Contacts of the helix formed by residues 202 - 214 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A GLY 5.8 0.9 - - - -
294A LYS* 3.5 35.8 + - - +
200F GLY 4.3 0.2 + - - -
201F TRP* 1.3 76.9 - - - +
203F VAL* 1.3 66.6 + - - +
204F HIS* 3.4 12.2 + - - -
205F ASP* 3.4 31.6 + - - +
206F ALA* 2.9 20.7 + - - +
225F THR* 4.6 1.1 - - - -
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Residues in contact with VAL 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ARG* 4.4 9.4 - - - +
266A ASP* 3.6 37.4 + - + +
292A GLY 3.5 25.1 + - - +
293A LEU* 3.8 9.6 - - + +
202F SER* 1.3 74.0 - - - +
204F HIS* 1.3 62.9 + - - +
206F ALA* 3.4 2.6 + - - +
207F ILE* 3.2 26.8 + - + +
225F THR* 4.5 4.8 - - + +
232F ALA* 4.4 10.1 - - + +
235F HIS* 3.7 20.4 - - + +
236F VAL* 4.2 20.7 - - + +
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Residues in contact with HIS 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ARG* 4.7 0.7 - - - -
219A GLU* 2.8 51.7 + - + +
220A PHE* 4.0 11.6 - + + -
243A PRO* 3.7 21.9 - - + +
245A VAL* 5.8 0.7 - - + -
266A ASP* 3.9 19.3 + - + +
267A MSE 4.4 27.3 - - + +
294A LYS* 6.0 4.2 - - + +
321A ASP* 4.6 6.7 - - - -
202F SER* 3.4 16.2 + - - -
203F VAL* 1.3 77.2 - - - +
205F ASP* 1.3 82.4 + - - +
207F ILE* 3.4 4.1 + - - +
208F ASN* 3.1 27.2 + - - -
2600F GOL 3.8 1.6 - - - -
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Residues in contact with ASP 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG* 5.8 0.2 + - - -
219A GLU* 4.1 2.1 - - - +
294A LYS* 5.2 5.2 + - - -
201F TRP* 4.3 12.4 - - + -
202F SER* 3.3 27.2 + - - +
204F HIS* 1.3 92.2 + - - +
206F ALA* 1.3 57.6 + - - +
208F ASN* 3.3 0.9 + - - +
209F MSE 2.8 41.3 + - + +
2600F GOL 2.5 39.1 + - - +
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Residues in contact with ALA 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F TRP* 3.7 29.0 - - + +
202F SER 2.9 18.0 + - - +
203F VAL 3.6 4.7 - - - +
205F ASP* 1.3 77.8 - - - +
207F ILE* 1.3 62.6 + - - +
209F MSE 4.1 0.2 - - - +
210F CYS* 3.0 32.4 + - - -
224F PRO* 4.1 8.7 - - + -
225F THR* 4.5 2.2 - - + -
236F VAL* 3.8 23.8 - - + -
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Residues in contact with ILE 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ARG* 5.3 0.4 - - - +
241A GLY 4.2 13.9 - - - +
243A PRO* 3.9 17.7 - - + -
266A ASP* 3.6 32.5 - - - +
203F VAL* 3.2 21.2 + - + +
204F HIS* 3.7 8.1 - - - +
205F ASP 3.3 0.2 - - - -
206F ALA* 1.3 78.2 - - - +
208F ASN* 1.3 62.3 + - - +
210F CYS* 3.8 2.8 - - - +
211F ARG* 3.2 21.3 + - + +
235F HIS* 4.8 4.0 - - + +
236F VAL* 4.5 7.2 - - + -
239F LYS* 3.7 42.2 - - + -
240F VAL* 3.7 14.5 - - + +
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Residues in contact with ASN 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ILE 4.2 6.3 - - - +
219A GLU* 2.9 27.5 + - - +
241A GLY 5.0 0.9 - - - +
243A PRO* 3.2 22.6 - - - +
204F HIS* 3.1 17.0 + - - +
207F ILE* 1.3 75.4 - - - +
209F MSE 1.3 65.5 + - - +
211F ARG* 3.1 19.7 + - - +
