Contacts of the helix formed by residues 205 - 226 (chain A) in PDB entry 1JRX
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 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A ILE 3.4 2.5 + - - -
204A ASN* 1.3 71.3 - - - +
206A PRO* 1.3 71.5 - - - +
207A ALA* 2.8 22.7 + - - +
208A LEU* 3.0 31.9 + - + +
209A VAL* 3.0 22.1 + - - +
357A LYS* 4.1 18.8 + - - +
512A ILE 4.8 3.5 - - - +
513A ASP* 6.0 0.5 - - - -
538A GLY* 2.8 18.1 + - - +
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Residues in contact with PRO 206 (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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193A PHE* 3.3 22.3 - - + -
197A MET* 4.1 20.4 - - + -
204A ASN 3.1 10.5 - - - +
205A ASP* 1.3 90.5 - - - +
207A ALA* 1.3 56.5 + - - +
209A VAL 3.4 0.2 + - - -
210A LYS* 2.9 25.1 + - - +
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Residues in contact with ALA 207 (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* 2.8 15.6 + - - +
206A PRO* 1.3 73.8 - - - +
208A LEU* 1.3 63.0 + - - +
210A LYS* 3.2 11.1 + - - +
211A VAL* 3.1 24.8 + - - +
514A THR* 3.6 21.8 - - + +
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Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ASP* 3.0 28.5 + - - +
207A ALA* 1.3 76.9 - - - +
209A VAL* 1.3 56.8 + - - +
211A VAL* 3.1 6.0 + - - +
212A LEU* 2.9 27.1 + - - +
357A LYS* 5.8 0.7 - - + +
512A ILE* 3.8 20.0 - - + +
513A ASP 3.6 32.5 - - - +
514A THR* 4.0 8.3 - - + +
537A GLY 3.9 12.1 - - - +
538A GLY* 3.8 28.0 - - - +
539A VAL* 4.1 15.0 - - + +
556A PHE* 3.6 23.4 - - + -
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Residues in contact with VAL 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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193A PHE* 3.3 34.1 - - + +
196A THR* 3.8 28.0 - - + -
197A MET* 3.8 5.8 - - - -
204A ASN* 3.4 19.5 - - + +
205A ASP 3.0 13.1 + - - +
206A PRO 3.8 1.6 - - - +
208A LEU* 1.3 73.2 - - - +
210A LYS* 1.3 56.0 + - - +
212A LEU* 3.2 8.4 - - + +
213A SER* 2.7 36.6 + - - -
539A VAL* 3.2 28.0 - - + +
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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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193A PHE* 3.7 11.2 - - + -
206A PRO 2.9 14.2 + - - +
207A ALA* 3.4 13.5 - - - +
208A LEU 3.2 0.2 - - - -
209A VAL* 1.3 77.2 - - - +
211A VAL* 1.3 63.7 + - + +
213A SER* 3.3 5.8 + - - +
214A SER* 2.8 45.3 + - - -
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Residues in contact with VAL 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 ALA 3.1 13.8 + - - +
208A LEU* 3.1 8.8 + - - +
210A LYS* 1.3 74.6 - - + +
212A LEU* 1.3 59.2 + - - +
214A SER* 3.8 6.1 - - - -
215A HIS* 2.8 57.5 + - + +
514A THR* 3.7 36.6 - - + +
555A THR* 3.7 15.3 - - + -
556A PHE* 3.6 23.1 - - + -
559A LEU* 4.9 3.4 - - + -
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Residues in contact with LEU 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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192A MET* 3.9 7.3 - - + +
196A THR* 4.0 17.5 - - + +
208A LEU 2.9 13.8 + - - +
209A VAL* 3.2 12.3 - - + +
211A VAL* 1.3 77.9 - - - +
213A SER* 1.3 61.7 + - - +
215A HIS* 4.3 0.7 - - - +
216A SER* 3.4 20.8 + - - -
539A VAL* 4.2 12.3 - - + -
540A HIS* 4.5 0.7 - - - +
548A ASN* 3.7 36.1 - - + +
