Contacts of the helix formed by residues 197 - 212 (chain D) in PDB entry 4UQJ
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 GLU 197 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D ASP* 4.7 4.1 + - - +
140D ASP* 5.6 4.9 - - + +
141D ARG* 3.5 16.0 - - - +
196D CYS* 1.3 76.0 - - - +
198D ARG* 1.3 65.9 + - - +
199D ASP* 3.0 12.8 + - + +
200D LYS* 3.4 8.4 + - + +
201D VAL* 3.0 24.9 + - - +
224D ASN* 4.7 1.3 - - - +
280D TYR* 6.1 1.6 - - - -
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Residues in contact with ARG 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D GLU* 1.3 73.5 - - - +
199D ASP* 1.3 67.0 + - - +
201D VAL* 4.1 5.1 - - - +
202D ASN* 3.7 27.0 + - - +
224D ASN* 4.5 14.0 - - - +
226D GLY 5.8 0.4 - - - +
229D ASP* 5.1 20.0 - - + +
230D GLY* 5.3 5.3 - - - +
280D TYR* 6.0 6.8 - - + -
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Residues in contact with ASP 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D GLU* 3.0 6.6 - - + +
198D ARG* 1.3 85.3 - - - +
200D LYS* 1.3 63.8 + - - +
201D VAL 3.0 5.4 + - - -
202D ASN* 3.1 14.9 + - - +
203D ASP* 3.2 19.3 + - - +
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Residues in contact with LYS 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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138D ASP* 4.1 15.7 - - - +
165D VAL* 5.9 4.0 - - + +
177D TYR* 5.0 0.3 + - - -
196D CYS* 3.6 25.6 - - + -
197D GLU* 3.4 7.7 + - + +
199D ASP* 1.3 78.7 - - - +
201D VAL* 1.3 60.6 + - - +
203D ASP* 3.7 12.2 + - - +
204D ILE* 3.2 29.0 + - + +
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Residues in contact with VAL 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D LEU* 4.6 10.3 - - + -
196D CYS* 3.8 26.0 - - + +
197D GLU 3.0 21.9 + - - +
198D ARG* 4.1 6.7 - - - +
199D ASP 3.0 0.8 - - - -
200D LYS* 1.3 75.8 - - - +
202D ASN* 1.3 66.1 + - - +
204D ILE* 3.2 7.7 + - - +
205D VAL* 2.8 42.5 + - + +
222D ILE* 4.0 36.3 - - + -
224D ASN* 4.6 3.1 - - - +
230D GLY* 6.4 1.1 - - - -
232D LEU* 6.5 0.7 - - + -
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Residues in contact with ASN 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D ARG 3.7 15.9 + - - +
199D ASP* 3.1 10.8 + - - +
201D VAL* 1.3 84.8 - - - +
203D ASP* 1.3 60.6 + - - +
205D VAL* 3.8 3.5 - - - +
206D ASP* 2.9 39.3 + - - +
230D GLY* 4.2 6.4 - - - -
231D ASP* 3.8 26.2 + - - +
232D LEU* 6.0 0.3 - - - +
234D LYS* 3.7 24.0 + - - +
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Residues in contact with ASP 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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170D ASN* 4.8 13.5 + - - +
177D TYR* 4.3 13.5 - - + +
199D ASP* 3.2 14.7 + - - +
200D LYS* 3.7 13.9 - - - +
201D VAL 3.2 0.4 - - - -
202D ASN* 1.3 80.9 - - - +
204D ILE* 1.3 60.9 + - - +
206D ASP* 3.4 7.6 + - - +
207D GLN* 3.1 28.3 + - - +
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Residues in contact with ILE 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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136D LEU* 4.5 5.6 - - + -
165D VAL* 4.1 19.5 - - + -
177D TYR* 3.9 22.9 - - + +
181D PHE* 4.8 10.5 - - + -
194D LEU* 3.6 43.3 - - + -
196D CYS* 4.0 18.8 - - - -
200D LYS* 3.2 16.1 + - + +
201D VAL* 3.2 7.2 + - - +
203D ASP* 1.3 73.2 - - - +
205D VAL* 1.3 56.0 + - - +
207D GLN* 3.1 7.4 + - - +
208D VAL* 2.8 50.6 + - + +
220D TYR* 5.8 0.7 - - + -
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Residues in contact with VAL 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D LEU* 4.6 9.9 - - + -
201D VAL* 2.8 37.7 + - + +
202D ASN* 3.8 8.3 - - - +
204D ILE* 1.3 72.4 - - - +
