Contacts of the helix formed by residues 215 - 225 (chain E) in PDB entry 3KQG
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214E LYS* 1.3 76.4 - - - +
216E TRP* 1.3 66.6 + - - +
217E TYR* 4.0 3.7 + - - +
218E SER* 3.3 25.4 + - - -
219E ALA* 2.9 20.3 + - - +
252E TRP* 3.6 0.2 - - - -
311E CYS 3.7 9.0 - - - -
312E ASP* 3.3 30.5 - - + +
313E LYS 3.1 7.9 - - - +
314E THR* 4.1 10.6 - - + +
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Residues in contact with TRP 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E THR* 1.3 73.6 - - - +
217E TYR* 1.3 92.9 + + + +
219E ALA* 3.4 3.8 - - - +
220E GLU* 3.0 25.7 + - + -
230E LEU* 3.5 17.7 - - + +
252E TRP* 3.3 43.9 - + + +
253E ILE 3.0 21.7 + - - -
254E GLY 4.1 3.1 - - - -
255E LEU 3.2 12.8 + - - -
256E THR* 3.6 30.7 - - + -
267E VAL* 4.0 34.1 - - + -
295E CYS* 3.4 28.7 - - + -
311E CYS* 3.1 17.0 + - + +
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Residues in contact with TYR 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E THR* 3.2 4.2 + - - +
216E TRP* 1.3 101.1 - + + +
218E SER* 1.3 68.1 + - - +
220E GLU* 3.1 13.3 + - + +
221E GLN* 2.9 60.9 + - + +
311E CYS 4.5 1.2 + - - +
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Residues in contact with SER 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214E LYS* 4.0 19.8 - - - +
215E THR* 3.3 22.0 + - - -
217E TYR* 1.3 79.2 - - - +
219E ALA* 1.3 63.1 + - - +
221E GLN* 3.2 17.4 + - - +
222E PHE* 3.0 21.8 + - - +
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Residues in contact with ALA 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E LYS* 3.8 13.3 - - + +
215E THR 2.9 17.8 + - - +
216E TRP* 3.4 7.6 - - - +
218E SER* 1.3 77.7 - - - +
220E GLU* 1.3 63.1 + - - +
222E PHE* 3.1 3.6 + - - +
223E CYS* 2.9 27.5 + - - -
230E LEU* 4.2 4.5 - - + -
252E TRP* 4.7 3.1 - - + -
317E PHE* 3.4 40.3 - - + -
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Residues in contact with GLU 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E TRP* 3.0 20.7 + - + +
217E TYR* 3.1 23.0 + - + +
219E ALA* 1.3 75.8 - - - +
221E GLN* 1.3 59.6 + - + +
223E CYS* 3.4 1.1 + - - +
224E VAL* 2.9 38.7 + - + +
229E HIS* 2.8 29.6 + - - -
230E LEU* 3.0 39.7 + - + +
267E VAL* 3.2 28.8 - - + +
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Residues in contact with GLN 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E TYR* 2.9 61.1 + - + +
218E SER* 3.2 17.7 + - - +
220E GLU* 1.3 76.3 - - + +
222E PHE* 1.3 61.3 + - - +
224E VAL* 3.1 10.4 + - + +
225E SER* 2.8 30.4 + - - -
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Residues in contact with PHE 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E TYR* 3.6 38.1 - + - -
212E ILE* 5.8 0.2 - - + -
214E LYS* 4.2 17.9 - - - -
218E SER 3.0 13.1 + - - +
219E ALA 3.1 7.6 + - - +
221E GLN* 1.3 74.7 - - - +
223E CYS* 1.3 64.6 + - - +
225E SER* 2.8 23.9 + - - -
226E ARG* 3.2 58.2 + - + +
317E PHE* 3.3 31.2 - + + -
319E CYS* 4.3 1.6 - - - -
247F GLY* 4.0 20.0 - - - -
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Residues in contact with CYS 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E ALA 2.9 15.9 + - - -
220E GLU 3.5 8.1 - - - +
222E PHE* 1.3 77.6 - - - +
224E VAL* 1.3 53.9 + - - +
226E ARG* 2.7 22.3 + - - -
228E SER* 3.0 29.6 + - - +
229E HIS 3.7 11.0 - - - -
230E LEU* 3.8 23.6 - - - +
317E PHE* 3.8 2.7 - - - -
319E CYS* 2.1 55.0 - - - -
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Residues in contact with VAL 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E GLU* 2.9 39.8 + - + +
221E GLN* 3.1 12.8 + - + +
223E CYS* 1.3 74.5 - - - +
225E SER* 1.3 58.2 + - - +
227E ASN* 3.2 16.6 + - - +
228E SER 3.2 13.0 - - - +
229E HIS* 3.8 12.6 - - + +
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Residues in contact with SER 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E GLN 2.8 17.7 + - - -
222E PHE* 2.8 17.4 + - - -
223E CYS 3.1 0.4 - - - -
224E VAL* 1.3 72.9 - - - +
226E ARG* 1.3 71.9 + - - +
227E ASN 3.4 1.7 + - - -
244F LYS* 3.4 20.9 + - - -
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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