Contacts of the helix formed by residues 203 - 218 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90K ASP* 3.6 33.8 + - + +
168K GLY* 5.5 4.6 - - - -
123N PHE* 3.8 13.0 - + - -
127N TYR* 4.5 6.9 + - - -
178N LEU* 3.7 22.6 + - + +
179N LYS* 3.7 26.9 + - + +
197N GLY 3.8 2.2 + - - -
200N CYS 3.0 12.0 + - - +
201N LEU 3.1 1.6 - - - -
202N GLY* 1.3 78.5 - - - +
204N PRO* 1.4 68.2 - - + +
205N LEU* 3.1 46.1 + - + +
206N ASN* 2.8 39.4 + - - +
207N ALA 3.7 0.5 + - - -
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Residues in contact with PRO 204 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108N ILE* 3.9 26.0 - - + -
110N LEU* 6.1 0.4 - - + -
178N LEU* 3.4 28.9 - - + +
197N GLY* 3.3 20.2 - - - +
200N CYS* 4.1 17.7 - - + +
203N HIS* 1.4 88.7 - - + +
205N LEU* 1.3 64.9 + - + +
207N ALA* 3.2 8.3 + - - +
208N ALA 3.2 15.1 + - - -
230N THR* 3.7 28.1 - - + +
233N LEU* 4.9 1.8 - - + -
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Residues in contact with LEU 205 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110N LEU* 3.7 22.9 - - + -
123N PHE* 3.5 25.1 - - + +
126N LEU* 3.7 12.3 - - + +
127N TYR* 3.6 50.5 - - + -
130N ILE* 3.6 25.6 - - + -
178N LEU* 4.2 11.2 - - + -
203N HIS* 3.1 16.2 + - + +
204N PRO* 1.3 75.8 - - + +
206N ASN* 1.3 60.4 + - - +
207N ALA 3.3 0.2 - - - -
208N ALA* 3.4 4.5 + - - +
209N VAL* 2.8 32.1 + - - +
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Residues in contact with ASN 206 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89K GLY* 3.6 10.0 - - - -
90K ASP 2.9 25.6 + - - -
91K ASN 4.6 0.2 + - - -
92K GLU* 3.7 23.5 + - - +
123N PHE* 3.4 21.2 - - - -
201N LEU* 3.0 34.3 + - + +
202N GLY* 4.3 0.6 - - - -
203N HIS* 2.8 18.2 + - - +
205N LEU* 1.3 75.5 - - - +
207N ALA* 1.3 59.8 + - - +
209N VAL* 3.3 6.6 + - - +
210N TRP* 2.9 30.0 + - - +
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Residues in contact with ALA 207 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61N VAL* 3.9 20.5 - - + +
64N THR* 4.5 2.0 - - + -
200N CYS* 4.5 5.8 - - - -
201N LEU* 3.9 18.0 - - + +
203N HIS 3.7 1.4 + - - -
204N PRO 3.2 9.5 + - - +
206N ASN* 1.3 77.9 - - - +
208N ALA* 1.3 55.9 + - - +
210N TRP* 3.4 3.4 + - - +
211N LEU* 3.0 29.6 + - - +
230N THR* 3.1 31.9 - - - +
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Residues in contact with ALA 208 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110N LEU* 3.8 23.6 - - + -
126N LEU* 3.5 30.9 - - + +
204N PRO 3.2 7.2 + - - +
205N LEU* 3.6 2.5 - - - +
206N ASN 3.3 0.2 - - - -
207N ALA* 1.3 78.9 - - - +
209N VAL* 1.3 55.8 + - - +
211N LEU* 3.3 6.0 + - - +
212N ALA* 2.9 30.7 + - - +
228N ILE* 4.5 16.8 - - + +
230N THR* 4.5 3.1 - - + +
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Residues in contact with VAL 209 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121N ILE* 3.6 13.7 - - + +
122N THR 4.3 1.1 - - - -
123N PHE* 3.8 34.1 - - + +
126N LEU* 4.1 20.2 - - + -
205N LEU 2.8 26.7 + - - +
206N ASN* 3.3 7.4 + - - +
208N ALA* 1.3 73.4 - - - +
210N TRP* 1.3 66.4 + - - +
212N ALA* 3.2 4.7 + - - +
213N ARG* 3.1 57.2 + - - +
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Residues in contact with TRP 210 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39N TYR* 4.4 6.1 - - - -
61N VAL* 4.3 5.8 - - + -
76N GLN* 3.7 30.7 + - - +
77N PRO* 3.5 38.9 - - + +
78N ASP* 3.6 38.6 - - - -
79N PHE* 4.2 13.5 - + + -
201N LEU* 4.5 7.6 - - + -
206N ASN 2.9 16.6 + - - +
207N ALA* 3.6 8.5 - - - +
209N VAL* 1.3 79.7 - - - +
211N LEU* 1.3 89.0 + - + +