206D ASP* 1.3 62.4 + - - +
208D VAL* 3.3 10.0 + - - +
209D ILE* 3.0 28.8 + - - +
222D ILE* 5.1 5.4 - - + -
231D ASP 4.9 2.0 - - - +
232D LEU* 6.6 0.7 - - + -
234D LYS* 3.7 23.6 - - + -
235D ILE* 3.5 40.4 - - + -
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Residues in contact with ASP 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 ASN* 2.9 26.4 + - - +
203D ASP* 3.6 8.1 - - - +
205D VAL* 1.3 75.9 - - - +
207D GLN* 1.3 63.4 + - + +
209D ILE* 3.3 9.2 + - - +
210D THR* 3.0 26.7 + - - +
234D LYS* 3.1 33.2 + - - +
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Residues in contact with GLN 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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173D LYS 4.1 10.3 + - - -
174D ASP* 3.3 26.1 + - - +
177D TYR* 3.9 42.9 - - + +
181D PHE* 5.0 4.7 - - + -
203D ASP 3.1 14.8 + - - +
204D ILE 3.1 8.2 + - - +
206D ASP* 1.3 76.9 - - + +
208D VAL* 1.3 62.0 + - - +
210D THR* 3.1 14.4 + - - +
211D ILE* 3.0 35.7 + - + +
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Residues in contact with VAL 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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181D PHE* 4.0 20.2 - - + -
194D LEU* 5.8 0.7 - - + -
204D ILE* 2.8 33.0 + - + +
205D VAL* 3.5 11.0 - - - +
207D GLN* 1.3 72.7 - - - +
209D ILE* 1.3 57.0 + - - +
211D ILE* 3.3 9.0 - - - +
212D GLY 3.0 6.4 + - - -
213D LYS* 2.8 57.0 + - + +
214D HIS* 3.7 11.4 - - + -
220D TYR* 3.2 28.9 - - + +
235D ILE* 4.8 3.1 - - + -
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Residues in contact with ILE 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ILE* 4.4 17.8 - - + +
210B THR* 5.2 4.0 - - - -
214B HIS* 3.9 7.4 + - - -
205D VAL* 3.0 18.5 + - + +
206D ASP* 3.7 8.7 - - - +
207D GLN 3.2 0.4 - - - -
208D VAL* 1.3 74.0 - - - +
210D THR* 1.3 66.3 + - - +
212D GLY* 3.1 12.3 + - - -
214D HIS* 3.3 29.7 + - + +
234D LYS* 3.4 42.8 - - + +
235D ILE* 3.4 24.0 - - + -
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Residues in contact with THR 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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209B ILE* 5.2 5.2 - - - -
214B HIS* 3.5 17.1 - - - -
233B LEU 5.7 2.2 - - - +
234B LYS* 4.9 13.1 - - - +
237B PHE* 4.9 14.5 - - + +
238B GLY* 4.6 6.2 + - - -
206D ASP 3.0 16.2 + - - -
207D GLN* 3.1 18.5 + - - +
209D ILE* 1.3 78.9 - - - +
211D ILE* 1.3 65.9 + - + +
212D GLY 3.3 0.9 + - - -
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Residues in contact with ILE 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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214B HIS* 5.0 1.6 - - - -
215B VAL* 5.3 1.0 - - - +
237B PHE* 4.9 15.2 - - + +
238B GLY 4.7 8.2 - - - +
177D TYR* 6.3 1.1 - - + -
178D ARG* 5.9 7.9 - - + -
181D PHE* 3.6 46.4 - - + -
207D GLN* 3.0 23.4 + - + +
208D VAL* 3.3 11.2 - - - +
210D THR* 1.3 80.5 - - + +
212D GLY* 1.3 58.8 + - - +
213D LYS* 3.6 27.1 + - + +
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Residues in contact with GLY 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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212B GLY* 6.3 0.2 - - - -
214B HIS* 4.4 10.5 - - - -
215B VAL* 4.6 13.0 - - - +
208D VAL 3.0 4.0 + - - -
209D ILE 3.1 11.2 + - - -
210D THR 3.1 5.2 - - - -
211D ILE* 1.3 78.4 - - - +
213D LYS* 1.3 57.4 + - - +
214D HIS* 3.1 18.0 + - - -
215D VAL* 3.7 23.4 - - - +
218D TYR* 4.7 0.9 - - - -
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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
------------------------------------------------------------
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