Contacts of the helix formed by residues 202 - 214 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292B GLY 5.8 0.7 - - - -
294B LYS* 3.4 38.0 + - - +
200G GLY 4.2 1.0 + - - -
201G TRP* 1.3 76.9 - - - +
203G VAL* 1.3 66.7 + - - +
204G HIS* 3.5 11.6 + - - -
205G ASP* 3.3 31.8 + - - +
206G ALA* 2.9 20.7 + - - +
225G THR* 4.6 0.2 - - - -
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Residues in contact with VAL 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ASP* 3.7 35.4 + - + +
292B GLY 3.6 23.7 + - - +
293B LEU* 4.0 8.7 - - + +
201G TRP 4.0 0.2 + - - -
202G SER* 1.3 74.6 - - - +
204G HIS* 1.3 63.4 + - - +
206G ALA* 3.4 2.9 + - - +
207G ILE* 3.1 24.1 + - + +
225G THR* 4.3 4.7 - - + +
232G ALA* 4.3 18.4 - - + +
235G HIS* 3.8 22.9 - - + +
236G VAL* 4.1 21.3 - - + +
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Residues in contact with HIS 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLU* 2.8 51.8 + - + -
220B PHE* 4.0 11.9 - + + -
243B PRO* 3.8 16.8 - - + +
245B VAL* 5.7 0.7 - - + -
266B ASP* 3.9 18.1 + - + +
267B MSE 4.2 30.1 - - + +
294B LYS* 6.0 2.0 - - + -
321B ASP* 4.4 6.7 - - - -
202G SER* 3.4 13.9 + - - -
203G VAL* 1.3 76.9 - - - +
205G ASP* 1.3 85.5 + - - +
207G ILE* 3.4 10.3 + - - +
208G ASN* 3.1 27.3 + - - -
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Residues in contact with ASP 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLU* 4.2 4.5 - - - +
294B LYS* 5.5 2.9 + - - -
201G TRP* 4.4 12.9 - - + -
202G SER* 3.3 28.5 + - - +
204G HIS* 1.3 99.3 + - - +
206G ALA* 1.3 61.4 + - - +
208G ASN* 3.9 5.2 + - - +
209G MSE 2.8 39.1 + - + +
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Residues in contact with ALA 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201G TRP* 3.8 29.5 - - + +
202G SER 2.9 18.4 + - - +
203G VAL 3.5 5.6 - - - +
204G HIS 3.3 0.2 - - - -
205G ASP* 1.3 76.9 - - - +
207G ILE* 1.3 62.3 + - - +
209G MSE 3.9 0.7 - - - +
210G CYS* 2.9 31.9 + - - -
224G PRO* 4.2 8.1 - - + -
225G THR* 4.5 1.3 - - + -
236G VAL* 3.9 25.1 - - + -
240G VAL* 4.6 0.4 - - - -
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Residues in contact with ILE 207 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B GLY 4.0 14.1 - - - +
243B PRO* 3.8 20.4 - - + -
266B ASP* 4.8 5.6 - - - +
203G VAL* 3.1 23.1 + - + +
204G HIS* 3.5 9.9 - - - +
206G ALA* 1.3 77.9 - - - +
208G ASN* 1.3 63.4 + - - +
210G CYS* 3.4 2.9 + - - +
211G ARG* 3.2 21.2 + - + +
235G HIS* 5.0 0.9 - - + +
236G VAL* 4.0 17.9 - - + -
239G LYS* 3.5 44.4 - - + +
240G VAL* 3.6 18.4 - - + +
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Residues in contact with ASN 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ILE 4.1 7.1 - - - +
219B GLU* 2.9 42.4 + - - +
241B GLY 5.0 0.5 - - - +
243B PRO* 3.1 23.6 - - - +
174G GLU* 5.9 1.3 - - - +
204G HIS* 3.1 19.2 + - - +
205G ASP* 3.9 5.4 + - - +
207G ILE* 1.3 77.4 - - - +
