Contacts of the helix formed by residues 202 - 214 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292F GLY 5.7 1.3 - - - -
294F LYS* 3.4 35.6 - - - +
201H TRP* 1.3 79.6 - - - +
203H VAL* 1.3 66.4 + - - +
204H HIS* 3.5 11.4 + - - -
205H ASP* 3.3 32.7 + - - +
206H ALA* 2.9 19.1 + - - +
225H THR* 4.6 0.9 - - - -
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Residues in contact with VAL 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F ARG* 4.4 9.4 - - - +
266F ASP* 3.8 24.9 + - - +
292F GLY 3.5 24.6 + - - +
293F LEU* 3.8 10.3 - - + +
202H SER* 1.3 73.9 - - - +
204H HIS* 1.3 63.2 + - - +
206H ALA* 3.3 2.9 + - - +
207H ILE* 3.2 27.2 + - + +
225H THR* 4.6 4.0 - - + +
232H ALA* 4.4 10.3 - - + +
235H HIS* 3.6 33.4 - - + +
236H VAL* 4.1 19.9 - - + +
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Residues in contact with HIS 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194F ARG* 4.7 0.2 - - - -
219F GLU* 2.8 51.3 + - + +
220F PHE* 3.8 13.3 - + + -
243F PRO* 3.8 22.1 - - + +
245F VAL* 5.8 0.7 - - + -
266F ASP* 4.0 16.8 + - + +
267F MSE 4.4 26.7 - - + +
294F LYS* 5.4 3.8 - - - -
321F ASP* 4.5 8.1 - - - -
202H SER* 3.4 14.6 + - - -
203H VAL* 1.3 78.2 - - - +
205H ASP* 1.3 84.8 + - - +
207H ILE* 3.5 4.2 + - - +
208H ASN* 3.1 29.9 + - - -
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Residues in contact with ASP 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F GLU* 4.3 5.0 - - - +
294F LYS* 4.6 6.9 + - - -
201H TRP* 4.3 12.1 - - + -
202H SER* 3.3 28.3 + - - +
203H VAL 3.3 0.6 - - - -
204H HIS* 1.3 97.1 + - - +
206H ALA* 1.3 61.8 + - - +
208H ASN* 3.4 6.2 + - - +
209H MSE 2.9 38.7 + - + +
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Residues in contact with ALA 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201H TRP* 3.6 28.2 - - + +
202H SER 2.9 18.3 + - - +
203H VAL 3.5 5.4 - - - +
205H ASP* 1.3 77.3 - - - +
207H ILE* 1.3 62.3 + - - +
209H MSE 3.4 0.9 + - - +
210H CYS* 3.0 32.2 + - - -
224H PRO* 4.1 8.1 - - + -
225H THR* 4.4 2.2 - - + -
236H VAL* 3.8 24.9 - - + -
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Residues in contact with ILE 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241F GLY 4.1 13.0 - - - +
243F PRO* 3.9 16.8 - - + -
266F ASP* 3.7 30.5 - - - +
203H VAL* 3.2 21.4 + - + +
204H HIS* 3.8 7.4 - - - +
205H ASP 3.3 0.2 - - - -
206H ALA* 1.3 78.4 - - - +
208H ASN* 1.3 63.4 + - - +
210H CYS* 3.4 2.9 + - - +
211H ARG* 3.2 21.9 + - + +
235H HIS* 4.8 4.0 - - + +
236H VAL* 4.5 7.2 - - + -
239H LYS* 3.7 39.9 - - + -
240H VAL* 3.8 18.7 - - + +
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Residues in contact with ASN 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F ILE 4.1 6.9 - - - +
219F GLU* 2.9 41.9 + - - +
241F GLY 5.1 0.5 - - - +
243F PRO* 3.3 22.9 - - - +
174H GLU* 5.8 1.6 - - - +
204H HIS* 3.1 23.2 + - - +
205H ASP* 4.0 6.3 + - - +
206H ALA 3.4 0.2 - - - -
207H ILE* 1.3 75.5 - - - +
