Contacts of the helix formed by residues 180 - 194 (chain D) in PDB entry 5JLH
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 ALA 180 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D HIS* 5.7 0.2 - - + -
155D GLY 3.8 6.7 - - - +
156D ASP 2.7 31.4 - - - +
157D GLY 3.2 16.2 - - - +
159D THR* 4.7 2.5 - - - -
179D LEU* 1.3 78.8 - - - +
181D GLY* 1.3 62.8 + - - +
182D ARG* 3.1 5.4 - - + +
183D ASP* 3.1 15.2 + - - +
184D LEU* 3.1 27.2 + - - +
260D LEU* 5.2 2.4 - - - +
302D THR* 4.6 5.2 - - - -
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Residues in contact with GLY 181 (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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155D GLY 3.3 12.0 + - - -
156D ASP* 3.7 7.2 - - - +
180D ALA* 1.3 73.3 - - - +
182D ARG* 1.3 56.5 + - - +
184D LEU* 3.2 4.7 + - - +
185D THR 2.9 14.4 + - - -
212D LYS* 2.5 26.3 + - - -
302D THR* 3.9 18.1 + - - -
401D ADP 3.4 17.7 - - - -
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Residues in contact with ARG 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D TYR* 3.4 25.6 - - + +
71D GLU* 2.8 54.8 + - - +
72D HIS* 5.4 2.9 + - + -
156D ASP* 3.2 35.7 + - - +
180D ALA* 3.1 3.3 - - + +
181D GLY* 1.3 76.5 - - - +
183D ASP* 1.3 65.9 + - - +
185D THR* 3.2 9.3 + - - -
186D ASP* 2.9 34.4 + - - +
205D ARG* 3.3 36.4 - - - +
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Residues in contact with ASP 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D HIS* 3.8 28.6 - - - -
178D ASP* 3.9 6.4 - - - +
179D LEU* 3.6 21.5 + - + -
180D ALA* 3.1 14.5 + - - +
182D ARG* 1.3 84.9 + - - +
184D LEU* 1.3 58.8 + - - +
186D ASP* 3.2 11.5 + - - +
187D TYR* 2.9 27.9 + - - +
266D LEU* 4.2 23.2 - - + +
268D MET* 5.2 3.8 - - + +
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Residues in contact with LEU 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D ALA 3.1 16.4 + - - +
181D GLY* 3.2 7.2 + - - +
183D ASP* 1.3 74.3 - - - +
185D THR* 1.3 58.2 + - - +
187D TYR* 3.2 6.9 + - + +
188D LEU* 2.8 30.3 + - - +
212D LYS* 4.0 6.1 - - + -
256D CYS* 3.3 36.9 - - - +
257D PRO* 4.5 3.6 - - + -
259D ALA* 3.6 20.0 - - + -
260D LEU* 3.9 27.4 - - + -
266D LEU* 5.1 4.9 - - + -
302D THR* 3.8 12.1 - - - +
305D TYR* 3.3 35.2 - - + +
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Residues in contact with THR 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D ASP* 5.5 0.2 + - - -
181D GLY 2.9 7.5 + - - -
182D ARG* 3.2 13.3 + - + +
184D LEU* 1.3 74.7 - - - +
186D ASP* 1.3 64.6 + - - +
188D LEU* 3.0 7.7 + - - +
189D MET* 2.9 24.1 + - - +
205D ARG* 3.9 29.4 - - + +
208D VAL* 3.7 25.3 - - + +
209D ARG* 4.1 12.3 - - + +
212D LYS* 2.5 33.3 + - - +
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Residues in contact with ASP 186 (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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283B LYS* 5.3 8.7 + - - +
182D ARG* 2.9 19.1 + - - +
183D ASP* 3.2 13.9 + - - +
185D THR* 1.3 77.0 - - - +
187D TYR* 1.3 60.9 + - - +
189D MET* 3.4 15.7 - - - +
190D LYS* 3.3 20.6 + - - +
205D ARG* 3.3 37.9 + - - -
266D LEU* 6.3 0.2 - - + -
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Residues in contact with TYR 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D ASP 2.9 13.9 + - - +
184D LEU* 3.4 11.7 - - + +
186D ASP* 1.3 75.3 - - - +
188D LEU* 1.3 65.4 + - - +
190D LYS* 3.1 32.4 + - - +
191D ILE* 2.9 49.2 + - + +
255D ARG* 4.0 28.0 + - + -
256D CYS* 4.1 23.1 - - - -
259D ALA* 4.9 4.0 - - + -
265D PHE* 4.0 40.6 - - + +
266D LEU* 3.6 28.0 - - + +
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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
