Contacts of the helix formed by residues 207 - 220 (chain A) in PDB entry 1JXQ
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 THR 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A LEU* 1.3 76.3 - - - +
208A ALA* 1.3 67.6 + - - +
209A LYS* 4.0 6.7 + - - +
210A LYS* 2.9 44.1 + - + +
211A MET* 3.0 8.0 + - - +
245A GLY* 3.8 0.2 - - - -
246A THR* 3.4 23.9 - - + +
247A ASP* 3.4 23.8 - - + +
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Residues in contact with ALA 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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207A THR* 1.3 69.8 - - - +
209A LYS* 1.3 63.2 + - - +
211A MET* 3.0 15.0 + - - +
212A VAL* 3.1 18.7 + - + +
245A GLY* 3.3 9.0 - - - -
247A ASP* 2.9 11.6 + - - +
254A CYS* 3.4 45.8 - - + +
255A PRO 4.4 1.1 - - - +
256A VAL* 3.6 18.7 - - + +
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Residues in contact with LYS 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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207A THR* 3.1 8.4 - - - +
208A ALA* 1.3 79.5 - - - +
210A LYS* 1.3 63.1 + - + +
212A VAL* 3.5 8.5 + - - +
213A LEU* 3.1 49.4 + - + +
247A ASP* 4.3 3.4 + - - +
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Residues in contact with LYS 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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205A ASP 5.6 0.7 - - - +
206A LEU* 3.9 31.4 - - + +
207A THR* 2.9 29.7 + - + +
209A LYS* 1.3 75.1 - - + +
211A MET* 1.3 60.9 + - - +
213A LEU* 3.2 18.6 + - + +
214A ALA* 2.8 29.5 + - - +
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Residues in contact with MET 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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168A ILE* 4.3 26.4 - - + +
170A ASN* 3.8 13.7 - - - +
206A LEU* 3.9 15.7 - - + -
207A THR 3.0 12.4 + - - +
208A ALA* 3.2 11.0 - - - +
210A LYS* 1.3 73.3 - - - +
212A VAL* 1.3 67.1 + - + +
214A ALA* 2.9 4.9 + - - +
215A LEU* 2.9 31.7 + - + +
234A ILE* 4.2 19.7 - - + -
236A SER* 5.5 0.2 - - - -
243A VAL* 3.9 27.8 - - + -
244A TYR 4.3 3.1 - - - +
245A GLY* 3.5 33.2 - - - -
256A VAL* 4.0 10.5 - - + -
261A ILE* 5.2 1.6 - - + -
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Residues in contact with VAL 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 ALA 3.1 14.1 + - - +
209A LYS* 3.7 9.0 - - - +
211A MET* 1.3 75.2 - - - +
213A LEU* 1.3 52.5 + - + +
215A LEU* 3.2 9.9 + - - +
216A LEU* 2.7 55.2 + - + +
256A VAL* 4.2 21.5 - - + -
260A LYS* 4.2 31.0 - - + +
264A ILE* 4.4 7.4 - - + -
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Residues in contact with LEU 213 (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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209A LYS* 3.1 47.7 + - + +
210A LYS* 3.3 23.8 - - + +
211A MET 3.1 0.6 - - - -
212A VAL* 1.3 77.5 - - + +
214A ALA* 1.3 62.4 - - - +
216A LEU* 3.2 16.3 + - + +
217A GLU* 3.0 24.9 + - - +
220A ARG* 5.1 2.5 + - - +
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Residues in contact with ALA 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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166A LEU* 4.2 15.8 - - + +
168A ILE* 4.6 2.9 - - + -
203A LYS* 4.2 33.0 + - + +
206A LEU* 4.6 9.4 - - + -
210A LYS 2.8 15.9 + - - +
211A MET 2.9 8.3 + - - +
213A LEU* 1.3 72.9 - - - +
215A LEU* 1.3 62.1 + - - +
217A GLU* 3.4 7.8 + - - +
218A LEU* 3.1 23.4 + - - +
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Residues in contact with LEU 215 (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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166A LEU* 4.1 18.4 - - + -
168A ILE* 4.5 12.1 - - + -
211A MET* 2.9 26.2 + - + +
212A VAL* 3.6 2.7 - - - +
214A ALA* 1.3 77.3 - - - +
216A LEU* 1.3 61.4 + - - +
218A LEU* 3.4 5.2 + - - +
219A ALA 3.1 17.5 + - - -
232A VAL* 4.1 21.1 - - + -
234A ILE* 4.9 1.8 - - + -
256A VAL* 5.4 1.3 - - + -
261A ILE* 3.5 39.7 - - + -
264A ILE* 3.6 29.1 - - + +
265A PHE* 3.7 23.1 - - + -
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Residues in contact with LEU 216 (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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212A VAL* 2.7 41.6 + - + +
213A LEU* 3.5 16.6 - - + +
215A LEU* 1.3 73.6 - - - +
217A GLU* 1.3 57.3 + - - +
219A ALA* 3.4 3.4 + - + +
220A ARG* 2.8 53.2 + - - +
264A ILE* 4.2 23.1 - - + -
269A SER* 5.5 4.7 - - - +
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Residues in contact with GLU 217 (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 GLU* 5.6 1.2 - - - +
203A LYS* 4.3 18.0 + - - -
213A LEU 3.0 15.5 + - - +
214A ALA* 3.7 6.3 - - - +
216A LEU* 1.3 74.5 - - - +
218A LEU* 1.3 66.6 + - - +
220A ARG* 3.1 30.0 + - - +
221A GLN* 3.2 31.7 + - + +
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Residues in contact with LEU 218 (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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164A HIS* 3.8 27.4 - - + +
166A LEU* 3.7 36.8 - - + +
201A GLU* 5.6 4.7 - - - +
214A ALA 3.1 13.8 + - - +
215A LEU* 3.5 9.0 - - - +
216A LEU 3.3 0.2 - - - -
217A GLU* 1.3 76.3 - - - +
219A ALA* 1.3 60.9 + - - +
221A GLN* 3.1 28.7 + - - +
224A HIS* 2.9 27.7 + - + -
230A CYS* 4.2 9.0 - - - -
231A VAL 4.8 1.1 - - - +
232A VAL* 3.9 9.6 - - + -
265A PHE* 3.8 24.2 - - + -
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Residues in contact with ALA 219 (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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215A LEU 3.1 4.3 + - - +
216A LEU* 3.9 2.9 - - + +
218A LEU* 1.3 74.5 - - - +
220A ARG* 1.3 58.5 + - - +
221A GLN 2.9 14.1 + - - +
224A HIS* 4.2 0.7 - - - -
264A ILE* 3.7 39.7 - - + +
265A PHE* 3.8 16.2 - - + -
269A SER* 4.3 9.4 - - - +
270A CYS* 3.3 34.3 - - + +
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Residues in contact with ARG 220 (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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213A LEU* 5.1 2.8 + - - +
216A LEU* 2.8 53.1 + - - +
217A GLU* 3.1 23.1 + - - +
219A ALA* 1.3 76.5 - - - +
221A GLN* 1.3 60.2 + - - +
269A SER 5.5 2.0 - - - -
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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