Contacts of the helix formed by residues 209 - 221 (chain A) in PDB entry 1WSQ
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 GLY 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A PRO 2.9 16.0 + - - -
206A GLN 4.6 0.8 - - - -
207A THR 3.4 2.6 - - - -
208A GLU* 1.3 83.1 - - - +
210A VAL* 1.3 64.9 + - - -
211A ASN 3.5 2.4 + - - -
212A ALA* 3.6 2.8 + - - -
213A VAL* 3.4 20.6 + - - +
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Residues in contact with VAL 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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205A PRO* 3.8 15.0 + - + +
209A GLY* 1.3 72.4 - - - -
211A ASN* 1.3 68.7 + - - +
213A VAL* 3.4 1.1 + - - -
214A GLU* 2.8 33.0 + - - +
233A LEU* 3.5 39.2 - - + +
234A TYR* 3.8 43.7 - - + +
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Residues in contact with ASN 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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209A GLY 3.5 0.4 - - - -
210A VAL* 1.3 86.6 - - - +
212A ALA* 1.3 61.7 + - - +
214A GLU* 3.2 17.7 + - - +
215A ASP* 3.0 34.5 + - - +
234A TYR* 4.9 2.9 + - - -
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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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203A GLN* 5.5 0.9 - - - -
208A GLU* 3.7 22.0 - - + +
209A GLY* 3.6 2.1 + - - -
210A VAL 3.3 0.4 - - - -
211A ASN* 1.3 78.8 - - - +
213A VAL* 1.3 61.6 + - + +
215A ASP* 3.5 8.6 + - - +
216A GLU* 3.3 19.9 + - - +
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Residues in contact with VAL 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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203A GLN* 4.0 32.1 - - + +
205A PRO* 4.0 17.7 - - + -
208A GLU* 3.9 23.8 - - + +
209A GLY 3.4 16.3 + - - +
210A VAL 3.9 2.9 - - - +
211A ASN 3.3 0.4 - - - -
212A ALA* 1.3 75.9 - - + +
214A GLU* 1.3 63.7 + - - +
216A GLU* 3.1 3.3 + - - +
217A ILE* 2.9 23.2 + - + +
233A LEU* 4.0 14.4 - - + -
239A ILE* 3.9 28.7 - - + -
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Residues in contact with GLU 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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210A VAL* 2.8 21.9 + - - +
211A ASN* 3.2 21.6 + - - +
213A VAL* 1.3 77.8 - - - +
215A ASP* 1.3 63.5 + - - +
217A ILE* 3.3 4.5 + - + +
218A LYS* 2.9 67.5 + - + +
233A LEU* 3.6 17.0 - - + +
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Residues in contact with ASP 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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211A ASN* 3.0 24.9 + - - +
212A ALA* 3.7 8.2 - - - +
214A GLU* 1.3 82.7 - - - +
216A GLU* 1.3 61.5 - - - +
218A LYS* 3.5 4.7 + - - +
219A LYS* 3.1 25.3 + - - +
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Residues in contact with GLU 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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82A HIS* 5.9 1.9 + - - -
89A ARG* 4.7 7.4 + - - -
175A ARG* 3.1 32.7 + - - +
199A THR* 5.0 3.1 + - - -
203A GLN* 3.2 28.8 + - - +
212A ALA 3.3 8.9 + - - +
213A VAL 3.1 9.4 + - - +
215A ASP* 1.3 79.6 - - - +
217A ILE* 1.3 62.4 + - - +
219A LYS* 3.2 3.0 + - - -
220A TYR* 3.0 52.7 + - + +
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Residues in contact with ILE 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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175A ARG* 4.4 9.0 - - - +
203A GLN* 4.3 11.4 - - - +
213A VAL* 2.9 30.9 + - + +
214A GLU* 3.8 7.6 - - - +
216A GLU* 1.3 76.6 - - - +
218A LYS* 1.3 59.9 + - + +
220A TYR* 5.3 0.2 - - - -
221A THR* 2.7 52.5 + - + +
226A ARG* 3.6 24.0 - - - +
230A MET* 4.0 48.9 - - + +
233A LEU* 4.9 0.7 - - + -
239A ILE* 4.1 14.6 - - + -
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Residues in contact with LYS 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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214A GLU* 2.9 51.2 + - + +
215A ASP* 4.2 4.9 - - - +
217A ILE* 1.3 79.8 - - + +
219A LYS* 1.3 62.1 + - - +
221A THR 4.1 7.6 - - - +
226A ARG* 3.8 31.2 + - - +
266A GLN* 5.3 9.4 + - - +
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Residues in contact with LYS 219 (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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82A HIS* 6.4 1.1 - - + -
83A ASP* 4.1 19.4 + - - -
215A ASP 3.1 18.4 + - - +
216A GLU* 3.2 5.1 + - - +
218A LYS* 1.3 79.1 - - - +
220A TYR* 1.3 101.8 + - + +
221A THR 3.7 0.6 - - - +
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Residues in contact with TYR 220 (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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82A HIS* 4.7 7.9 - + - -
83A ASP* 4.2 5.5 + - - -
86A VAL* 3.8 32.2 - - + +
89A ARG* 6.0 2.0 - - - -
175A ARG* 3.6 24.1 - - - +
176A ASP* 4.1 6.5 - - - +
196A GLY 3.7 19.1 - - - -
197A SER* 2.6 46.2 + - - +
216A GLU* 3.0 45.4 + - + +
219A LYS* 1.3 122.6 + - + +
221A THR* 1.3 63.5 + - + +
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Residues in contact with THR 221 (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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175A ARG* 3.4 28.0 - - + +
176A ASP* 4.4 0.9 - - - -
217A ILE* 2.7 32.4 + - + +
218A LYS 4.1 5.4 - - - +
219A LYS 5.0 0.5 - - - -
220A TYR* 1.3 83.1 - - + +
222A THR* 1.3 62.9 + - - +
223A LEU 3.9 0.2 + - - -
226A ARG* 2.8 42.4 + - - -
230A MET* 4.0 28.5 - - + -
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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