Contacts of the helix formed by residues 186 - 202 (chain D) in PDB entry 4BL5
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 HIS 186 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D LEU* 5.8 2.6 - - + +
73D VAL* 3.8 27.0 - - + +
74D GLY* 3.3 18.1 + - - -
75D GLY* 3.7 15.7 - - - -
76D LEU 5.1 0.4 - - - -
172D ASN* 5.0 16.6 - - + +
173D VAL 4.8 15.0 + - - +
178D ASP* 4.8 10.9 + - - -
179D ASN 4.6 0.4 + - - -
185D GLY* 1.3 76.1 - - - -
187D VAL* 1.3 70.5 + - + +
188D LEU 3.3 1.5 + - - +
189D PRO* 3.4 17.4 - - + +
190D GLY* 3.0 21.5 + - - -
217D PHE* 6.5 0.4 - - + -
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Residues in contact with VAL 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D ASN* 5.6 3.8 - - - +
186D HIS* 1.3 77.8 - - + +
188D LEU* 1.3 58.3 + - + +
190D GLY* 3.6 1.0 - - - -
191D LEU* 2.7 63.0 + - + +
207D VAL* 6.1 0.4 - - + -
215D ARG* 5.6 1.8 - - + +
217D PHE* 3.7 34.3 - - + -
252D ILE* 4.0 30.1 - - + -
255D ALA* 5.6 0.9 - - + -
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Residues in contact with LEU 188 (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 PHE* 3.5 36.1 - - + -
186D HIS* 4.6 0.2 - - - +
187D VAL* 1.3 75.1 - - + +
189D PRO* 1.4 68.2 - - + +
190D GLY 3.1 1.3 - - - -
191D LEU* 3.2 4.9 + - + +
192D ILE* 2.8 41.6 + - + +
217D PHE* 3.5 41.5 - - + -
255D ALA* 3.9 28.3 - - + +
259D VAL* 4.0 20.9 - - + -
301D PHE* 4.3 9.4 - - + -
305D VAL* 5.0 4.9 - - + -
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Residues in contact with PRO 189 (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 VAL 5.6 0.7 - - - +
174D PHE* 5.2 2.9 - - + -
178D ASP* 3.5 26.7 - - - +
179D ASN 3.6 22.4 - - - +
180D PHE* 3.2 43.0 - - + +
186D HIS* 3.4 22.9 - - + +
188D LEU* 1.4 95.5 - - + +
190D GLY* 1.3 56.8 + - - +
192D ILE* 4.0 2.9 - - + -
193D HIS* 3.1 28.8 + - - +
308D THR* 6.2 0.4 - - + -
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Residues in contact with GLY 190 (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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179D ASN 5.3 0.2 + - - -
180D PHE* 4.7 1.7 + - - +
181D ASN 5.0 1.7 + - - -
182D ILE* 3.7 25.9 - - - +
186D HIS 3.0 19.1 + - - +
187D VAL* 3.6 1.3 - - - -
189D PRO* 1.3 78.4 - - - +
191D LEU* 1.3 56.2 + - - +
193D HIS 3.4 0.9 + - - -
194D LYS* 3.0 39.0 + - - +
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Residues in contact with LEU 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D VAL* 2.7 47.7 + - + +
188D LEU* 3.2 7.2 + - + +
190D GLY* 1.3 69.6 - - - +
192D ILE* 1.3 66.8 + - - +
194D LYS* 3.6 25.0 - - + +
195D VAL* 3.0 31.3 + - + +
205D LEU* 4.6 5.8 - - + -
207D VAL* 4.1 28.5 - - + -
208D TRP 5.5 0.2 - - - +
252D ILE* 4.9 2.7 - - + +
255D ALA* 4.5 2.9 - - + -
256D ALA* 3.6 37.9 - - + +
259D VAL* 4.1 14.8 - - + -
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Residues in contact with ILE 192 (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 PHE* 6.1 1.3 - - + -
180D PHE* 4.1 3.1 - - + -
188D LEU* 2.8 38.8 + - + +
189D PRO* 3.8 8.7 - - + +
190D GLY 3.3 0.2 - - - -
191D LEU* 1.3 73.8 - - - +
193D HIS* 1.3 62.0 + - - +
195D VAL 3.6 0.2 + - - -
196D HIS* 3.0 22.3 + - - +
259D VAL* 3.9 17.0 - - + -
263D MET* 3.8 14.7 - - - +
305D VAL* 5.2 2.9 - - + -
308D THR* 3.8 29.4 - - + -
309D CYS* 3.6 27.1 - - - -
312D PHE* 3.6 35.9 - - + -
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Residues in contact with HIS 193 (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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180D PHE* 2.8 25.0 + - - +
182D ILE* 3.7 21.0 - - + +
189D PRO 3.1 20.3 + - - +
192D ILE* 1.3 76.4 - - - +
194D LYS* 1.3 58.1 + - - +
196D HIS* 3.1 1.6 + - + +
197D LEU* 2.9 46.4 + - + +
312D PHE* 3.9 25.6 - + + -
316D TYR* 3.4 24.8 + + - -
