Contacts of the helix formed by residues 179 - 195 (chain A) in PDB entry 1JX6
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 ASP 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A TYR* 3.6 25.9 + - + +
161A THR* 2.6 30.2 + - - +
162A THR* 3.8 12.8 - - - +
177A GLY 3.9 0.2 - - - -
178A PHE* 1.3 67.5 - - - +
180A HIS* 1.3 66.3 + - - +
181A ALA* 3.5 12.5 + - - +
182A GLU* 3.0 34.9 + - + +
183A GLY 3.1 18.7 + - - -
185A ARG* 4.5 3.3 + - - -
337A SER* 2.9 21.9 + - - +
340A PHE* 3.2 10.5 - - + -
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Residues in contact with HIS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ASN* 2.8 46.1 + - - -
160A ILE* 4.9 1.3 - - - -
161A THR* 5.2 1.8 - - + -
178A PHE 3.1 11.2 + - - -
179A ASP* 1.3 72.0 + - - +
181A ALA* 1.3 64.4 - - - +
184A SER* 2.9 31.7 + - - -
210A TYR* 3.5 30.5 - + - -
211A ILE* 3.5 15.0 - - + +
214A VAL* 3.4 23.6 - - + -
215A ARG* 2.9 40.0 + - + -
289A TRP* 3.5 7.9 - - - -
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A THR* 6.1 3.4 - - + -
179A ASP* 3.4 12.7 + - - +
180A HIS* 1.3 78.7 - - - +
182A GLU* 1.3 58.0 + - - +
184A SER* 3.4 1.2 + - - -
185A ARG* 2.8 53.9 + - - +
214A VAL* 4.0 13.7 + - + +
218A THR* 3.9 14.2 - - + +
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Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASP* 3.0 27.4 + - + +
180A HIS 3.3 0.2 - - - -
181A ALA* 1.3 76.3 - - - +
183A GLY* 1.3 64.8 + - - +
185A ARG* 2.9 33.8 + - - +
186A GLU* 2.6 58.0 + - - +
340A PHE* 4.1 11.7 - - + -
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Residues in contact with GLY 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASP 3.1 8.7 + - - -
182A GLU* 1.3 79.1 - - - +
184A SER* 1.3 61.5 + - - +
186A GLU* 3.3 4.8 + - - +
187A LEU* 3.1 26.7 + - - +
289A TRP* 3.8 20.0 - - - -
308A VAL* 3.9 19.9 - - - +
340A PHE* 3.7 10.0 - - - -
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Residues in contact with SER 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A HIS 2.9 18.5 + - - -
181A ALA 3.8 3.4 - - - -
183A GLY* 1.3 73.2 - - - +
185A ARG* 1.3 61.7 + - - +
187A LEU* 3.4 3.7 + - - +
188A ALA* 2.9 28.8 + - - +
215A ARG* 3.2 23.6 - - - -
218A THR* 4.1 15.7 - - - -
219A PHE* 3.8 6.6 - - - +
262A TYR* 3.1 26.0 + - - -
289A TRP* 3.3 8.0 + - - +
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Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLN* 5.8 6.1 - - - +
179A ASP* 4.5 3.2 + - - -
181A ALA* 2.8 46.1 + - - +
182A GLU* 2.9 40.3 + - - +
184A SER* 1.3 73.8 - - - +
186A GLU* 1.3 60.8 + - + +
188A ALA* 3.2 1.4 + - - -
189A THR* 2.9 34.7 + - - +
218A THR* 4.0 13.9 - - + +
222A GLN* 3.3 25.9 + - - +
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Residues in contact with GLU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLU* 2.6 46.9 + - - +
183A GLY 3.6 7.4 - - - +
184A SER 3.2 0.2 - - - -
185A ARG* 1.3 77.8 - - + +
187A LEU* 1.3 62.4 + - - +
189A THR* 3.4 7.7 + - - -
190A GLU* 3.2 25.8 + - - +
308A VAL* 3.9 3.0 - - + +
340A PHE* 3.7 34.3 + - - +
342A ILE* 3.9 30.2 + - + +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLY 3.1 17.1 + - - +
184A SER 3.4 4.7 + - - +
186A GLU* 1.3 77.7 - - - +
188A ALA* 1.3 61.3 + - - +
190A GLU* 3.1 5.0 + - - +
