Contacts of the helix formed by residues 203 - 218 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123Q PHE* 3.8 12.6 - + - -
127Q TYR* 4.5 6.5 + - - -
178Q LEU* 3.6 21.9 + - + +
179Q LYS* 3.6 36.7 + - + +
197Q GLY 3.8 1.6 - - - -
200Q CYS 3.0 11.6 + - - +
201Q LEU 3.1 2.2 + - - -
202Q GLY* 1.3 78.6 - - - +
204Q PRO* 1.3 68.4 - - + +
205Q LEU* 3.1 46.7 + - + +
206Q ASN* 2.8 39.0 + - - +
207Q ALA 3.7 0.7 + - - -
90T ASP* 3.6 26.6 + - + +
168T GLY* 5.6 4.8 + - - -
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Residues in contact with PRO 204 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108Q ILE* 3.8 27.1 - - + -
110Q LEU* 6.1 0.2 - - + -
178Q LEU* 3.4 28.9 - - + +
197Q GLY* 3.3 20.4 - - - +
200Q CYS* 3.7 17.2 - - + +
203Q HIS* 1.3 89.8 - - + +
205Q LEU* 1.3 64.4 + - + +
207Q ALA* 3.2 15.1 + - - +
208Q ALA 3.2 8.5 + - - -
230Q THR* 3.7 27.9 - - + +
233Q LEU* 4.9 1.8 - - + -
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Residues in contact with LEU 205 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Q LEU* 3.7 21.8 - - + -
123Q PHE* 3.4 24.9 - - + +
126Q LEU* 3.7 12.8 - - + -
127Q TYR* 3.6 50.5 - - + -
130Q ILE* 3.6 25.4 - - + -
178Q LEU* 4.2 11.9 - - + -
203Q HIS* 3.0 16.9 + - + +
204Q PRO* 1.3 74.5 - - + +
206Q ASN* 1.3 60.2 + - - +
208Q ALA* 3.6 4.1 - - - +
209Q VAL* 2.8 32.7 + - - +
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Residues in contact with ASN 206 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123Q PHE* 3.4 21.0 - - - -
201Q LEU* 3.0 34.9 + - + +
202Q GLY* 4.1 0.8 - - - -
203Q HIS* 2.8 17.4 + - - +
205Q LEU* 1.3 75.8 - - - +
207Q ALA* 1.3 60.1 + - - +
209Q VAL* 3.2 6.2 + - - +
210Q TRP* 2.9 30.5 + - - +
89T GLY* 3.5 5.5 - - - -
90T ASP 3.0 24.8 + - - -
91T ASN 4.7 0.2 - - - -
92T GLU* 3.5 29.7 + - - +
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Residues in contact with ALA 207 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Q VAL* 3.9 20.0 - - + +
64Q THR* 4.5 4.3 - - + -
200Q CYS* 4.6 3.6 - - - -
201Q LEU* 3.9 17.8 - - + +
203Q HIS 3.7 1.8 + - - -
204Q PRO 3.2 9.3 + - - +
206Q ASN* 1.3 76.9 - - - +
208Q ALA* 1.3 59.4 + - - +
210Q TRP* 3.4 3.9 + - - +
211Q LEU* 3.0 29.6 + - - +
230Q THR* 3.1 31.9 - - - +
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Residues in contact with ALA 208 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Q LEU* 3.8 23.1 - - + -
126Q LEU* 3.4 32.0 - - + +
204Q PRO 3.2 6.5 + - - +
205Q LEU* 3.6 2.9 - - - +
206Q ASN 3.3 0.2 - - - -
207Q ALA* 1.3 76.5 - - - +
209Q VAL* 1.3 58.6 + - - +
211Q LEU* 3.3 5.8 + - - +
212Q ALA* 2.9 31.0 + - - +
228Q ILE* 4.6 16.4 - - + +
230Q THR* 4.5 3.3 - - + +
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Residues in contact with VAL 209 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121Q ILE* 3.6 13.0 - - + +
122Q THR 4.3 1.1 - - - -
123Q PHE* 3.8 33.7 - - + +
126Q LEU* 4.1 19.7 - - + -
205Q LEU 2.8 23.1 + - - +
206Q ASN* 3.7 7.0 - - - +
208Q ALA* 1.3 74.1 - - - +
210Q TRP* 1.3 65.5 + - - +
212Q ALA* 3.2 4.1 + - - +
213Q ARG* 3.0 58.4 + - - +
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Residues in contact with TRP 210 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Q TYR* 4.4 6.3 - - - -
61Q VAL* 4.2 8.7 - - + -
76Q GLN* 3.7 26.7 + - - +
77Q PRO* 3.5 44.0 - - + +
78Q ASP* 3.7 37.9 - - - -
79Q PHE* 4.3 12.6 - + + -
201Q LEU* 4.5 7.2 - - + -
206Q ASN 2.9 17.0 + - - +
207Q ALA* 3.6 6.5 - - - +
