Contacts of the helix formed by residues 196 - 214 (chain A) in PDB entry 5JJA
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 LEU 196 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LYS* 6.6 0.2 - - + -
159A ILE* 3.5 24.2 - - + +
160A ASP* 3.8 5.2 - - - -
161A GLN* 3.7 40.2 - - + +
164A VAL* 3.9 20.4 - - + -
189A ILE* 4.0 10.3 - - + -
193A PHE* 3.0 30.6 + - + +
195A GLY* 1.3 79.9 - - - +
197A ARG* 1.3 58.8 + - - +
198A ALA 3.5 1.8 - - - -
199A TYR* 3.2 9.1 + - + +
200A ILE* 2.9 41.6 + - + +
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Residues in contact with ARG 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A TYR* 2.8 64.5 + - + +
191A GLY 3.0 24.2 + - - -
193A PHE 3.7 6.5 - - - +
194A LEU* 3.2 33.7 + - - +
195A GLY 3.5 0.2 - - - -
196A LEU* 1.3 77.8 - - - +
198A ALA* 1.3 63.9 + - - +
200A ILE 3.3 1.4 + - - -
201A ARG* 3.1 30.1 + - - +
672C ILE* 3.5 23.2 - - - +
673C ILE 3.1 24.2 + - - -
674C GLU* 4.2 2.0 - - - +
675C ASP* 3.7 26.1 - - - +
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Residues in contact with ALA 198 (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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194A LEU 4.8 0.8 + - - -
195A GLY 5.2 2.4 + - - +
196A LEU 3.5 0.2 - - - -
197A ARG* 1.3 78.2 - - - +
199A TYR* 1.3 62.6 + - - +
201A ARG* 3.5 25.2 + - - +
202A LYS* 3.1 24.1 + - - +
242A GLU* 5.1 3.8 - - - +
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Residues in contact with TYR 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLN* 3.5 65.7 - - + +
164A VAL* 3.8 26.0 - - + -
165A LEU* 3.4 23.8 - - - +
195A GLY 5.3 1.5 + - - +
196A LEU* 3.2 15.0 + - + +
198A ALA* 1.3 79.6 - - - +
200A ILE* 1.3 62.9 + - - +
202A LYS* 3.3 11.1 + - + +
203A GLN* 3.0 33.5 + - + +
356B MET* 3.7 8.4 - - + +
357B SER* 5.6 2.5 - - - -
360B SER* 2.7 34.3 + - - -
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Residues in contact with ILE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A VAL* 3.7 25.8 - - + -
168A LEU* 4.5 2.0 - - + +
186A LEU* 4.1 25.1 - - + -
189A ILE* 4.5 5.6 - - + -
190A TYR* 3.7 44.9 - - + +
196A LEU* 2.9 35.3 + - + +
197A ARG 3.7 3.8 - - - +
199A TYR* 1.3 78.2 - - + +
201A ARG* 1.3 62.5 + - - +
203A GLN* 3.3 2.8 + - - +
204A ILE* 3.0 44.6 + - + +
227A ILE* 5.9 1.6 - - + -
231A ILE* 5.7 1.3 - - + -
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Residues in contact with ARG 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A TYR* 2.8 42.4 + - + +
197A ARG* 3.1 29.7 + - - +
198A ALA* 3.8 22.7 - - - +
199A TYR 3.3 0.2 - - - -
200A ILE* 1.3 76.9 - - + +
202A LYS* 1.3 63.6 + - - +
204A ILE* 3.5 7.6 + - - +
205A ASN* 3.1 32.0 + - - +
228A LEU* 5.1 15.2 - - + +
231A ILE* 4.7 10.5 - - + -
235A PHE* 5.0 2.8 - - - -
240A LYS* 6.1 0.8 - - - +
242A GLU* 2.9 43.2 + - - +
243A HIS* 3.7 24.1 - - - -
674C GLU* 5.5 5.1 + - - +
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Residues in contact with LYS 202 (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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198A ALA 3.1 17.5 + - - +
199A TYR* 3.7 11.9 - - + +
201A ARG* 1.3 78.4 - - - +
203A GLN* 1.3 57.2 + - - +
205A ASN* 3.2 11.6 + - + +
206A ASN* 3.0 39.3 + - - +
242A GLU* 5.5 0.6 + - - -
357B SER* 3.9 28.3 + - - -
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Residues in contact with GLN 203 (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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165A LEU* 3.3 23.5 - - + +
168A LEU* 3.7 26.4 - - + +
169A GLU* 4.6 6.7 + - - -
199A TYR* 3.0 33.3 + - + +
200A ILE 3.3 0.2 + - - -
202A LYS* 1.3 74.2 - - - +
204A ILE* 1.3 65.2 + - - +
206A ASN* 2.8 31.6 + - - +
207A ILE* 3.0 36.2 + - + +
360B SER* 3.1 32.3 + - - -
363B ALA* 5.1 0.8 - - - +
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Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 4.0 19.1 - - + -
186A LEU* 4.6 5.2 - - + -
200A ILE* 3.0 38.9 + - + +
201A ARG* 3.8 5.4 - - - +
203A GLN* 1.3 77.3 - - - +
205A ASN* 1.3 57.5 + - - +
207A ILE* 3.2 9.4 + - - +
208A PHE* 2.9 58.8 + - + -
224A LEU* 4.0 23.6 - - + +
227A ILE* 5.0 8.5 - - + -
228A LEU* 3.7 28.7 - - + -
231A ILE* 5.9 1.1 - - + -
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Residues in contact with ASN 205 (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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201A ARG* 3.1 22.0 + - - +