212F LYS* 3.0 29.2 + - - +
2600F GOL 2.9 46.8 + - - +
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Residues in contact with MSE 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F GLU* 3.7 28.5 - - + +
177F ASP* 3.6 38.4 - - + +
178F LEU* 4.6 5.8 - - + -
201F TRP* 3.7 40.6 - - + +
205F ASP* 2.8 25.6 + - + +
206F ALA 4.1 0.2 - - - +
208F ASN* 1.3 73.0 - - - +
210F CYS* 1.3 62.8 + - - +
212F LYS* 3.1 6.7 + - - +
213F LEU* 2.9 44.5 + - + +
2600F GOL 3.2 27.8 - - - +
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Residues in contact with CYS 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F TRP* 4.7 5.1 - - - -
206F ALA* 3.0 25.0 + - - +
207F ILE 3.8 0.2 - - - +
209F MSE 1.3 74.8 - - - +
211F ARG* 1.3 62.7 + - - +
213F LEU 3.3 0.3 + - - -
214F GLU* 3.1 29.1 + - - +
221F ILE* 3.5 27.1 - - - -
224F PRO* 5.7 0.4 - - - -
236F VAL* 5.2 1.8 - - - -
240F VAL* 3.5 41.5 - - + -
241F GLY 5.3 0.9 - - - +
242F ILE* 3.3 15.4 - - + +
244F ILE* 4.4 10.1 - - - -
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Residues in contact with ARG 211 (chain F).
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* 5.3 17.7 + - - -
217A ASP* 2.9 36.0 + - - +
218A ILE 5.0 4.6 + - - +
241A GLY* 4.8 14.4 + - - -
207F ILE* 3.2 10.8 + - + +
208F ASN* 3.1 22.8 + - - +
210F CYS* 1.3 81.0 - - - +
212F LYS* 1.3 84.6 + - - +
213F LEU 3.5 0.3 + - - -
214F GLU* 3.7 25.7 + - - +
215F LYS* 4.9 1.2 + - - -
2600F GOL 5.0 1.0 + - - -
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Residues in contact with LYS 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ASP* 3.1 38.0 + - - -
174F GLU* 2.7 39.3 + - + +
178F LEU* 3.5 29.8 - - + +
208F ASN 3.0 15.0 + - - +
209F MSE 3.1 8.2 + - - +
211F ARG* 1.3 97.7 - - - +
213F LEU* 1.3 59.6 + - - +
214F GLU 3.5 0.4 - - - -
215F LYS* 3.9 24.5 - - - +
216F TYR* 4.1 0.2 - - - -
2600F GOL 2.9 25.0 + - - +
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Residues in contact with LEU 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F VAL* 5.0 4.5 - - + -
177F ASP* 4.5 5.4 - - + +
178F LEU* 3.7 22.0 - - + -
181F THR* 3.5 36.1 - - + +
195F LEU* 3.6 24.0 - - + -
201F TRP* 3.9 25.6 - - + -
209F MSE 2.9 28.4 + - + +
210F CYS 4.0 2.7 - - - +
211F ARG 3.3 0.2 - - - -
212F LYS* 1.3 76.7 - - - +
214F GLU* 1.3 64.4 + - - +
215F LYS 3.2 2.9 - - - -
216F TYR* 3.0 23.8 + - + +
218F ILE* 3.5 8.7 - - - +
221F ILE* 4.1 6.3 - - + -
242F ILE* 4.3 8.1 - - + -
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Residues in contact with GLU 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F CYS 3.1 25.1 + - - +
211F ARG* 3.7 20.9 - - - +
212F LYS 3.5 0.8 - - - -
213F LEU* 1.3 76.5 - - - +
215F LYS* 1.3 59.1 + - - +
216F TYR 2.9 6.2 + - - -
217F ASP* 2.9 15.6 + - - -
218F ILE* 4.5 2.3 + - - +
241F GLY* 3.7 28.8 - - - -
242F ILE* 3.8 19.1 - - + +
211H ARG* 4.6 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
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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