Contacts of the helix formed by residues 215 - 226 (chain A) in PDB entry 2JIL
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 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A GLY* 4.2 1.1 - - - -
170A ALA* 3.7 22.4 - - + +
171A HIS* 5.5 1.6 - - - -
213A GLY 3.8 1.3 + - - +
214A THR* 1.3 76.8 - - - +
216A HIS* 1.3 64.2 + - - +
217A ALA* 3.5 8.8 + - - +
218A GLU* 2.8 45.2 + - - +
219A ALA* 2.9 21.1 + - - +
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Residues in contact with HIS 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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166A ILE* 3.4 34.4 - - + +
167A ARG* 4.0 3.3 - - - -
168A GLY 2.8 28.9 + - - +
169A GLY* 3.9 6.4 - - - -
170A ALA 4.4 1.4 + - - +
215A THR* 1.3 72.9 - - - +
217A ALA* 1.3 60.5 + - - +
219A ALA* 3.2 6.6 + - - +
220A MET* 2.9 31.3 + - + +
239B SER* 3.3 42.8 + - - +
240B GLU 3.8 2.4 + - - -
241B THR* 2.6 32.2 + - - -
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Residues in contact with ALA 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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215A THR* 3.2 8.9 + - - +
216A HIS* 1.3 81.2 - - - +
218A GLU* 1.3 58.3 + - + +
220A MET* 3.2 12.1 - - + +
221A SER* 2.8 33.7 + - - +
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Residues in contact with GLU 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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213A GLY 4.0 2.9 - - - +
214A THR* 3.3 18.7 - - + +
215A THR* 2.8 49.4 + - - +
217A ALA* 1.3 74.0 - - + +
219A ALA* 1.3 59.7 + - - +
221A SER* 3.2 6.8 + - - -
222A ILE* 2.8 39.4 + - + +
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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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166A ILE* 4.3 13.2 - - + -
180A VAL* 4.4 10.3 - - + -
211A LEU* 4.2 21.4 - - + +
214A THR* 4.2 12.4 - - - +
215A THR 2.9 13.1 + - - +
216A HIS* 3.6 9.2 - - - +
218A GLU* 1.3 76.3 - - - +
220A MET* 1.3 61.9 + - - +
222A ILE* 3.3 12.3 + - - +
223A LEU* 3.0 29.5 + - - +
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Residues in contact with MET 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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166A ILE* 4.4 4.6 - - + +
216A HIS* 2.9 18.2 + - + +
217A ALA* 3.2 18.4 - - + +
219A ALA* 1.3 72.0 - - - +
221A SER* 1.3 86.7 + - - +
223A LEU* 3.2 4.5 + - - +
224A LYS* 2.9 37.7 + - + +
241B THR* 4.5 28.5 - - + +
243B VAL* 4.6 16.5 - - + +
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Residues in contact with SER 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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217A ALA* 2.8 23.5 + - - +
218A GLU* 3.6 7.4 - - - -
220A MET* 1.3 93.7 - - - +
222A ILE* 1.3 60.4 + - - +
224A LYS* 3.6 3.3 - - - +
225A GLN* 2.9 53.0 + - - +
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Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A VAL* 3.6 33.0 - - + -
209A ILE* 3.7 43.1 - - + -
211A LEU* 3.9 16.2 - - + -
214A THR* 4.1 15.5 - - + -
218A GLU* 2.8 23.3 + - + +
219A ALA* 3.3 5.6 + - - +
221A SER* 1.3 76.7 - - - +
223A LEU* 1.3 62.1 + - - +
225A GLN* 3.4 3.8 + - - +
226A CYS* 3.2 25.2 + - + +
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Residues in contact with LEU 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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157A LYS* 2.9 22.3 + - - +
160A ASN 5.3 0.2 - - - +
162A PHE* 3.5 34.2 - - + -
164A PHE* 4.3 11.7 - - + -
166A ILE* 4.0 24.5 - - + -
203A LEU* 4.1 15.9 - - + -
206A VAL* 3.8 27.8 - - + -
211A LEU* 5.3 0.2 - - + -
219A ALA* 3.0 20.6 + - + +
220A MET 3.6 6.1 - - - +
222A ILE* 1.3 74.6 - - - +
224A LYS* 1.3 57.8 + - - +
226A CYS* 3.4 9.8 - - - -
232A LEU* 4.4 4.5 - - + -
243B VAL* 4.1 26.0 - - + -
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Residues in contact with LYS 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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157A LYS* 3.0 15.2 + - - +
160A ASN* 3.1 36.0 + - - +
220A MET* 2.9 29.5 + - + +
221A SER* 3.3 9.2 + - - +
223A LEU* 1.3 78.1 - - - +
225A GLN* 1.3 64.3 + - + +
226A CYS 4.3 0.2 - - - +
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Residues in contact with GLN 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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220A MET* 6.0 0.2 - - - +
221A SER* 2.9 33.6 + - - +
222A ILE* 3.9 3.5 - - - +
224A LYS* 1.3 83.9 - - + +
226A CYS* 1.3 65.6 + - - +
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Residues in contact with CYS 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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157A LYS* 2.9 20.9 + - - -
160A ASN* 4.7 0.3 - - - +
162A PHE* 3.7 24.9 - - - -
206A VAL* 4.1 11.7 - - + -
207A ASP* 3.3 19.5 - - - +
209A ILE* 6.3 2.0 - - + -
222A ILE* 3.2 14.0 + - + +
223A LEU 3.4 19.1 - - - -
224A LYS 3.5 0.6 - - - +
225A GLN* 1.3 80.3 - - - +
227A GLY* 1.3 69.2 + - - +
230A ALA* 3.8 9.0 - - - -
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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