Contacts of the helix formed by residues 202 - 214 (chain A) in PDB entry 2PGW
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 SER 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A GLY 4.3 0.6 + - - -
201A TRP* 1.3 78.4 - - - +
203A VAL* 1.3 65.7 + - - +
204A HIS* 3.6 11.6 + - - -
205A ASP* 3.5 31.3 + - - +
206A ALA* 3.0 18.4 + - - +
225A THR* 4.5 0.9 - - - -
292E GLY 5.7 1.8 - - - -
294E LYS* 3.4 37.7 + - - +
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Residues in contact with VAL 203 (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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202A SER* 1.3 75.2 - - - +
204A HIS* 1.3 64.7 + - - +
206A ALA* 3.4 2.8 + - - +
207A ILE* 3.2 24.2 + - + +
225A THR* 4.4 8.5 - - + +
232A ALA* 4.5 12.3 - - + +
235A HIS* 3.6 38.1 - - + +
236A VAL* 4.0 21.1 - - + +
266E ASP* 3.7 22.6 + - + +
292E GLY 3.5 24.2 + - - +
293E LEU* 4.0 10.0 - - + +
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Residues in contact with HIS 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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202A SER* 3.5 13.8 + - - -
203A VAL* 1.3 77.6 - - - +
205A ASP* 1.3 86.2 + - - +
207A ILE* 3.4 10.4 + - - +
208A ASN* 3.1 29.6 + - - -
219E GLU* 2.8 52.5 + - + +
220E PHE* 4.0 11.7 - + + -
243E PRO* 3.7 18.5 - - + +
245E VAL* 5.8 0.7 - - + -
266E ASP* 4.0 15.4 + - + +
267E MSE 4.5 26.2 - - + +
294E LYS* 6.0 2.7 - - + +
321E ASP* 4.7 6.1 - - - -
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Residues in contact with ASP 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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201A TRP* 4.3 13.4 - - + -
202A SER* 3.4 28.3 + - - +
203A VAL 3.3 0.4 - - - -
204A HIS* 1.3 98.2 + - - +
206A ALA* 1.3 56.2 + - - +
208A ASN* 4.0 5.4 + - - +
209A MSE 2.7 44.1 + - + +
192E ARG* 5.8 0.7 + - - -
219E GLU* 4.3 4.5 - - - +
294E LYS* 5.4 3.8 + - - -
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Residues in contact with ALA 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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201A TRP* 3.8 28.9 - - + +
202A SER 3.0 19.5 + - - +
203A VAL 3.5 4.5 - - - +
204A HIS 3.3 0.2 - - - -
205A ASP* 1.3 78.6 - - - +
207A ILE* 1.3 62.1 + - - +
209A MSE 4.0 0.5 - - - +
210A CYS* 3.0 31.6 + - - -
224A PRO* 4.1 7.9 - - + -
225A THR* 4.6 1.6 - - + -
236A VAL* 3.9 24.7 - - + -
240A VAL* 4.6 1.1 - - - -
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Residues in contact with ILE 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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203A VAL* 3.2 22.4 + - + +
204A HIS* 3.6 8.7 - - - +
205A ASP 3.2 0.2 - - - -
206A ALA* 1.3 77.6 - - - +
208A ASN* 1.3 63.5 + - - +
210A CYS* 3.7 2.6 - - - +
211A ARG* 3.1 21.7 + - + +
235A HIS* 4.8 2.9 - - + +
236A VAL* 4.8 6.1 - - + -
239A LYS* 3.8 39.5 - - + -
240A VAL* 3.8 15.4 - - + +
241E GLY 4.2 13.5 - - - +
243E PRO* 3.9 18.4 - - + -
266E ASP* 3.5 33.0 - - - +
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Residues in contact with ASN 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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174A GLU* 5.8 1.6 - - - +
