Contacts of the helix formed by residues 203 - 218 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A PHE* 3.8 12.6 - + - -
127A TYR* 4.5 6.3 + - - -
178A LEU* 3.6 22.6 + - + +
179A LYS* 3.6 28.2 + - + +
197A GLY 3.8 2.2 + - - -
200A CYS 3.0 11.0 + - - +
201A LEU 3.1 2.0 + - - -
202A GLY* 1.3 79.4 - - - +
204A PRO* 1.3 69.4 - - + +
205A LEU* 3.1 46.7 + - + +
206A ASN* 2.8 39.4 + - - +
207A ALA 3.7 0.5 + - - -
90B ASP* 3.6 34.0 + - + +
168B GLY* 5.5 4.6 - - - -
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Residues in contact with PRO 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ILE* 3.9 26.7 - - + -
110A LEU* 6.1 0.2 - - + -
178A LEU* 3.4 28.0 - - + +
197A GLY* 3.3 21.1 - - - +
200A CYS* 3.7 17.5 - - + +
203A HIS* 1.3 88.8 - - + +
205A LEU* 1.3 65.8 + - + +
207A ALA* 3.2 8.0 + - - +
208A ALA 3.2 15.2 + - - -
230A THR* 3.7 27.3 - - + +
233A LEU* 4.9 1.6 - - + -
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 3.7 22.2 - - + -
123A PHE* 3.5 25.4 - - + +
126A LEU* 3.8 12.1 - - + -
127A TYR* 3.6 52.3 - - + +
130A ILE* 3.6 24.0 - - + -
178A LEU* 4.2 11.9 - - + -
203A HIS* 3.1 16.2 + - + +
204A PRO* 1.3 77.4 - - + +
206A ASN* 1.3 60.0 + - - +
207A ALA 3.3 0.2 - - - -
208A ALA* 3.6 4.5 - - - +
209A VAL* 2.8 31.9 + - - +
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Residues in contact with ASN 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PHE* 3.4 20.4 - - - -
201A LEU* 3.0 34.7 + - + +
202A GLY* 4.1 0.8 - - - -
203A HIS* 2.8 18.8 + - - +
205A LEU* 1.3 75.9 - - - +
207A ALA* 1.3 59.8 + - - +
209A VAL* 3.7 5.8 - - - +
210A TRP* 2.9 31.0 + - - +
89B GLY* 3.5 10.7 - - - -
90B ASP 2.9 24.6 + - - -
91B ASN 4.6 0.2 - - - -
92B GLU* 3.5 25.7 + - - +
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Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 3.9 22.3 - - + +
64A THR* 4.5 4.3 - - + -
200A CYS* 4.6 4.0 - - - -
201A LEU* 3.9 18.4 - - + +
203A HIS 3.7 1.6 + - - -
204A PRO 3.2 9.7 + - - +
206A ASN* 1.3 75.2 - - - +
208A ALA* 1.3 60.0 + - - +
210A TRP* 3.4 3.1 + - - +
211A LEU* 3.0 29.5 + - - +
230A THR* 3.2 29.6 - - - +
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 3.8 22.7 - - + -
126A LEU* 3.5 31.5 - - + +
204A PRO 3.2 7.6 + - - +
205A LEU* 3.6 2.9 - - - +
206A ASN 3.3 0.2 - - - -
207A ALA* 1.3 78.8 - - - +
209A VAL* 1.3 57.9 + - - +
211A LEU* 3.4 5.4 + - - +
212A ALA* 2.9 30.8 + - - +
228A ILE* 4.5 16.6 - - + +
230A THR* 4.5 3.9 - - + +
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 3.6 14.3 - - + +
122A THR 4.3 1.1 - - - -
123A PHE* 3.8 33.7 - - + +
126A LEU* 4.1 20.0 - - + -
205A LEU 2.8 23.8 + - - +
206A ASN* 3.2 6.7 + - - +
208A ALA* 1.3 70.8 - - - +
210A TRP* 1.3 67.4 + - - +
212A ALA* 3.2 4.8 + - - +
213A ARG* 3.1 58.6 + - - +
92B GLU* 6.2 0.4 - - - +
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Residues in contact with TRP 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR* 4.3 6.5 - - - -
61A VAL* 4.2 9.0 - - + -
76A GLN* 3.7 28.0 + - - +
77A PRO* 3.5 44.5 - - + +
78A ASP* 3.6 37.5 - - - -
79A PHE* 4.2 12.8 - + + -
201A LEU* 4.5 6.7 - - + -
206A ASN 2.9 16.3 + - - +