209Q VAL* 1.3 78.6 - - - +
211Q LEU* 1.3 89.3 + - + +
213Q ARG* 3.5 10.3 + - - +
214Q LYS* 3.1 47.3 + - + +
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Residues in contact with LEU 211 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59Q ARG* 3.8 24.5 - - + +
61Q VAL* 3.9 15.0 - - + -
79Q PHE* 3.7 30.3 - - + -
207Q ALA 3.0 18.3 + - - +
208Q ALA 3.7 3.1 - - - +
210Q TRP* 1.3 82.9 - - + +
212Q ALA* 1.3 66.1 + - - +
213Q ARG 3.2 0.2 + - - -
214Q LYS* 3.2 2.8 + - - +
215Q MET* 2.9 46.1 + - + +
222Q LEU* 4.2 5.8 - - + -
228Q ILE* 3.7 40.2 - - + -
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Residues in contact with ALA 212 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116Q LEU* 4.1 33.1 - - + +
118Q ALA 4.6 0.6 - - - +
121Q ILE* 3.8 19.1 - - + -
126Q LEU* 4.4 4.5 - - + -
208Q ALA 2.9 21.0 + - - +
209Q VAL 3.6 4.7 - - - +
211Q LEU* 1.3 72.4 - - - +
213Q ARG* 1.3 57.6 + - - +
215Q MET* 3.6 1.7 + - - +
216Q ALA* 3.1 29.9 + - - +
222Q LEU* 3.9 15.0 + - + +
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Residues in contact with ARG 213 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118Q ALA 4.6 0.7 - - - -
119Q THR* 3.4 26.7 - - - +
120Q ASP* 4.0 11.8 + - - +
121Q ILE* 2.8 38.3 + - + -
122Q THR* 4.3 7.5 - - - +
123Q PHE 5.2 0.4 - - - +
209Q VAL* 3.0 35.3 + - - +
210Q TRP* 3.6 8.5 - - + +
212Q ALA* 1.3 74.5 - - - +
214Q LYS* 1.3 66.3 + - - +
216Q ALA* 3.2 6.3 + - - +
217Q SER* 2.9 25.5 + - - -
84T ALA 5.3 2.8 + - - -
87T CYS 4.7 10.7 + - - -
92T GLU* 6.0 0.4 + - - -
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Residues in contact with LYS 214 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Q TYR* 4.3 23.4 + - - -
76Q GLN* 4.4 20.1 - - - +
79Q PHE* 4.5 7.1 - - + -
210Q TRP* 3.1 38.2 + - + +
211Q LEU* 3.5 9.4 - - - +
213Q ARG* 1.3 78.0 - - - +
215Q MET* 1.3 74.6 + - + +
217Q SER* 3.0 12.2 + - - +
218Q LEU* 2.9 46.9 + - + +
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Residues in contact with MET 215 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Q ARG* 3.8 32.1 - - - -
79Q PHE* 3.2 47.6 - - + -
211Q LEU* 2.9 26.4 + - + +
212Q ALA 4.0 3.4 - - - +
214Q LYS* 1.3 86.0 - - + +
216Q ALA* 1.3 60.2 + - - +
218Q LEU* 3.3 14.3 + - + +
220Q GLU* 2.9 50.1 + - - +
222Q LEU* 3.8 30.5 - - + +
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Residues in contact with ALA 216 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116Q LEU 4.0 4.5 - - - +
117Q PRO 3.4 28.6 - - - +
118Q ALA 3.8 9.9 - - - +
119Q THR* 3.8 14.1 - - + +
212Q ALA 3.1 19.3 + - - +
213Q ARG 3.2 4.7 + - - +
215Q MET* 1.3 75.1 - - - +
217Q SER* 1.3 57.7 + - - +
219Q GLY* 3.2 17.0 + - - -
221Q PRO* 4.2 13.3 - - - +
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Residues in contact with SER 217 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119Q THR* 4.0 17.0 - - - -
213Q ARG 2.9 14.4 + - - -
214Q LYS* 3.0 19.3 + - - +
216Q ALA* 1.3 72.7 - - - +
218Q LEU* 1.3 67.3 + - - +
219Q GLY 3.1 5.1 + - - -
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Residues in contact with LEU 218 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Q TYR* 5.9 2.9 - - + -
79Q PHE* 4.0 17.9 - - + -
214Q LYS* 2.9 29.0 + - + +
215Q MET* 3.7 31.9 - - + +
216Q ALA 3.2 0.4 - - - -
217Q SER* 1.3 86.0 + - - +
219Q GLY* 1.3 60.5 + - - +
220Q GLU* 3.5 21.0 + - + +
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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