Contacts of the helix formed by residues 199 - 214 (chain D) in PDB entry 3G33
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 PRO 199 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D GLU* 3.9 13.2 - - + +
39D VAL* 4.5 6.7 - - + -
197D MET 3.6 4.7 - - - +
198D TYR* 1.3 88.0 - - + +
200D PRO* 1.3 76.5 - - + +
201D SER* 4.0 7.0 - - - +
202D MET* 3.0 41.3 + - + +
203D ILE* 3.2 10.4 + - - +
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Residues in contact with PRO 200 (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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35D GLU* 3.4 27.8 - - + +
38D TYR 5.0 2.7 - - - +
39D VAL* 3.9 15.3 - - + -
155D VAL 3.2 22.0 - - - +
156D ILE* 3.6 6.7 - - - -
157D ALA* 3.3 39.0 - - + +
160D PHE* 3.8 9.9 - - + -
198D TYR 3.5 4.2 - - - +
199D PRO* 1.3 81.8 - - + +
201D SER* 1.3 56.0 + - - +
203D ILE* 3.2 6.4 + - + -
204D ALA* 2.9 25.6 + - - +
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Residues in contact with SER 201 (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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32D LEU* 3.9 11.7 - - - +
35D GLU* 2.7 39.2 + - - -
160D PHE* 3.5 24.2 - - - -
199D PRO* 4.0 6.8 - - - +
200D PRO* 1.3 75.0 - - - +
202D MET* 1.3 58.4 + - - +
204D ALA* 3.4 1.0 + - - +
205D THR* 2.8 34.8 + - - +
233D THR* 4.4 12.1 - - - +
235D THR* 4.6 8.4 - - - +
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Residues in contact with MET 202 (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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198D TYR* 3.9 18.8 - - + -
199D PRO* 3.0 33.0 + - + +
201D SER* 1.3 78.4 + - - +
203D ILE* 1.3 60.4 + - - +
205D THR* 3.3 11.7 - - + +
206D GLY* 2.8 28.1 + - - -
235D THR* 4.8 15.0 - - + -
239D CYS* 4.3 27.6 - - + -
240D LEU* 5.1 7.0 - - + -
243D CYS* 3.7 33.2 - - + -
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Residues in contact with ILE 203 (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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157D ALA* 3.6 17.5 - - + -
186D LEU* 4.1 7.6 - - + +
189D CYS* 3.6 30.7 - - + -
195D PHE* 3.5 33.2 - - + +
196D ALA 5.5 0.4 - - - +
198D TYR* 3.6 32.5 - - + +
199D PRO 3.2 6.7 + - - +
200D PRO* 3.5 10.3 - - + +
202D MET* 1.3 75.8 - - - +
204D ALA* 1.3 52.6 + - - +
207D SER* 2.7 38.6 + - - -
243D CYS* 4.8 5.4 - - - -
247D ILE* 4.2 2.3 - - - +
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Residues in contact with ALA 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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157D ALA* 3.2 27.8 - - - +
160D PHE* 3.5 20.6 - - + -
161D LEU* 5.0 5.2 - - + +
164D ILE* 4.1 5.4 - - + -
186D LEU* 4.1 7.4 - - + -
200D PRO 2.9 13.8 + - - +
201D SER 3.6 2.5 - - - +
203D ILE* 1.3 73.6 - - - +
205D THR* 1.3 60.8 + - - +
206D GLY 3.0 1.6 - - - -
207D SER* 3.4 5.0 + - - -
208D ILE* 2.9 35.0 + - - +
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Residues in contact with THR 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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164D ILE* 4.0 4.8 - - - +
201D SER 2.8 28.7 + - - +
202D MET* 3.3 14.8 - - + +
204D ALA* 1.3 73.1 - - - +
206D GLY* 1.3 61.0 + - - +
208D ILE* 3.3 20.5 - - - +
209D GLY* 3.4 4.7 + - - -
229D LEU* 3.4 41.2 + - - +
233D THR* 4.0 24.7 - - - +
235D THR* 4.4 4.9 - - - +
240D LEU* 3.3 20.3 - - + +
244D GLN* 5.3 0.2 - - - +
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Residues in contact with GLY 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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202D MET 2.8 20.1 + - - -
203D ILE 3.9 0.2 - - - -
205D THR* 1.3 76.0 - - - +
207D SER* 1.3 59.3 + - - +
208D ILE 3.2 1.6 - - - -
209D GLY* 3.3 1.0 + - - -
210D ALA* 3.1 22.5 + - - +
240D LEU* 3.7 12.8 - - - -
243D CYS* 4.6 2.0 - - - -
244D GLN* 3.5 21.3 - - - +
247D ILE* 3.8 11.0 - - - -