207A ALA* 3.6 5.8 - - - +
209A VAL* 1.3 79.6 - - - +
211A LEU* 1.3 90.2 + - + +
213A ARG* 3.4 10.2 + - - +
214A LYS* 3.1 46.5 + - + +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ARG* 3.7 26.0 - - + -
61A VAL* 3.8 14.8 - - + -
79A PHE* 3.7 29.6 - - + -
207A ALA 3.0 17.3 + - - +
208A ALA 3.7 3.1 - - - +
210A TRP* 1.3 83.0 - - + +
212A ALA* 1.3 64.7 + - - +
213A ARG 3.2 0.2 + - - -
214A LYS* 3.2 2.2 + - - +
215A MET* 2.9 49.1 + - + +
222A LEU* 4.1 6.1 - - + -
228A ILE* 3.7 40.6 - - + -
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 4.1 32.4 - - + +
118A ALA 4.6 0.8 - - - +
121A ILE* 3.9 18.8 - - + -
126A LEU* 4.4 3.8 - - + -
208A ALA 2.9 18.8 + - - +
209A VAL 3.2 4.7 + - - +
211A LEU* 1.3 75.0 - - - +
213A ARG* 1.3 58.2 + - - +
215A MET* 3.6 1.7 + - - +
216A ALA* 3.1 29.2 + - - +
222A LEU* 3.9 15.5 - - + +
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Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ALA 4.6 0.7 - - - -
119A THR* 3.4 25.8 - - - +
120A ASP* 4.0 7.8 + - - +
121A ILE* 2.8 41.9 + - + +
122A THR* 4.3 7.3 - - - +
123A PHE 5.2 0.4 - - - +
209A VAL* 3.1 32.0 + - - +
210A TRP* 3.6 12.1 - - - +
212A ALA* 1.3 74.1 - - - +
214A LYS* 1.3 66.8 + - - +
216A ALA* 3.2 7.2 + - - +
217A SER* 2.9 24.9 + - - -
84B ALA 5.3 3.2 + - - -
87B CYS 4.8 10.9 + - - -
92B GLU* 5.9 0.6 + - - -
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Residues in contact with LYS 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR* 4.2 25.9 + - - -
76A GLN* 4.3 20.5 - - - +
79A PHE* 4.5 7.1 - - + -
210A TRP* 3.1 36.3 + - + +
211A LEU* 3.5 10.3 - - - +
213A ARG* 1.3 77.8 - - - +
215A MET* 1.3 74.4 + - + +
217A SER* 3.0 12.9 + - - +
218A LEU* 2.9 46.1 + - + +
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Residues in contact with MET 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ARG* 3.8 33.2 - - - -
79A PHE* 3.1 47.8 - - + -
211A LEU* 2.9 27.1 + - + +
212A ALA 4.0 2.9 - - - +
214A LYS* 1.3 85.5 - - + +
216A ALA* 1.3 60.6 + - - +
218A LEU* 3.3 13.2 + - + +
220A GLU* 3.0 50.2 + - - +
222A LEU* 3.8 30.3 - - + +
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Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU 4.0 7.9 - - - +
117A PRO* 3.4 24.2 - - + +
118A ALA 3.9 9.6 - - - +
119A THR* 3.8 15.3 - - + +
212A ALA 3.1 19.5 + - - +
213A ARG 3.5 4.5 - - - +
215A MET* 1.3 77.6 - - - +
217A SER* 1.3 61.1 + - - +
219A GLY* 3.2 13.7 + - - -
221A PRO* 4.2 14.3 - - - +
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Residues in contact with SER 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A THR* 3.9 16.5 - - - +
213A ARG 2.9 13.9 + - - -
214A LYS* 3.0 19.1 + - - +
216A ALA* 1.3 76.7 - - - +
218A LEU* 1.3 67.1 + - - +
219A GLY 3.2 2.3 + - - -
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR* 5.8 2.9 - - + -
79A PHE* 3.9 32.1 - - + -
214A LYS* 2.9 27.9 + - + +
215A MET* 3.7 18.2 - - + +
216A ALA 3.2 0.4 - - - -
217A SER* 1.3 83.7 + - - +
219A GLY* 1.3 59.9 + - - +
220A GLU* 3.5 20.5 + - + +
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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