Contacts of the helix formed by residues 203 - 218 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ASP* 3.6 34.2 + - + +
168C GLY* 5.5 4.9 - - - -
123E PHE* 3.9 13.2 - + - -
127E TYR* 4.5 6.1 + - - -
178E LEU* 3.6 26.0 + - + +
179E LYS* 3.6 27.3 + - + +
197E GLY 3.8 1.7 + - - -
200E CYS 3.0 11.2 + - - +
201E LEU 3.1 1.8 + - - -
202E GLY* 1.3 79.2 - - - +
204E PRO* 1.3 68.0 - - + +
205E LEU* 3.1 42.7 + - + +
206E ASN* 2.8 39.1 + - - +
207E ALA 3.7 0.7 + - - -
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Residues in contact with PRO 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E ILE* 3.8 26.9 - - + -
110E LEU* 6.0 0.4 - - + -
178E LEU* 3.4 29.2 - - + +
197E GLY* 3.3 19.1 - - - +
200E CYS* 3.7 17.7 - - + +
203E HIS* 1.3 91.3 - - + +
205E LEU* 1.3 66.4 + - + +
207E ALA* 3.2 15.2 + - - +
208E ALA 3.2 8.5 + - - -
230E THR* 3.7 27.2 - - + +
233E LEU* 4.9 1.3 - - + -
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Residues in contact with LEU 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E LEU* 3.7 21.5 - - + -
123E PHE* 3.5 24.0 - - + +
126E LEU* 3.8 11.7 - - + -
127E TYR* 3.6 51.6 - - + +
130E ILE* 3.6 25.1 - - + -
178E LEU* 4.2 11.4 - - + -
203E HIS* 3.1 16.6 + - + +
204E PRO* 1.3 76.5 - - + +
206E ASN* 1.3 59.3 + - - +
208E ALA* 3.7 4.4 - - - +
209E VAL* 2.8 32.4 + - - +
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Residues in contact with ASN 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C GLY* 3.5 10.4 - - - -
90C ASP 2.9 26.4 + - - -
91C ASN 4.6 0.2 - - - -
92C GLU* 3.5 26.5 + - - +
123E PHE* 3.4 21.5 - - - -
201E LEU* 3.0 34.5 + - + +
202E GLY* 4.1 0.4 - - - -
203E HIS* 2.8 18.3 + - - +
205E LEU* 1.3 76.2 - - - +
207E ALA* 1.3 59.8 + - - +
209E VAL* 3.3 6.0 + - - +
210E TRP* 2.9 30.1 + - - +
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Residues in contact with ALA 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E VAL* 3.9 20.5 - - + +
64E THR* 4.5 3.8 - - + -
200E CYS* 4.5 4.3 - - - -
201E LEU* 3.9 18.0 - - + +
203E HIS 3.7 1.8 + - - -
204E PRO 3.2 9.7 + - - +
206E ASN* 1.3 78.5 - - - +
208E ALA* 1.3 56.7 + - - +
210E TRP* 3.5 3.9 + - - +
211E LEU* 3.0 30.0 + - - +
230E THR* 3.1 31.4 - - - +
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Residues in contact with ALA 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E LEU* 3.7 23.3 - - + -
126E LEU* 3.5 30.5 - - + +
204E PRO 3.2 7.4 + - - +
205E LEU* 3.7 2.9 - - - +
206E ASN 3.3 0.2 - - - -
207E ALA* 1.3 79.4 - - - +
209E VAL* 1.3 57.3 + - - +
211E LEU* 3.4 6.2 + - - +
212E ALA* 2.9 30.8 + - - +
228E ILE* 4.5 16.2 - - + +
230E THR* 4.5 3.5 - - + +
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Residues in contact with VAL 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C GLU* 6.1 0.7 - - - +
121E ILE* 3.7 13.5 - - + +
122E THR 4.3 0.7 - - - -
123E PHE* 3.8 33.7 - - + +
126E LEU* 4.0 20.2 - - + -
205E LEU 2.8 22.9 + - - +
206E ASN* 3.7 6.3 - - - +
208E ALA* 1.3 71.7 - - - +
210E TRP* 1.3 67.6 + - - +
212E ALA* 3.2 4.5 + - - +
213E ARG* 3.1 57.9 + - - +
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Residues in contact with TRP 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E TYR* 4.4 5.6 - - - -
61E VAL* 4.2 8.5 - - + -
76E GLN* 3.7 26.1 + - - +
77E PRO* 3.5 44.0 - - + +
78E ASP* 3.6 38.4 - - - -
79E PHE* 4.2 13.5 - + + -
201E LEU* 4.5 7.2 - - + -
206E ASN 2.9 17.8 + - - +