191A PHE* 3.0 31.7 + - + -
219A PHE* 3.8 3.4 - - + -
262A TYR* 3.8 14.6 - - + +
287A ASN* 3.7 32.1 - - + +
288A GLY 4.0 4.7 - - - +
289A TRP* 3.7 26.0 - - + +
306A ILE* 4.0 26.7 - - + -
307A THR* 4.1 5.4 - - - -
308A VAL* 4.0 26.0 - - + +
342A ILE* 4.1 4.0 - - + -
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A SER 2.9 18.5 + - - +
185A ARG* 3.6 1.3 - - - +
187A LEU* 1.3 76.2 - - - +
189A THR* 1.3 57.9 + - - +
191A PHE* 3.9 1.2 - - - +
192A GLY* 2.9 26.7 + - - -
219A PHE* 3.4 28.9 - - + +
222A GLN* 3.3 35.7 + - + +
223A VAL* 4.3 9.2 - - + +
227A ASN* 4.9 2.3 + - - -
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Residues in contact with THR 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ARG* 2.9 18.1 + - - +
186A GLU* 3.6 8.5 - - - -
187A LEU 3.2 0.2 - - - -
188A ALA* 1.3 76.5 - - - +
190A GLU* 1.3 66.2 + - - +
192A GLY* 3.3 3.1 + - - -
193A LYS* 3.2 42.7 + - + +
222A GLN* 3.3 13.1 + - - +
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Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLU 3.2 12.5 + - - +
187A LEU* 3.1 9.5 + - - +
189A THR* 1.3 80.7 - - - +
191A PHE* 1.3 66.3 + - + +
193A LYS* 2.9 40.2 + - - +
194A PHE* 3.0 49.2 + - + -
306A ILE* 3.4 25.8 - - + -
342A ILE* 4.2 20.4 - - + +
344A THR* 5.5 0.7 - - + -
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Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 3.0 36.2 + - + +
188A ALA 4.1 3.1 - - - +
190A GLU* 1.3 77.8 - - + +
192A GLY* 1.3 62.6 + - - +
194A PHE* 4.1 5.8 - - - -
195A PHE* 3.0 30.9 + + - -
219A PHE* 4.0 22.4 - + + -
223A VAL* 5.0 0.2 - - + -
229A PHE* 3.6 14.9 - - + -
260A PHE* 3.3 50.0 - + + -
261A ILE 4.7 1.3 - - - -
262A TYR* 5.2 0.4 - + - -
285A MET* 3.2 37.7 - - + -
287A ASN* 3.9 32.8 - - + -
306A ILE* 3.9 10.1 - - + -
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Residues in contact with GLY 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ALA 2.9 16.0 + - - -
189A THR* 3.6 6.5 - - - -
190A GLU 3.1 0.6 - - - -
191A PHE* 1.3 78.6 - - - +
193A LYS* 1.3 56.9 + - - +
195A PHE 3.2 16.1 - - - +
227A ASN* 3.4 33.0 - - - +
229A PHE* 3.9 5.1 - - - -
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Residues in contact with LYS 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A THR* 3.5 29.0 - - + +
190A GLU* 2.9 37.5 + - - +
192A GLY* 1.3 78.5 - - - +
194A PHE* 1.3 70.8 + - + +
195A PHE 3.5 1.5 - - - +
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Residues in contact with PHE 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A GLU* 3.0 54.4 + - + +
191A PHE* 3.1 1.3 + - - +
193A LYS* 1.3 87.9 - - + +
195A PHE* 1.3 82.1 + - + +
196A PRO* 4.6 1.0 - - - +
285A MET* 3.4 38.1 - - + -
306A ILE* 4.1 7.6 - - + -
344A THR* 5.0 9.9 - - + -
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Residues in contact with PHE 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A PHE* 3.0 19.3 + + - -
192A GLY 3.2 18.4 - - - +
193A LYS 4.6 1.0 - - - -
194A PHE* 1.3 91.7 - - + +
196A PRO* 1.3 69.3 - - + +
199A THR* 3.2 24.5 - - + +
227A ASN* 5.4 0.3 - - - +
229A PHE* 3.8 11.7 - - + -
259A ASP* 3.7 43.1 - - + -
260A PHE* 3.7 23.3 - + + -
285A MET* 3.8 33.4 - - + -
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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