.1 3.4 + - - -
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Residues in contact with LEU 218 (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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39D TYR* 5.9 2.5 - - + -
79D PHE* 4.0 18.4 - - + -
214D LYS* 2.9 29.5 + - + +
215D MET* 3.7 32.3 - - + +
216D ALA 3.2 0.6 - - - -
217D SER* 1.3 85.8 + - - +
219D GLY* 1.3 60.8 + - - +
220D GLU* 3.5 20.9 + - + +
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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