213N ARG* 3.5 9.6 + - - +
214N LYS* 3.1 46.0 + - + +
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Residues in contact with LEU 211 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59N ARG* 3.7 25.4 - - + -
61N VAL* 3.9 14.4 - - + -
79N PHE* 3.8 28.7 - - + -
207N ALA 3.0 16.8 + - - +
208N ALA 3.7 3.8 - - - +
210N TRP* 1.3 83.7 - - + +
212N ALA* 1.3 65.7 + - - +
213N ARG 3.2 0.2 + - - -
214N LYS* 3.2 2.4 + - - +
215N MET* 2.9 46.5 + - + +
222N LEU* 4.1 6.1 - - + -
228N ILE* 3.7 39.7 - - + -
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Residues in contact with ALA 212 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N LEU* 4.0 33.7 - - + +
118N ALA 4.6 1.1 - - - +
121N ILE* 3.8 18.4 - - + -
126N LEU* 4.4 4.5 - - + -
208N ALA 2.9 17.6 + - - +
209N VAL 3.2 4.2 + - - +
211N LEU* 1.3 76.1 - - - +
213N ARG* 1.3 57.3 + - - +
215N MET* 3.6 1.4 + - - +
216N ALA* 3.1 30.0 + - - +
222N LEU* 3.9 14.9 + - + +
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Residues in contact with ARG 213 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I MET* 2.9 42.2 - - - +
87K CYS 5.0 5.9 + - - -
92K GLU* 5.9 1.4 + - - -
118N ALA 4.6 1.8 - - - -
119N THR* 3.4 24.0 - - - +
120N ASP* 4.0 6.3 - - - +
121N ILE* 2.8 38.2 + - + -
122N THR* 4.3 4.4 - - - +
123N PHE 5.3 0.2 - - - +
209N VAL* 3.1 35.1 + - - +
210N TRP* 3.6 8.0 - - - +
212N ALA* 1.3 73.4 - - - +
214N LYS* 1.3 66.4 + - - +
216N ALA* 3.2 6.4 + - - +
217N SER* 2.9 24.9 + - - -
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Residues in contact with LYS 214 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39N TYR* 4.2 25.3 + - - -
76N GLN* 4.4 20.6 - - - +
79N PHE* 4.5 7.2 - - + -
210N TRP* 3.1 36.5 + - + +
211N LEU* 3.5 9.9 - - - +
213N ARG* 1.3 77.9 - - - +
215N MET* 1.3 73.6 + - + +
217N SER* 3.1 12.9 + - - +
218N LEU* 2.9 47.8 + - + +
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Residues in contact with MET 215 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59N ARG* 3.8 33.7 - - - -
79N PHE* 3.1 46.9 - - + -
211N LEU* 2.9 25.4 + - + +
212N ALA 3.9 3.4 - - - +
214N LYS* 1.3 84.3 - - + +
216N ALA* 1.3 60.4 + - - +
218N LEU* 3.3 15.0 + - + +
220N GLU* 3.0 50.0 + - - +
222N LEU* 3.8 30.7 - - + +
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Residues in contact with ALA 216 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N LEU 4.0 4.3 - - - +
117N PRO 3.4 28.7 - - - +
118N ALA 3.9 9.2 - - - +
119N THR* 3.8 14.0 - - + +
212N ALA 3.1 19.0 + - - +
213N ARG 3.5 4.9 - - - +
214N LYS 3.2 0.2 - - - -
215N MET* 1.3 77.3 - - - +
217N SER* 1.3 57.3 + - - +
219N GLY* 3.1 17.5 + - - -
221N PRO* 4.2 14.0 - - - +
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Residues in contact with SER 217 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119N THR* 3.9 17.0 - - - +
213N ARG 2.9 14.8 + - - -
214N LYS* 3.1 18.7 + - - +
216N ALA* 1.3 75.1 - - - +
218N LEU* 1.3 66.0 + - - +
219N GLY 3.2 3.8 + - - -
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Residues in contact with LEU 218 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39N TYR* 5.9 2.9 - - + -
79N PHE* 3.9 18.8 - - + -
214N LYS* 2.9 28.3 + - + +
215N MET* 3.7 32.3 - - + +
216N ALA 3.2 0.4 - - - -
217N SER* 1.3 85.1 + - - +
219N GLY* 1.3 59.1 - - - +
220N GLU* 3.5 20.2 + - + +
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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
------------------------------------------------------------
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