Contacts of the helix formed by residues 216 - 227 (chain C) in PDB entry 3KL8
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 216 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214C ASP* 2.8 7.4 + - - +
215C GLU* 1.3 78.5 - - + +
217C GLN* 1.3 72.1 + - - +
218C HIS* 3.7 18.9 + - - +
219C ARG* 3.0 43.3 + - + +
220C LEU* 3.0 11.3 + - - +
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Residues in contact with GLN 217 (chain C).
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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176C PRO* 4.0 22.4 - - + +
214C ASP 5.2 0.4 - - - -
215C GLU 3.8 4.2 + - - -
216C ASP* 1.3 74.9 + - - +
218C HIS* 1.3 68.1 + - + +
220C LEU* 3.0 27.6 - - + +
221C TYR* 2.8 59.0 + - + +
293H LYS* 4.5 19.1 + - - +
295H VAL* 4.4 8.1 - - - +
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Residues in contact with HIS 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ASP* 3.1 14.1 + - - +
217C GLN* 1.3 84.5 - - + +
219C ARG* 1.3 67.2 + - - +
220C LEU 2.9 2.0 + - - -
221C TYR* 3.8 17.9 - + + +
222C ALA* 3.0 24.1 + - - +
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Residues in contact with ARG 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C ASP* 2.9 37.6 + - - +
216C ASP* 3.2 25.1 - - + +
218C HIS* 1.3 77.4 - - - +
220C LEU* 1.3 59.7 + - - +
222C ALA* 3.3 12.3 - - - +
223C GLN* 3.2 21.0 + - - +
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Residues in contact with LEU 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C PRO* 4.2 14.1 - - + +
177C GLY* 4.1 24.5 - - - +
212C PHE* 3.6 16.2 - - + +
213C TRP* 3.4 42.4 - - + +
214C ASP* 4.2 14.3 - - - +
216C ASP 3.0 9.2 + - - +
217C GLN* 3.0 17.5 - - + +
218C HIS 2.9 1.8 - - - -
219C ARG* 1.3 73.1 - - - +
221C TYR* 1.3 62.5 + - + +
222C ALA 2.9 0.9 - - - -
223C GLN* 2.6 29.6 + - - +
224C ILE* 2.9 18.3 + - + +
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Residues in contact with TYR 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C PHE* 4.7 10.4 - + - -
176C PRO* 3.9 16.2 - - + +
179C LEU* 4.1 14.8 - - + +
184C LEU* 3.3 45.9 - - + +
217C GLN* 2.8 67.5 + - + -
218C HIS* 3.4 20.8 + + + +
220C LEU* 1.3 80.9 - - + +
222C ALA* 1.3 55.5 + - - +
224C ILE* 3.3 9.1 + - + +
225C LYS* 2.8 41.8 + - - +
295H VAL* 4.4 6.6 - - - +
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Residues in contact with ALA 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C HIS 3.0 12.9 + - - +
219C ARG* 3.3 21.5 - - - +
220C LEU 2.8 0.6 + - - -
221C TYR* 1.3 77.6 - - - +
223C GLN* 1.3 58.5 + - - +
225C LYS* 3.3 11.1 + - - +
226C ALA* 2.9 32.4 + - - +
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Residues in contact with GLN 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C PRO 3.5 19.0 + - - -
212C PHE* 3.6 8.7 - - + +
213C TRP 3.3 33.3 + - - +
214C ASP* 4.3 4.9 + - - +
219C ARG* 3.2 8.5 + - - +
220C LEU* 2.6 14.9 + - - +
222C ALA* 1.3 76.4 - - - +
224C ILE* 1.3 59.4 + - - +
226C ALA* 3.4 1.7 + - - -
227C GLY 3.2 2.6 + - - -
228C ALA* 2.9 67.9 + - + +
281H LYS* 4.5 8.5 - - - +
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Residues in contact with ILE 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C GLY* 4.4 19.7 - - - +
179C LEU* 3.5 30.5 - - + +
181C PRO* 4.0 24.4 - - + +
184C LEU* 3.8 20.9 - - + -
196C TRP* 4.4 7.6 - - + -
212C PHE* 3.6 33.2 - - + -
220C LEU* 2.9 28.5 + - + +
221C TYR* 3.4 10.3 - - + +
223C GLN* 1.3 73.6 - - - +
225C LYS* 1.3 59.3 + - - +
227C GLY* 2.7 27.2 + - - -
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Residues in contact with LYS 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C PRO* 4.2 8.5 - - - +
184C LEU* 3.6 38.2 + - + +
185C LYS* 3.8 47.2 + - + +
221C TYR* 2.8 29.2 + - - +
222C ALA* 3.8 7.6 - - - +
224C ILE* 1.3 75.4 - - - +
226C ALA* 1.3 61.0 + - - +
227C GLY 3.4 0.2 + - - -
253C VAL* 4.0 10.6 - - - +
108G SER* 5.1 1.0 - - - -
109G GLU* 5.2 5.0 + - - +
238G THR* 5.1 12.0 + - - +
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Residues in contact with ALA 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C ALA 2.9 18.7 + - - +
223C GLN* 3.6 7.2 - - - +
224C ILE 3.0 0.2 - - - -
225C LYS* 1.3 78.5 - - - +
227C GLY* 1.3 56.6 + - - +
228C ALA* 4.3 10.3 - - + +
108G SER* 3.1 13.4 - - - -
109G GLU* 3.3 23.4 + - + -
110G ALA* 3.0 27.9 + - + +
240G THR* 6.1 2.7 - - + -
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Residues in contact with GLY 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C TRP* 5.0 3.4 - - - -
212C PHE* 4.4 8.3 - - - -
224C ILE 2.7 22.3 + - - -
225C LYS 3.2 0.4 + - - -
226C ALA* 1.3 73.5 - - - +
228C ALA* 1.3 57.3 + - - +
229C TYR* 3.2 20.1 + - - +
253C VAL* 3.7 23.5 - - - +
108G SER* 4.3 2.8 + - - -
110G ALA* 3.6 9.5 - - - +
111G ASP* 5.4 3.6 - - - +
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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