Contacts of the helix formed by residues 202 - 214 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200D GLY 4.3 0.6 + - - -
201D TRP* 1.3 80.7 - - - +
203D VAL* 1.3 66.0 + - - +
204D HIS* 3.3 24.3 + - - -
205D ASP* 3.4 19.3 + - - +
206D ALA* 2.9 18.9 + - - +
225D THR* 4.4 0.4 - - - -
226D VAL* 6.0 2.9 - - - -
292G GLY 5.8 1.3 - - - -
294G LYS* 3.5 35.8 + - - -
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Residues in contact with VAL 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D SER* 1.3 74.8 - - - +
204D HIS* 1.3 63.6 + - - +
206D ALA* 3.4 2.9 + - - +
207D ILE* 3.2 28.9 + - + +
225D THR* 4.3 8.9 - - + +
232D ALA* 4.3 13.2 - - + +
235D HIS* 3.6 31.0 - - + +
236D VAL* 3.9 26.1 - - + +
263G ARG* 4.5 2.5 - - - +
266G ASP* 3.7 22.2 + - + +
292G GLY 3.5 24.2 + - - +
293G LEU* 3.8 9.2 - - + -
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Residues in contact with HIS 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D SER* 3.3 18.7 + - - -
203D VAL* 1.3 76.9 - - - +
205D ASP* 1.3 83.0 + - - +
207D ILE* 3.3 10.4 + - - +
208D ASN* 3.0 27.7 + - - -
2400D GOL 3.8 1.6 - - - -
194G ARG* 4.6 0.2 + - - -
219G GLU* 3.0 49.0 + - + +
220G PHE* 4.0 12.6 - + + -
243G PRO* 3.7 19.2 - - + +
245G VAL* 5.8 0.7 - - + -
266G ASP* 3.9 17.8 + - + +
267G MSE 4.3 24.7 - - + +
294G LYS* 5.8 4.0 - - + +
321G ASP* 4.7 6.5 - - - -
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Residues in contact with ASP 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D TRP* 4.2 13.8 - - + -
202D SER* 3.3 27.6 + - - +
204D HIS* 1.3 94.2 + - - +
206D ALA* 1.3 60.5 + - - +
208D ASN* 3.9 0.3 - - - +
209D MSE 2.8 37.3 + - + +
2400D GOL 2.7 40.2 + - - -
192G ARG* 5.7 0.9 + - - -
219G GLU* 4.2 1.9 - - - +
294G LYS* 5.4 4.2 + - - -
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Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D TRP* 3.6 28.4 - - + +
202D SER 2.9 19.1 + - - +
203D VAL 3.6 5.6 - - - +
205D ASP* 1.3 77.6 - - - +
207D ILE* 1.3 57.3 + - - +
209D MSE 3.9 0.7 - - - +
210D CYS* 3.0 36.3 + - - -
224D PRO* 4.1 8.5 - - + -
225D THR* 4.5 2.2 - - + -
236D VAL* 3.9 22.4 - - + -
240D VAL* 4.6 0.9 - - - -
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Residues in contact with ILE 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D VAL* 3.2 22.3 + - + +
204D HIS* 3.6 8.5 - - - +
205D ASP 3.2 0.2 - - - -
206D ALA* 1.3 79.4 - - - +
208D ASN* 1.3 62.8 + - - +
210D CYS* 3.5 2.4 + - - +
211D ARG* 3.2 21.2 + - + +
235D HIS* 4.8 1.3 - - + +
236D VAL* 4.7 6.3 - - + -
239D LYS* 4.3 31.6 - - + +
240D VAL* 3.8 21.3 - - + +
241G GLY 4.2 15.0 - - - +
242G ILE 5.7 0.2 - - - -
243G PRO* 4.1 16.6 - - + -
266G ASP* 3.6 32.8 - - - +
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Residues in contact with ASN 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D HIS* 3.0 17.2 + - - +
207D ILE* 1.3 77.4 - - - +
209D MSE 1.3 63.7 + - - +
211D ARG* 3.4 20.3 + - - +
212D LYS* 3.1 28.1 + - - +
2400D GOL 2.9 43.2 + - - +
