Contacts of the helix formed by residues 215 - 224 (chain N) in PDB entry 5KZ5
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 ILE 215 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203N MET 4.1 4.9 - - - +
204N THR* 3.9 39.5 - - + +
212N LYS* 6.3 0.2 - - + -
213N GLN* 3.2 9.0 + - + +
214N PRO* 1.4 70.5 - - - +
216N ALA* 1.3 56.6 + - - +
218N ILE* 5.0 0.7 - - + -
219N GLY* 2.9 31.2 + - - -
229N PHE* 4.2 12.5 - - + -
231N THR* 4.1 13.7 - - + -
247N MET* 3.6 39.7 - - + -
248N LYS* 4.4 7.8 - - + +
249N ILE* 3.8 25.8 - - + -
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Residues in contact with ALA 216 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214N PRO* 3.2 4.0 - - + -
215N ILE* 1.3 78.5 - - - +
217N GLU* 1.3 58.8 + - + +
220N ARG* 3.4 16.6 + - - +
247N MET* 5.7 0.2 - - - -
248N LYS* 3.4 28.9 + - - +
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Residues in contact with GLU 217 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186N LEU* 4.5 27.4 - - + -
214N PRO* 3.3 21.7 + - + +
216N ALA* 1.3 75.8 - - + +
218N ILE* 1.4 65.4 + - - +
220N ARG* 3.1 42.4 + - - +
221N ILE* 3.4 17.4 - - + +
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Residues in contact with ILE 218 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184N ILE* 4.2 8.3 - - + -
186N LEU* 4.5 6.5 - - + -
189N LEU* 4.0 20.4 - - + -
200N VAL* 4.2 2.9 - - + -
202N VAL* 3.8 39.9 - - + -
203N MET 5.1 0.2 - - - +
213N GLN* 4.2 4.9 - - + -
214N PRO* 3.1 39.6 + - + +
215N ILE* 4.4 0.7 - - + +
217N GLU* 1.4 75.1 - - - +
219N GLY* 1.3 60.2 + - - +
221N ILE* 3.3 17.2 + - + +
222N CYS* 3.2 22.6 + - - -
229N PHE* 3.4 31.9 - - + -
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Residues in contact with GLY 219 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215N ILE 2.9 20.3 + - - -
218N ILE* 1.3 73.0 - - - +
220N ARG* 1.4 58.2 + - - +
221N ILE 3.3 0.2 - - - -
222N CYS* 3.5 11.4 - - - +
223N SER* 2.9 28.6 + - - -
229N PHE* 4.1 7.3 - - - -
248N LYS* 3.5 26.4 - - - +
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Residues in contact with ARG 220 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190N GLU* 3.2 26.5 + - - -
216N ALA 3.4 19.8 + - - +
217N GLU* 3.1 31.5 + - - +
219N GLY* 1.4 74.3 - - - +
221N ILE* 1.4 73.7 + - - +
223N SER* 3.0 19.5 + - - +
224N SER* 3.2 19.4 + - - -
248N LYS* 4.2 8.7 - - - +
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Residues in contact with ILE 221 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186N LEU 5.4 1.6 - - - +
189N LEU* 3.9 27.8 - - + -
190N GLU* 3.4 45.1 - - + +
193N ILE* 3.5 34.8 - - + -
217N GLU* 3.4 22.0 - - + +
218N ILE* 3.4 9.2 - - - +
220N ARG* 1.4 86.6 - - - +
222N CYS* 1.4 63.0 + - - +
224N SER* 3.4 7.7 + - - -
225N ARG* 3.3 27.2 + - - +
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Residues in contact with CYS 222 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193N ILE* 5.0 0.9 - - - +
200N VAL* 3.7 38.8 - - - -
218N ILE 3.2 18.5 + - - -
219N GLY* 3.5 8.7 - - - +
221N ILE* 1.4 80.8 - - - +
223N SER* 1.4 55.7 + - - +
225N ARG* 3.3 2.3 + - - +
226N LYS 3.1 7.6 + - - -
227N VAL* 3.0 46.9 + - + +
229N PHE* 3.7 29.4 - - + -
248N LYS* 5.6 1.8 - - + +
250N ASP* 5.9 0.2 - - - +
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Residues in contact with SER 223 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219N GLY 2.9 18.5 + - - -
220N ARG* 3.0 18.0 + - - +
222N CYS* 1.4 68.5 - - - +
224N SER* 1.3 64.9 + - - +
226N LYS* 3.1 24.1 + - - +
227N VAL 5.0 1.1 - - - -
248N LYS* 4.1 18.3 - - - +
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Residues in contact with SER 224 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220N ARG* 3.2 20.5 + - - -
221N ILE* 3.6 7.9 - - - -
222N CYS 3.4 0.2 - - - -
223N SER* 1.3 80.5 + - - +
225N ARG* 1.4 70.5 + - - +
226N LYS* 3.2 24.7 + - - +
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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