209H MSE 1.3 64.4 + - + +
211H ARG* 3.3 18.8 + - - +
212H LYS* 3.1 41.2 + - - +
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Residues in contact with MSE 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174H GLU* 3.6 44.6 - - + +
177H ASP* 3.6 38.6 - - + +
178H LEU* 4.5 6.1 - - + -
201H TRP* 3.7 38.8 - - + +
205H ASP* 2.9 24.3 + - + +
206H ALA 4.0 1.3 - - - +
208H ASN* 1.3 75.2 - - + +
210H CYS* 1.3 61.6 + - - +
212H LYS* 3.2 5.1 + - - +
213H LEU* 2.9 50.3 + - + +
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Residues in contact with CYS 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201H TRP* 4.5 7.0 - - - -
206H ALA* 3.0 26.1 + - - +
207H ILE 3.7 0.9 - - - +
208H ASN 3.3 0.2 - - - -
209H MSE 1.3 76.2 - - - +
211H ARG* 1.3 63.1 + - - +
214H GLU* 3.1 30.0 + - - +
221H ILE* 3.5 25.8 - - - -
224H PRO* 5.7 0.7 - - - -
236H VAL* 5.1 2.0 - - - -
240H VAL* 3.7 39.5 - - + -
241H GLY 5.3 0.9 - - - +
242H ILE* 3.2 16.4 - - + +
244H ILE* 4.4 9.0 - - - -
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Residues in contact with ARG 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F GLU* 4.6 21.2 + - - -
217F ASP* 2.8 36.6 + - - +
218F ILE 4.9 5.6 + - - +
241F GLY* 5.1 9.4 + - - -
207H ILE* 3.2 14.0 + - + +
208H ASN* 3.4 22.3 + - - +
209H MSE 3.2 0.4 - - - -
210H CYS* 1.3 80.7 - - - +
212H LYS* 1.3 86.1 + - - +
213H LEU 3.4 0.2 + - - -
214H GLU* 3.6 28.0 + - - +
215H LYS 4.8 0.9 + - - -
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Residues in contact with LYS 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F ARG* 6.3 0.6 - - - +
217F ASP* 3.3 22.7 + - - -
174H GLU* 2.9 44.5 + - + +
178H LEU* 3.6 30.7 - - + +
208H ASN* 3.1 26.5 + - + +
209H MSE 3.2 7.4 + - - +
211H ARG* 1.3 110.3 - - - +
213H LEU* 1.3 58.2 + - - +
214H GLU 3.5 0.2 - - - -
215H LYS* 3.8 22.2 - - - +
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Residues in contact with LEU 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170H VAL* 5.1 3.6 - - + -
177H ASP* 4.5 4.0 - - + +
178H LEU* 3.6 23.1 - - + -
181H THR* 3.7 35.0 - - + +
195H LEU* 3.6 24.7 - - + -
201H TRP* 3.9 25.4 - - + -
209H MSE 2.9 30.5 + - + +
210H CYS 4.1 2.9 - - - +
211H ARG 3.3 0.2 - - - -
212H LYS* 1.3 75.9 - - - +
214H GLU* 1.3 65.0 + - - +
215H LYS 3.2 2.9 - - - -
216H TYR* 3.0 24.0 + - + +
218H ILE* 3.5 7.7 - - + +
221H ILE* 4.3 5.4 - - + -
242H ILE* 4.2 9.6 - - + -
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Residues in contact with GLU 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E ARG* 4.8 22.7 + - - +
210H CYS 3.1 20.0 + - - +
211H ARG* 3.7 26.2 - - - +
212H LYS 3.5 1.0 - - - -
213H LEU* 1.3 76.3 - - - +
215H LYS* 1.3 58.8 + - - +
216H TYR 2.8 6.4 + - - -
217H ASP* 3.0 15.6 + - - -
218H ILE* 4.5 1.9 + - - +
241H GLY* 4.3 20.8 + - - -
242H ILE* 3.6 23.8 - - + +
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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