551A SER* 3.8 10.6 + - - +
552A ASP* 3.4 44.9 - - + +
555A THR* 4.4 8.6 + - - -
556A PHE* 4.3 8.3 - - + -
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Residues in contact with SER 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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175A ALA 4.4 1.0 - - - +
189A PRO* 3.2 38.9 + - - +
192A MET* 4.0 15.5 - - - -
193A PHE* 3.7 22.6 - - - +
209A VAL* 2.7 23.6 + - - -
210A LYS* 3.3 7.6 + - - +
212A LEU* 1.3 70.9 - - - +
214A SER* 1.3 69.5 + - - +
216A SER* 2.7 23.4 + - - -
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Residues in contact with SER 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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175A ALA 5.6 0.2 - - - +
189A PRO* 4.3 14.0 - - - +
210A LYS* 2.8 42.4 + - - -
211A VAL* 3.8 1.4 - - - -
213A SER* 1.3 76.2 + - - +
215A HIS* 1.3 74.9 + - - -
216A SER 3.5 0.5 + - - -
217A LYS* 4.5 5.0 + - - +
218A ASP* 4.0 9.4 + - - +
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Residues in contact with HIS 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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211A VAL* 2.8 47.1 + - + +
214A SER* 1.3 95.4 - - - +
216A SER* 1.3 53.3 + - - +
217A LYS 3.3 2.5 - - - -
218A ASP* 3.1 19.3 + - + +
219A SER* 2.7 35.8 + - - +
555A THR* 3.4 25.9 + - + +
559A LEU* 4.6 20.1 - - + +
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Residues in contact with SER 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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172A MET* 4.7 0.5 - - - +
173A ASN 3.7 8.5 - - - -
174A ALA* 3.4 27.2 - - - +
175A ALA 3.0 21.1 + - - -
192A MET* 3.6 6.5 - - - -
212A LEU 3.4 17.0 + - - -
213A SER 2.7 18.2 + - - -
214A SER 3.4 0.2 - - - -
215A HIS* 1.3 78.2 - - - +
217A LYS* 1.3 57.5 + - - +
219A SER* 3.2 5.1 + - - -
220A VAL* 3.0 23.7 + - - +
551A SER* 3.9 4.5 - - - -
555A THR* 4.3 5.6 - - - -
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Residues in contact with LYS 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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175A ALA 3.6 16.5 + - - +
176A TRP 3.3 24.0 - - - +
177A THR* 4.1 21.8 - - + +
178A ASP* 4.0 26.5 + - - -
181A LYS* 5.5 2.7 - - - +
214A SER 4.5 5.1 + - - +
215A HIS 3.3 0.4 - - - -
216A SER* 1.3 79.9 + - - +
218A ASP* 1.3 55.4 + - - +
220A VAL* 3.1 4.0 + - - +
221A ASP* 2.6 68.2 + - - +
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Residues in contact with ASP 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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214A SER 4.0 13.1 - - - +
215A HIS* 3.2 19.8 + - + +
217A LYS* 1.3 80.9 + - - +
219A SER* 1.4 51.4 - - - +
221A ASP* 3.2 11.3 + - - +
222A TRP* 2.8 36.6 + - - +
558A ARG* 3.9 16.2 + - - +
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Residues in contact with SER 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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172A MET* 3.7 18.6 - - - -
215A HIS* 2.7 16.3 + - - +
216A SER* 3.5 5.8 - - - -
218A ASP* 1.4 71.8 - - - +
220A VAL* 1.3 63.7 + - - +
222A TRP* 3.3 7.0 + - - +
223A MET* 3.0 27.7 + - - +
551A SER* 4.9 0.9 - - - -
554A ILE* 3.9 12.1 + - - +
555A THR* 2.5 40.2 + - - -
558A ARG* 4.9 6.9 + - - +