202A LYS* 3.4 11.3 - - + +
204A ILE* 1.3 78.5 - - - +
206A ASN* 1.3 57.9 + - - +
208A PHE* 3.1 7.0 + - - +
209A TYR* 2.8 51.1 + - + -
228A LEU* 5.2 1.0 - - - +
242A GLU* 5.7 3.8 + - - +
246A PHE* 3.2 45.7 - - - +
250A VAL* 4.2 10.1 - - + +
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Residues in contact with ASN 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LYS* 3.0 30.8 + - - +
203A GLN* 2.8 35.9 + - - +
205A ASN* 1.3 75.1 - - - +
207A ILE* 1.3 63.4 + - - +
209A TYR* 3.4 12.4 + - - +
210A ARG* 3.1 24.9 + - - +
357B SER* 4.8 3.0 + - - +
360B SER* 4.2 4.4 - - - +
361B ASP* 3.5 44.7 + - - +
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 3.9 47.1 - - + +
169A GLU* 5.0 7.4 - - - +
203A GLN* 3.0 27.6 + - + +
204A ILE* 3.5 9.2 - - - +
206A ASN* 1.3 76.4 - - - +
208A PHE* 1.3 67.4 + - + +
210A ARG* 3.4 5.6 + - - +
211A PHE* 3.0 22.0 + - - +
218A HIS* 3.6 34.2 - - + +
221A ILE* 4.9 0.4 - - + -
224A LEU* 4.1 17.0 - - + -
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Residues in contact with PHE 208 (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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204A ILE* 2.9 30.3 + - + +
205A ASN* 3.1 7.6 + - - +
207A ILE* 1.3 79.8 - - + +
209A TYR* 1.3 57.0 + - - +
211A PHE* 3.3 5.3 + - - +
212A ILE* 2.9 38.7 + - + +
221A ILE* 3.8 34.5 - - + -
224A LEU* 3.8 28.7 - - + -
225A LEU* 3.9 26.5 - - + -
228A LEU* 3.5 25.6 - - + -
246A PHE* 4.8 1.6 - + - -
250A VAL* 3.6 32.1 - - + -
251A LEU* 5.1 0.2 - - + -
254A LEU* 4.1 9.9 - - + -
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Residues in contact with TYR 209 (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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205A ASN* 2.8 43.8 + - + +
206A ASN* 3.8 13.0 - - - +
208A PHE* 1.3 70.2 - - - +
210A ARG* 1.3 61.0 + - - +
212A ILE* 4.5 4.3 - - + +
213A TYR* 2.9 59.1 + + + +
245A ILE* 5.2 4.7 - - - +
249A LYS* 3.7 33.0 - - + +
250A VAL* 3.4 21.8 - - + +
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Residues in contact with ARG 210 (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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206A ASN 3.1 16.9 + - - +
207A ILE* 3.9 4.9 - - - +
209A TYR* 1.3 73.8 - - - +
211A PHE* 1.3 60.6 + - - +
213A TYR* 5.4 0.2 - - - -
214A GLU* 2.8 72.0 + - + +
215A THR* 3.0 21.3 + - + +
361B ASP* 2.9 36.5 + - - +
362B ASN* 4.4 7.5 + - - +
363B ALA 5.3 0.6 - - - +
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Residues in contact with PHE 211 (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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207A ILE 3.0 14.8 + - - +
208A PHE* 3.4 9.4 - - - +
210A ARG* 1.3 76.9 - - - +
212A ILE* 1.3 63.7 + - + +
215A THR* 3.7 7.6 - - - -
216A GLU* 2.8 36.4 + - - +
217A HIS* 3.4 28.5 - - - -
218A HIS* 3.6 31.0 - - + -
221A ILE* 3.9 20.6 - - + -
254A LEU* 3.7 22.7 - - + -
257A VAL* 3.7 22.4 - - + -
259A SER* 3.7 13.7 - - - -
263A TYR* 3.6 29.4 - + - -
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Residues in contact with ILE 212 (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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208A PHE* 2.9 31.5 + - + +
209A TYR* 4.0 6.7 - - + +
211A PHE* 1.3 73.5 - - - +
213A TYR* 1.3 93.2 + - + +
216A GLU* 4.0 14.6 - - - +
249A LYS 5.0 1.3 - - - +
250A VAL* 3.9 26.9 - - + +
253A PRO* 4.3 11.7 - - + +
254A LEU* 3.8 29.6 - - + +
256A LYS* 4.0 22.4 + - - -
257A VAL* 4.1 17.8 - - + +
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Residues in contact with TYR 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A TYR* 2.9 54.7 + + + +
212A ILE* 1.3 97.6 - - + +
214A GLU* 1.3 59.5 + - - +
216A GLU* 5.9 0.2 - - - -
249A LYS 4.6 2.9 + - - -
253A PRO* 4.2 18.9 - - - +
256A LYS* 4.4 15.4 - - - -
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Residues in contact with GLU 214 (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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210A ARG* 2.8 56.0 + - + +
212A ILE 3.6 1.0 - - - -
213A TYR* 1.3 80.0 - - - +
215A THR* 1.3 73.0 + - + +
216A GLU* 3.6 7.5 - - - +
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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