204A HIS* 3.1 24.9 + - - +
205A ASP* 4.0 5.2 + - - +
207A ILE* 1.3 76.0 - - - +
209A MSE 1.3 66.5 + - + +
211A ARG* 3.2 32.5 + - - +
212A LYS* 2.9 34.2 + - + +
218E ILE 4.1 3.4 - - - +
219E GLU* 2.9 37.0 + - - +
241E GLY 4.9 0.5 - - - +
243E PRO* 3.4 19.2 - - - +
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Residues in contact with MSE 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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174A GLU* 3.6 47.3 - - + +
177A ASP* 3.8 32.8 - - + +
178A LEU* 4.4 6.3 - - + -
201A TRP* 3.6 39.3 - - + +
205A ASP* 2.7 29.8 + - + +
208A ASN* 1.3 74.4 - - + +
210A CYS* 1.3 57.4 + - - +
212A LYS* 3.2 3.9 + - + +
213A LEU* 2.9 57.9 + - + +
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Residues in contact with CYS 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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201A TRP* 4.6 5.8 - - - -
206A ALA* 3.0 26.0 + - - +
207A ILE 3.7 0.4 - - - +
209A MSE 1.3 76.0 - - - +
211A ARG* 1.3 63.9 - - - +
213A LEU* 3.2 0.9 + - - -
214A GLU* 3.1 28.6 + - - +
221A ILE* 3.5 26.7 - - - -
224A PRO* 5.7 0.7 - - - -
236A VAL* 5.1 2.0 - - - -
240A VAL* 3.6 38.8 - - + -
241A GLY 5.3 0.4 - - - +
242A ILE* 3.4 16.8 - - + +
244A ILE* 4.5 9.4 - - - -
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Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A ILE* 3.1 12.2 + - + +
208A ASN* 3.2 31.1 + - - +
210A CYS* 1.3 81.0 - - - +
212A LYS* 1.3 83.6 + - - +
213A LEU 3.5 0.2 + - - -
214A GLU* 3.5 31.2 - - - +
215A LYS 4.9 0.7 + - - -
214E GLU* 5.1 14.5 + - - -
217E ASP* 3.0 33.8 + - - +
218E ILE 4.3 9.3 + - - +
241E GLY* 4.8 14.7 + - - -
242E ILE* 6.3 0.8 - - - +
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Residues in contact with LYS 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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174A GLU* 2.7 48.5 + - + +
178A LEU* 3.4 29.4 - - + +
208A ASN* 2.9 24.1 + - - +
209A MSE 3.2 7.6 + - + +
211A ARG* 1.3 96.7 - - - +
213A LEU* 1.3 59.7 + - - +
215A LYS* 3.9 18.1 - - - +
216A TYR* 4.1 0.3 - - - -
217E ASP* 3.1 38.9 + - - -
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Residues in contact with LEU 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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170A VAL* 5.2 2.7 - - + -
177A ASP* 4.5 4.9 - - + +
178A LEU* 3.6 19.5 - - + -
181A THR* 3.7 29.4 - - + +
195A LEU* 3.8 25.4 - - + -
201A TRP* 3.7 29.4 - - + -
209A MSE 2.9 34.5 + - + +
210A CYS 3.2 3.5 + - - +
212A LYS* 1.3 76.1 - - - +
214A GLU* 1.3 65.4 + - - +
215A LYS 3.2 2.9 - - - -
216A TYR* 3.0 23.6 + - + +
218A ILE* 3.6 8.6 - - + +
221A ILE* 4.1 6.1 - - + -
242A ILE* 4.4 6.5 - - + -
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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 CYS 3.1 17.0 + - - +
211A ARG* 3.5 29.2 + - - +
212A LYS 3.4 1.0 - - - -
213A LEU* 1.3 75.6 - - - +
215A LYS* 1.3 58.8 + - - +
216A TYR 3.0 6.6 + - - -
217A ASP* 3.2 13.9 + - - -
218A ILE* 4.6 2.0 + - - +
241A GLY* 4.4 20.2 + - - -
242A ILE* 4.0 21.1 - - + +
211F ARG* 5.3 18.4 + - - -
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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