207E ALA* 3.6 5.4 - - - +
209E VAL* 1.3 78.9 - - - +
211E LEU* 1.3 89.4 + - + +
213E ARG* 3.5 9.8 + - - +
214E LYS* 3.1 46.5 + - + +
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Residues in contact with LEU 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ARG* 3.8 24.7 - - + -
61E VAL* 3.9 15.0 - - + -
79E PHE* 3.7 29.8 - - + -
207E ALA 3.0 17.5 + - - +
208E ALA 3.7 3.1 - - - +
210E TRP* 1.3 82.4 - - + +
212E ALA* 1.3 67.9 + - - +
213E ARG 3.2 0.2 + - - -
214E LYS* 3.2 2.2 + - - +
215E MET* 2.9 45.9 + - + +
222E LEU* 4.1 5.4 - - + -
228E ILE* 3.7 40.2 - - + -
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Residues in contact with ALA 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E LEU* 4.0 33.4 - - + +
118E ALA 4.6 0.4 - - - +
121E ILE* 3.8 18.8 - - + -
126E LEU* 4.4 4.5 - - + -
208E ALA 2.9 17.6 + - - +
209E VAL 3.6 4.3 - - - +
211E LEU* 1.3 76.1 - - - +
213E ARG* 1.3 56.3 - - - +
215E MET* 3.9 1.6 - - - +
216E ALA* 3.1 30.0 + - - +
222E LEU* 3.9 15.3 + - + +
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Residues in contact with ARG 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C CYS 4.7 8.5 + - - -
92C GLU* 5.9 1.6 + - - -
118E ALA 4.6 0.7 - - - -
119E THR* 3.4 25.5 - - - +
120E ASP 4.0 0.4 - - - -
121E ILE* 2.7 39.0 + - + +
122E THR* 4.2 4.8 - - - +
123E PHE 5.2 0.4 - - - +
209E VAL* 3.1 33.0 + - - +
210E TRP* 3.6 11.2 - - - +
212E ALA* 1.3 74.1 - - - +
214E LYS* 1.3 66.0 + - - +
216E ALA* 3.2 6.4 + - - +
217E SER* 2.9 25.4 + - - -
1M MET* 2.8 46.3 - - - +
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Residues in contact with LYS 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E TYR* 4.2 24.5 + - - -
76E GLN* 4.3 21.5 - - - +
79E PHE* 4.5 7.4 - - + -
210E TRP* 3.1 37.8 + - + +
211E LEU* 3.2 10.5 + - - +
213E ARG* 1.3 76.8 - - - +
215E MET* 1.3 75.9 + - + +
217E SER* 3.0 13.0 + - - +
218E LEU* 2.9 46.3 + - + +
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Residues in contact with MET 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ARG* 3.8 31.2 - - - -
79E PHE* 3.2 48.9 - - + -
211E LEU* 2.9 26.3 + - + +
212E ALA 3.9 3.1 - - - +
214E LYS* 1.3 84.3 - - + +
216E ALA* 1.3 61.7 + - - +
218E LEU* 3.3 15.4 + - + +
220E GLU* 3.0 50.1 + - - +
222E LEU* 3.9 30.3 - - + +
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Residues in contact with ALA 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E LEU 4.0 4.0 - - - +
117E PRO 3.4 28.2 - - - +
118E ALA 3.9 9.9 - - - +
119E THR* 3.8 14.5 - - + +
212E ALA 3.1 19.3 + - - +
213E ARG 3.5 4.9 - - - +
215E MET* 1.3 76.8 - - - +
217E SER* 1.3 59.9 + - - +
219E GLY* 3.2 13.9 + - - -
221E PRO* 4.2 14.6 - - - +
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Residues in contact with SER 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E THR* 4.0 15.9 - - - -
213E ARG 2.9 14.6 + - - -
214E LYS* 3.0 18.2 + - - +
216E ALA* 1.3 75.4 - - - +
218E LEU* 1.3 67.8 + - - +
219E GLY 3.1 4.0 + - - -
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Residues in contact with LEU 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E TYR* 5.9 2.9 - - + -
79E PHE* 3.9 18.4 - - + -
214E LYS* 2.9 28.8 + - + +
215E MET* 3.7 32.8 - - + +
216E ALA 3.2 0.4 - - - -
217E SER* 1.3 85.6 + - - +
219E GLY* 1.3 60.2 + - - +
220E GLU* 3.5 19.8 + - + +
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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