----------------------------------------------------------
184D LEU 2.8 19.8 + - - +
185D THR* 3.0 6.9 + - - +
187D TYR* 1.3 71.8 - - - +
189D MET* 1.3 67.9 + - - +
191D ILE* 2.9 29.9 + - + +
192D LEU* 2.9 32.8 + - + +
208D VAL* 3.9 20.0 - - + +
211D ILE* 4.4 9.4 - - + -
212D LYS* 3.8 32.8 - - + +
216D CYS* 4.3 9.9 - - - -
249D ILE* 6.3 2.0 - - + -
252D GLU* 4.1 9.2 - - + +
253D ARG* 5.5 0.9 - - - -
256D CYS* 3.5 28.0 - - + -
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Residues in contact with MET 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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185D THR 2.9 13.7 + - - +
186D ASP* 3.4 30.1 - - - +
188D LEU* 1.3 77.1 - - - +
190D LYS* 1.3 62.1 + - - +
192D LEU* 3.5 14.1 + - - +
193D THR* 3.3 19.3 + - - +
197D TYR 4.9 0.2 - - - +
199D PHE* 2.9 39.1 + - + +
200D THR* 4.7 8.5 - - - +
201D THR 5.9 0.2 - - - +
205D ARG* 3.8 34.5 - - + -
208D VAL* 4.3 19.2 - - + +
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Residues in contact with LYS 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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109B LEU* 4.5 27.1 - - + +
171B PRO* 4.6 24.0 + - - +
172B HIS* 4.8 14.1 - - - +
174B ILE 5.6 1.8 - - - +
186D ASP 3.3 13.5 + - - +
187D TYR* 3.1 40.1 + - - +
188D LEU 3.1 0.6 - - - -
189D MET* 1.3 78.3 - - - +
191D ILE* 1.3 63.5 + - - +
193D THR* 2.3 33.8 + - - +
194D GLU* 4.1 0.7 + - - +
265D PHE 5.0 6.2 + - - -
266D LEU* 5.9 2.0 - - - +
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Residues in contact with ILE 191 (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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187D TYR* 2.9 43.7 + - + +
188D LEU* 2.9 35.3 + - + +
190D LYS* 1.3 80.5 - - - +
192D LEU* 1.3 59.9 + - - +
194D GLU* 2.9 53.8 - - - +
252D GLU* 3.6 27.3 - - + +
255D ARG* 3.8 24.2 - - + +
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Residues in contact with LEU 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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188D LEU* 2.9 49.3 + - + +
189D MET* 3.8 10.5 - - - +
190D LYS 3.3 0.4 - - - -
191D ILE* 1.3 75.3 - - - +
193D THR* 1.3 56.2 + - - +
195D ARG* 2.7 33.6 + - - +
196D GLY 3.4 2.9 + - - -
197D TYR* 3.6 26.1 + - + +
199D PHE* 3.5 37.2 - - + -
208D VAL* 4.1 7.4 - - + -
211D ILE* 4.9 7.0 - - + -
247D ILE* 4.9 7.9 - - + -
249D ILE* 5.2 1.8 - - + -
252D GLU* 2.9 33.0 - - - +
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Residues in contact with THR 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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109B LEU* 3.9 31.9 + - + +
111B PRO* 3.5 18.6 - - - +
176B ARG* 5.6 2.2 - - - +
189D MET 3.3 17.3 - - - +
190D LYS* 2.3 27.9 + - - +
192D LEU* 1.3 77.6 - - - +
194D GLU* 1.3 58.4 + - - +
196D GLY* 3.0 15.4 + - - -
197D TYR 3.3 16.2 - - - +
198D SER* 4.4 16.0 + - - +
199D PHE 5.1 2.2 - - - +
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Residues in contact with GLU 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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109B LEU 5.3 0.9 - - - -
110B ASN 4.3 5.6 - - - +
111B PRO* 3.4 9.6 - - - +
112B LYS* 2.8 60.7 + - + +
113B ALA* 4.5 0.7 + - - +
190D LYS 5.3 0.4 - - - +
191D ILE* 2.9 38.2 + - - +
192D LEU 3.0 1.0 - - - -
193D THR* 1.3 82.2 + - - +
195D ARG* 1.3 59.5 + - + +
196D GLY 3.4 0.2 - - - -
251D ASN* 5.2 0.5 - - - +
252D GLU* 4.8 5.9 - - - +
255D ARG* 2.4 34.9 + - - -
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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
------------------------------------------------------------
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