321D LYS* 3.8 30.7 - - + -
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Residues in contact with LYS 194 (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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182D ILE* 3.7 37.7 - - + -
190D GLY 3.0 22.0 + - - +
191D LEU* 3.6 15.6 - - + +
192D ILE 3.2 0.2 - - - -
193D HIS* 1.3 75.3 - - - +
195D VAL* 1.3 53.6 + - - +
197D LEU* 2.8 10.0 + - + +
198D ALA* 2.6 36.2 + - - +
205D LEU* 3.4 16.8 - - + -
206D THR* 2.8 30.1 + - - +
208D TRP* 3.3 43.2 - - - +
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Residues in contact with VAL 195 (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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191D LEU* 3.0 18.2 + - + +
192D ILE 3.9 3.6 - - - +
194D LYS* 1.3 78.0 - - - +
196D HIS* 1.3 58.0 + - - +
198D ALA* 3.5 8.7 - - - +
199D LYS* 2.8 32.0 + - + +
205D LEU* 3.6 30.2 - - + +
259D VAL* 4.0 14.1 - - + +
260D VAL* 4.4 8.3 - - + -
263D MET* 4.1 25.1 - - + -
265D PHE* 3.7 31.0 - - + -
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Residues in contact with HIS 196 (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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192D ILE 3.0 15.4 + - - +
193D HIS 3.3 8.7 + - - +
194D LYS 2.9 0.2 + - - -
195D VAL* 1.3 77.9 - - - +
197D LEU* 1.3 69.5 + - + +
199D LYS* 3.3 11.1 + - + +
200D SER* 3.3 18.6 + - - -
263D MET* 4.0 17.7 - - + +
312D PHE* 3.9 18.6 - + + -
313D THR* 4.8 17.8 + - + +
316D TYR* 3.2 46.1 + + - +
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Residues in contact with LEU 197 (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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182D ILE* 3.9 28.5 - - + -
193D HIS* 2.9 23.6 + - + +
194D LYS* 2.8 11.9 + - - +
196D HIS* 1.3 77.8 - - + +
198D ALA* 1.3 55.9 + - - +
200D SER* 3.4 7.1 + - - -
201D SER* 2.9 34.0 + - - -
316D TYR* 4.2 17.3 - - - +
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Residues in contact with ALA 198 (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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194D LYS 2.6 18.7 + - - +
195D VAL* 3.5 13.0 - - - +
197D LEU* 1.3 73.5 - - - +
199D LYS* 1.3 53.3 + - - +
201D SER* 3.3 2.6 + - - -
202D GLY* 2.8 32.2 + - - -
203D SER* 3.2 28.4 + - - +
204D ALA 3.9 13.7 - - - +
205D LEU* 4.7 3.1 - - - +
265D PHE* 3.9 14.0 - - + -
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Residues in contact with LYS 199 (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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195D VAL* 2.8 30.4 + - + +
196D HIS* 3.7 6.7 - - + +
198D ALA* 1.3 73.9 - - - +
200D SER* 1.3 65.3 + - - +
202D GLY* 3.4 8.2 + - - -
263D MET* 4.9 10.8 - - + +
264D ASP 5.4 1.3 - - - +
265D PHE* 3.7 30.5 - - + -
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Residues in contact with SER 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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196D HIS* 3.3 14.7 + - - -
197D LEU* 3.7 10.8 - - - -
199D LYS* 1.3 79.5 - - - +
201D SER* 1.3 63.3 + - - +
202D GLY 3.3 0.9 + - - -
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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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197D LEU 2.9 20.2 + - - -
198D ALA 3.9 2.5 - - - -
200D SER* 1.3 77.2 - - - +
202D GLY* 1.3 60.7 + - - +
203D SER* 3.5 16.0 + - - -
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Residues in contact with GLY 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 ALA 2.8 10.7 + - - -
199D LYS* 3.4 6.1 + - - -
200D SER 3.2 5.2 + - - -
201D SER* 1.3 76.4 - - - +
203D SER* 1.3 60.9 + - - -
265D PHE* 6.2 0.2 - - - -
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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