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Residues in contact with SER 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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161D LEU* 5.7 0.5 - - - +
182D ALA* 4.1 4.0 + - - +
185D PHE* 3.3 38.2 - - - -
186D LEU* 3.0 23.1 - - - +
189D CYS* 4.9 0.9 - - - -
203D ILE 2.7 22.8 + - - -
204D ALA 3.4 2.3 + - - -
206D GLY* 1.3 75.5 - - - +
208D ILE* 1.3 59.9 + - - +
209D GLY 3.2 0.2 - - - -
210D ALA* 3.5 6.0 + - - +
211D ALA* 3.1 25.8 + - - +
247D ILE* 3.6 14.4 - - - +
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Residues in contact with ILE 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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161D LEU* 3.7 20.0 - - + -
164D ILE* 3.3 39.9 - - + +
165D LEU* 3.5 34.8 - - + -
168D LEU* 5.1 1.8 - - + -
178D VAL* 5.2 1.6 - - + -
182D ALA* 4.3 14.8 - - + -
204D ALA 2.9 20.3 + - - +
205D THR* 3.3 11.7 - - - +
207D SER* 1.3 77.7 + - - +
209D GLY* 1.3 60.9 + - - +
211D ALA* 3.8 1.0 - - - +
212D VAL* 3.2 31.2 + - + +
229D LEU* 4.0 16.1 - - + +
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Residues in contact with GLY 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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205D THR 3.4 2.1 + - - -
206D GLY 3.3 7.2 + - - -
207D SER 3.2 0.2 - - - -
208D ILE* 1.3 81.4 - - - +
210D ALA* 1.3 63.4 + - - +
211D ALA 3.1 1.3 - - - -
212D VAL* 4.2 2.6 - - - +
213D GLN* 3.0 22.2 + - - +
225D LEU* 5.0 3.6 - - - +
229D LEU* 3.6 23.8 - - - -
244D GLN* 3.1 20.2 + - - -
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Residues in contact with ALA 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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181D HIS* 4.8 0.5 + - - -
185D PHE* 4.0 26.0 - - + -
206D GLY 3.1 13.4 + - - +
207D SER* 3.7 11.2 - - - +
208D ILE 3.5 0.2 - - - -
209D GLY* 1.3 76.3 - - - +
211D ALA* 1.3 61.5 + - - +
213D GLN* 4.2 2.2 - - - +
214D GLY* 3.3 16.5 + - - -
244D GLN* 3.3 12.0 - - + +
247D ILE* 5.0 2.0 - - + -
248D GLU* 3.7 31.9 - - + +
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Residues in contact with ALA 211 (chain D).
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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178D VAL* 4.1 7.4 - - + +
181D HIS* 3.7 18.2 - - + -
182D ALA* 3.7 34.5 - - + +
185D PHE* 4.0 1.8 - - + -
207D SER 3.1 16.9 + - - +
208D ILE 3.9 4.3 - - - +
209D GLY 3.1 0.6 - - - -
210D ALA* 1.3 75.4 - - - +
212D VAL* 1.3 65.7 + - - +
214D GLY* 3.0 11.8 + - - -
215D LEU* 3.1 21.7 + - + +
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Residues in contact with VAL 212 (chain D).
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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168D LEU* 5.1 10.1 - - + -
170D LEU* 4.6 20.2 - - + -
178D VAL* 3.6 25.1 - - + -
208D ILE* 3.2 22.9 + - + +
209D GLY 4.2 2.0 - - - +
211D ALA* 1.3 78.3 - - - +
213D GLN* 1.3 57.9 + - - +
215D LEU* 3.2 7.0 + - - +
216D GLY 2.9 34.5 + - - -
225D LEU* 3.7 30.1 - - + -
229D LEU* 6.2 1.6 - - + -
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Residues in contact with GLN 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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252B ARG* 5.3 2.9 - - - +
209D GLY 3.0 15.5 + - - +
210D ALA* 4.3 2.9 - - - +
212D VAL* 1.3 77.3 - - - +
214D GLY* 1.3 59.7 + - - +
215D LEU 3.2 0.7 + - - -
216D GLY* 3.8 8.3 + - - +
221D SER 6.2 0.4 - - - -
222D GLY* 4.2 26.8 - - - +
225D LEU* 4.4 14.9 - - + +
226D THR* 5.2 3.3 - - - +
244D GLN* 2.9 23.6 + - - +
248D GLU* 5.3 3.8 - - - +
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Residues in contact with GLY 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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251B LEU* 3.6 19.4 - - - +
252B ARG* 3.4 24.3 + - - +
181D HIS* 5.2 5.4 - - - -
210D ALA 3.3 10.6 + - - -
211D ALA 3.0 9.3 + - - -
213D GLN* 1.3 77.2 - - - +
215D LEU* 1.3 59.9 + - - +
216D GLY 3.7 0.4 - - - -
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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