209G MSE 1.3 67.3 + - + +
211G ARG* 3.2 23.1 + - - +
212G LYS* 3.1 35.8 + - + +
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Residues in contact with MSE 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G GLU* 3.6 40.2 - - - +
177G ASP* 3.8 32.1 - - + +
178G LEU* 4.1 13.9 - - + -
201G TRP* 3.5 37.7 - - + +
205G ASP* 2.8 27.6 + - + +
206G ALA 4.0 1.3 - - - +
208G ASN* 1.3 73.4 - - + +
210G CYS* 1.3 63.4 + - - +
212G LYS* 3.2 5.8 + - + +
213G LEU* 2.9 50.4 + - + +
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Residues in contact with CYS 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201G TRP* 4.7 6.1 - - - -
206G ALA* 2.9 24.8 + - - +
209G MSE 1.3 75.8 - - - +
211G ARG* 1.3 63.6 + - - +
213G LEU* 3.3 0.8 + - - +
214G GLU* 3.1 28.4 + - - +
221G ILE* 3.6 26.5 - - - -
224G PRO* 5.7 0.9 - - - -
236G VAL* 5.1 2.5 - - - -
240G VAL* 3.5 40.6 - - + -
241G GLY 5.3 0.7 - - - +
242G ILE* 3.4 15.8 - - + +
244G ILE* 4.4 9.6 - - - -
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Residues in contact with ARG 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLU* 4.1 34.7 + - - +
217B ASP* 3.1 35.0 + - - +
218B ILE 4.5 11.7 + - - +
241B GLY* 5.2 9.1 + - - -
207G ILE* 3.2 14.4 + - + +
208G ASN* 3.5 20.9 + - - +
209G MSE 3.2 0.2 - - - -
210G CYS* 1.3 80.3 - - - +
212G LYS* 1.3 83.8 - - - +
213G LEU 3.4 0.3 + - - -
214G GLU* 3.5 29.8 + - - +
215G LYS 4.8 0.7 + - - -
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Residues in contact with LYS 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ASP 6.0 0.2 + - - -
217B ASP* 3.1 37.8 + - - -
174G GLU* 2.9 46.0 + - + +
178G LEU* 3.6 28.6 - - + +
208G ASN* 3.1 25.1 + - + +
209G MSE 3.8 7.4 - - + +
211G ARG* 1.3 97.6 - - - +
213G LEU* 1.3 58.9 + - - +
214G GLU 3.5 0.2 - - - -
215G LYS* 3.9 21.0 - - - +
216G TYR* 4.1 0.7 - - - -
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Residues in contact with LEU 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170G VAL* 5.2 3.1 - - + -
177G ASP* 4.4 4.3 - - + +
178G LEU* 3.8 17.7 - - + -
181G THR* 3.5 36.6 - - + +
195G LEU* 3.8 22.7 - - + -
201G TRP* 3.8 26.7 - - + -
209G MSE 2.9 32.1 + - + +
210G CYS 3.3 3.3 + - - +
212G LYS* 1.3 76.0 - - - +
214G GLU* 1.3 65.9 + - - +
215G LYS 3.2 3.1 - - - -
216G TYR* 3.0 19.9 + - + +
218G ILE* 3.6 14.4 - - + +
221G ILE* 4.2 5.4 - - + -
242G ILE* 4.4 7.2 - - + -
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Residues in contact with GLU 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D ARG* 4.6 23.6 + - - -
210G CYS 3.1 17.7 + - - +
211G ARG* 3.5 26.3 + - - +
213G LEU* 1.3 77.8 - - - +
215G LYS* 1.3 61.6 + - - +
216G TYR 3.1 1.4 + - - -
217G ASP* 3.1 14.9 + - - -
218G ILE* 4.6 1.5 + - - +
241G GLY* 4.6 21.7 + - - -
242G ILE* 3.8 21.1 - - + +
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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