218G ILE 4.0 7.5 - - - +
219G GLU* 2.8 30.9 + - - +
241G GLY 4.9 0.9 - - - +
243G PRO* 3.1 24.9 - - - +
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Residues in contact with MSE 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D GLU* 3.5 31.0 - - + +
177D ASP* 3.7 36.6 - - + +
178D LEU* 4.3 8.1 - - + -
201D TRP* 3.7 34.8 - - + +
205D ASP 2.8 28.8 + - - +
206D ALA 4.0 1.1 - - - +
208D ASN* 1.3 69.7 - - - +
210D CYS* 1.3 61.7 + - - +
212D LYS* 3.2 5.1 + - - +
213D LEU* 2.9 52.9 + - + +
2400D GOL 3.4 26.5 - - - +
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Residues in contact with CYS 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D TRP* 4.6 5.6 - - - -
206D ALA* 3.0 23.8 + - - +
207D ILE 3.8 0.2 - - - +
209D MSE 1.3 75.4 - - - +
211D ARG* 1.3 62.9 + - - +
213D LEU* 3.2 0.9 + - - -
214D GLU* 3.0 29.4 + - - +
221D ILE* 3.5 27.6 - - - -
224D PRO* 5.7 0.7 - - - -
236D VAL* 5.2 2.2 - - - -
240D VAL* 3.6 39.3 - - + -
241D GLY 5.3 0.9 - - - +
242D ILE* 3.3 15.3 - - + +
244D ILE* 4.3 10.5 - - - -
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Residues in contact with ARG 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D ILE* 3.2 11.1 + - - +
208D ASN* 3.4 26.0 + - - +
210D CYS* 1.3 82.2 - - - +
212D LYS* 1.3 87.9 + - - +
213D LEU 3.4 0.2 + - - -
214D GLU* 3.5 28.4 + - - +
215D LYS* 4.7 0.9 + - - +
2400D GOL 4.8 0.4 + - - -
214G GLU* 4.6 22.9 + - - -
217G ASP* 3.0 34.0 + - - +
218G ILE 4.6 6.5 + - - +
241G GLY 5.0 11.1 + - - -
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Residues in contact with LYS 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D GLU* 2.8 37.8 + - + +
178D LEU* 3.8 27.9 - - + +
208D ASN 3.1 16.4 + - - +
209D MSE 3.2 7.2 + - - +
211D ARG* 1.3 99.5 - - - +
213D LEU* 1.3 60.3 + - - +
214D GLU 3.7 0.2 + - - -
215D LYS* 3.7 20.3 - - - +
216D TYR* 4.1 0.7 - - - -
2400D GOL 2.8 25.6 + - - +
217G ASP* 2.9 37.1 + - - -
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Residues in contact with LEU 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D VAL* 5.0 3.1 - - + -
177D ASP* 4.4 5.2 - - + +
178D LEU* 3.8 17.7 - - + -
181D THR* 3.5 32.8 - - + +
195D LEU* 3.7 28.3 - - + -
201D TRP* 3.8 27.4 - - + -
209D MSE 2.9 31.8 + - + +
210D CYS 3.2 3.3 + - - +
212D LYS* 1.3 75.6 - - - +
214D GLU* 1.3 66.2 + - - +
215D LYS 3.2 2.9 - - - -
216D TYR* 2.9 20.2 + - + -
218D ILE* 3.5 11.9 - - + +
221D ILE* 4.0 7.4 - - + -
242D ILE* 4.4 5.8 - - + -
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Residues in contact with GLU 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C ARG* 4.3 27.1 + - - -
210D CYS 3.0 19.8 + - - +
211D ARG* 3.5 23.2 - - - +
212D LYS 3.4 1.4 - - - -
213D LEU* 1.3 75.6 - - - +
215D LYS* 1.3 58.1 + - - +
216D TYR 2.8 6.6 + - - -
217D ASP* 3.0 14.9 + - - -
218D ILE* 4.4 2.5 + - - +
241D GLY* 4.3 21.1 + - - -
242D ILE* 3.7 24.0 - - + +
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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