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Residues in contact with VAL 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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172A MET* 3.7 25.6 - - + -
174A ALA* 3.3 32.1 - - + -
177A THR* 4.4 4.3 - - + -
179A GLN* 3.7 34.8 - - - +
216A SER 3.0 4.6 + - - +
217A LYS 3.5 7.0 - - - +
219A SER* 1.3 75.8 - - - +
221A ASP* 1.3 57.4 + - - +
223A MET* 3.2 2.1 + - - +
224A THR* 2.9 31.1 + - - -
230A LEU* 4.0 18.3 - - + +
245A HIS* 4.2 14.4 - - + +
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Residues in contact with ASP 221 (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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178A ASP* 4.8 6.2 + - - +
179A GLN* 4.5 13.5 + - - +
217A LYS* 2.6 59.5 + - - +
218A ASP* 3.4 14.2 - - - +
220A VAL* 1.3 72.1 - - - +
222A TRP* 1.3 52.8 + - - +
224A THR* 3.2 6.6 + - - -
225A ALA* 2.6 38.4 + - - +
521B ALA* 6.1 0.9 - - - +
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Residues in contact with TRP 222 (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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140A SER* 3.4 44.0 - - - -
143A ILE* 4.1 15.0 - - + -
144A SER* 4.2 10.8 - - - -
147A ASP* 4.9 8.9 + - + +
218A ASP 2.8 17.4 + - - +
219A SER 3.4 3.1 - - - +
221A ASP* 1.3 75.4 - - - +
223A MET* 1.4 66.5 + - - +
225A ALA* 3.3 9.5 + - + +
226A MET* 3.0 58.5 + - + +
268A ARG* 6.1 0.2 - - - +
554A ILE* 3.7 19.1 - - + -
558A ARG* 3.3 63.9 - - + +
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Residues in contact with MET 223 (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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172A MET* 4.5 7.0 - - + -
219A SER 3.0 20.2 + - - +
220A VAL 3.7 3.4 - - - +
222A TRP* 1.4 78.1 - - - +
224A THR* 1.3 56.9 + - - +
226A MET* 2.9 25.0 + - + +
227A GLY 3.2 0.7 + - - -
228A ALA* 2.8 36.2 + - + +
230A LEU* 3.8 9.9 - - + -
257A VAL* 3.8 27.6 - - + +
260A VAL* 4.1 17.7 - - + +
261A LEU* 3.7 33.2 - - + -
554A ILE* 3.8 33.0 - - + -
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Residues in contact with THR 224 (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 GLN* 3.4 26.5 + - - +
220A VAL* 2.9 19.9 + - - +
221A ASP* 3.5 7.0 - - - -
223A MET* 1.3 73.6 - - - +
225A ALA* 1.3 58.6 - - - +
227A GLY* 2.9 21.0 + - - -
228A ALA 3.3 23.9 + - - +
230A LEU* 4.3 8.4 + - - +
231A THR* 6.3 2.2 - - + -
521B ALA* 5.5 11.7 - - + -
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Residues in contact with ALA 225 (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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221A ASP 2.6 19.8 + - - +
222A TRP* 3.5 10.5 - - + +
223A MET 3.2 0.2 - - - -
224A THR* 1.3 73.7 - - - +
226A MET* 1.3 59.8 + - + +
227A GLY* 3.5 1.0 + - - -
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Residues in contact with MET 226 (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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143A ILE* 4.0 17.5 - - + -
222A TRP* 3.0 65.9 + - + +
223A MET* 2.9 25.6 + - - +
225A ALA* 1.3 78.3 - - + +
227A GLY* 1.3 56.7 + - - +
260A VAL* 3.4 8.6 - - + +
261A LEU* 4.1 7.4 - - + -
264A ASN* 2.8 60.8 + - - +
268A ARG* 4.6 7.0 - - - +
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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