Contacts of the helix formed by residues 215 - 224 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203P MET 4.2 4.7 - - - +
204P THR* 3.9 37.2 - - + +
212P LYS* 5.7 4.5 - - + -
213P GLN* 3.3 12.1 + - + +
214P PRO* 1.3 68.8 - - - +
216P ALA* 1.3 59.7 + - - +
218P ILE* 4.3 4.0 - - + +
219P GLY* 3.0 27.7 + - - -
229P PHE* 4.4 7.5 - - + -
231P THR* 4.1 13.2 - - + -
247P MET* 3.8 30.3 - - + -
248P LYS* 4.3 6.6 - - + +
249P ILE* 3.7 26.5 - - + -
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Residues in contact with ALA 216 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214P PRO* 5.1 1.8 - - + -
215P ILE* 1.3 77.5 - - - +
217P GLU* 1.4 57.3 + - - +
220P ARG* 3.1 28.6 + - - +
248P LYS* 3.5 25.7 + - - +
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Residues in contact with GLU 217 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186P LEU* 5.9 7.4 - - + -
214P PRO* 3.4 22.7 + - + +
215P ILE 3.4 0.4 - - - -
216P ALA* 1.4 77.5 - - - +
218P ILE* 1.4 66.9 + - + +
220P ARG* 3.2 41.7 + - - +
221P ILE* 3.4 22.5 + - + +
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Residues in contact with ILE 218 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183P ILE* 6.0 0.9 - - + -
184P ILE* 5.5 2.5 - - + -
186P LEU* 5.6 6.5 - - + -
189P LEU* 4.8 12.8 - - + -
193P ILE* 5.8 0.3 - - - +
200P VAL* 4.2 3.8 - - + -
202P VAL* 3.7 39.9 - - + -
203P MET 4.9 1.1 - - - +
213P GLN* 4.0 15.5 - - + +
214P PRO* 3.3 33.7 + - + +
215P ILE* 4.3 1.6 - - + +
217P GLU* 1.4 75.1 - - + +
219P GLY* 1.4 57.3 + - - +
221P ILE* 3.3 14.8 + - + +
222P CYS* 3.2 34.4 + - - -
229P PHE* 3.5 32.3 - - + -
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Residues in contact with GLY 219 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215P ILE 3.0 18.8 + - - -
218P ILE* 1.4 76.7 - - - +
220P ARG* 1.4 56.9 + - - +
221P ILE 3.3 0.2 - - - -
222P CYS* 3.6 2.7 - - - +
223P SER* 3.0 32.7 + - - -
229P PHE* 4.1 14.5 - - - -
248P LYS* 3.6 25.3 - - - +
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Residues in contact with ARG 220 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190P GLU* 4.9 4.6 + - - -
216P ALA 3.1 19.9 + - - +
217P GLU* 3.2 32.9 + - - +
218P ILE 3.3 0.2 - - - -
219P GLY* 1.4 74.1 - - - +
221P ILE* 1.4 79.1 + - - +
223P SER* 3.0 20.2 + - - +
224P SER* 3.3 19.6 + - - -
248P LYS* 4.2 8.3 - - - +
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Residues in contact with ILE 221 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189P LEU* 5.4 8.3 - - + -
190P GLU* 3.4 32.3 - - + +
193P ILE* 3.8 42.2 - - + -
217P GLU* 3.4 26.5 - - + +
218P ILE* 3.5 11.9 - - + +
219P GLY 3.3 0.4 - - - -
220P ARG* 1.4 94.1 - - - +
222P CYS* 1.3 64.1 + - - +
224P SER* 3.5 6.3 + - - -
225P ARG* 3.4 31.3 + - - +
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Residues in contact with CYS 222 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193P ILE* 5.7 1.3 - - - -
200P VAL* 3.8 39.5 - - - -
218P ILE* 3.2 27.0 + - - -
219P GLY* 3.6 7.2 - - - +
221P ILE* 1.3 77.2 - - - +
223P SER* 1.4 61.3 + - - +
225P ARG* 3.3 3.8 + - - -
226P LYS 3.1 4.3 + - - -
227P VAL* 3.0 47.9 + - + +
229P PHE* 3.8 29.2 - - + -
248P LYS 5.6 0.7 - - - +
250P ASP* 5.6 0.7 - - - +
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Residues in contact with SER 223 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219P GLY 3.0 14.9 + - - -
220P ARG* 3.0 20.3 + - - +
222P CYS* 1.4 73.5 - - - +
224P SER* 1.4 62.9 + - - +
226P LYS* 3.2 21.6 + - - +
227P VAL 5.1 1.1 - - - -
248P LYS* 4.5 13.0 - - - +
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Residues in contact with SER 224 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220P ARG* 3.3 21.1 + - - -
221P ILE* 3.5 8.7 - - - -
222P CYS 3.3 0.2 - - - -
223P SER* 1.4 81.6 + - - +
225P ARG* 1.4 69.4 + - - +
226P LYS* 3.3 23.5 + - - +
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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
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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