Contacts of the helix formed by residues 204 - 218 (chain E) in PDB entry 1K7L
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 LYS 204 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202E ASP 1.9 25.1 + - - +
203E LEU 1.3 69.2 - - - -
205E SER* 1.3 58.8 + - - +
206E LEU 3.0 1.8 - - - -
207E ALA* 3.0 31.8 - - + +
208E LYS* 3.9 2.6 + - - +
407E VAL* 4.5 9.3 + - + +
410E LEU* 3.0 53.7 + - - +
411E HIS* 4.6 3.0 - - + +
414E SER* 5.6 1.2 + - - -
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Residues in contact with SER 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E ASP* 2.7 42.8 + - - +
203E LEU 3.7 0.3 + - - -
204E LYS* 1.3 75.5 - - - +
206E LEU* 1.3 62.9 + - - -
207E ALA 2.8 6.6 + - - -
208E LYS* 3.1 8.7 + - - +
209E ARG* 3.0 24.2 + - - +
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Residues in contact with LEU 206 (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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203E LEU* 4.0 34.0 - - + +
204E LYS 3.5 0.6 - - - +
205E SER* 1.3 81.2 + - - +
207E ALA* 1.3 60.5 + - - +
209E ARG* 3.6 4.9 + - - +
210E ILE* 3.1 46.7 + - + +
294E ILE* 5.4 0.7 - - + -
295E PRO* 3.2 36.3 - - + +
403E GLY* 3.9 19.7 - - - +
404E ILE* 4.3 9.4 - - + +
407E VAL* 3.7 23.8 - - + -
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Residues in contact with ALA 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E LYS* 3.0 21.8 + - + +
205E SER 2.8 1.0 - - - -
206E LEU* 1.3 77.1 - - - +
208E LYS* 1.3 70.6 + - - +
209E ARG 3.1 4.3 + - - -
210E ILE* 3.2 4.7 + - - +
211E TYR* 2.9 27.9 + - - +
377E LEU* 3.9 30.1 - - + +
407E VAL* 4.4 13.4 - - + +
411E HIS* 5.4 4.3 - - + -
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Residues in contact with LYS 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E LYS 3.9 1.7 + - - +
205E SER* 3.1 11.4 + - - +
207E ALA* 1.3 85.8 - - - +
209E ARG* 1.3 49.9 + - - +
211E TYR* 3.2 39.9 - - + +
212E GLU* 2.5 38.9 + - - +
373E SER* 4.0 19.0 + - - +
377E LEU* 5.8 1.0 - - - +
411E HIS* 4.1 17.9 + - - -
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Residues in contact with ARG 209 (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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205E SER 3.0 16.3 + - - +
206E LEU* 3.7 5.8 - - - +
208E LYS* 1.3 74.5 - - - +
210E ILE* 1.3 68.8 + - - +
211E TYR 3.0 0.9 - - - -
212E GLU* 2.8 38.5 + - - +
213E ALA* 2.9 16.3 + - - +
293E ALA* 3.0 49.7 + - - +
295E PRO* 4.2 20.0 - - + +
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Residues in contact with ILE 210 (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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206E LEU* 3.1 40.8 + - + +
207E ALA 3.6 3.6 - - - +
209E ARG* 1.3 80.2 - - - +
211E TYR* 1.3 60.4 + - - +
213E ALA* 3.4 6.0 + - - -
214E TYR* 3.2 19.2 + - - +
290E PHE* 3.2 28.8 - - + -
293E ALA 5.5 0.9 - - - -
294E ILE* 4.3 16.2 - - + -
295E PRO* 4.6 10.3 - - + -
376E SER* 3.8 18.6 - - - +
377E LEU* 4.1 15.5 - - + -
380E ALA* 4.0 20.6 - - + -
404E ILE* 4.2 9.6 - - + -
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Residues in contact with TYR 211 (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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207E ALA 2.9 16.7 + - - +
208E LYS* 3.2 40.4 - - + +
209E ARG 3.0 0.2 - - - -
210E ILE* 1.3 76.8 - - - +
212E GLU* 1.3 63.6 + - - +
214E TYR* 3.4 2.8 + + - +
215E LEU* 3.2 49.4 + - + +
372E ASP* 3.6 20.4 - - + +
373E SER* 3.5 37.6 + - - -
376E SER* 3.7 15.3 - - - +
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Residues in contact with GLU 212 (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 LYS* 2.5 34.4 + - - +
209E ARG* 3.0 33.8 + - - +
211E TYR* 1.3 75.3 - - + +
213E ALA* 1.3 65.0 + - - +
214E TYR 3.1 0.2 - - - -
215E LEU* 3.4 7.7 + - - +
216E LYS* 2.9 26.0 + - - +
212G GLU* 4.7 20.1 - - - +
216G LYS* 5.4 5.0 - - + +
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Residues in contact with ALA 213 (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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209E ARG* 2.9 17.7 + - - +
210E ILE* 3.6 12.1 - - - +
212E GLU* 1.3 77.0 - - - +
214E TYR* 1.3 56.8 + - - +
216E LYS* 3.5 4.0 - - - +
217E ASN* 2.7 41.1 + - - +
290E PHE* 3.7 14.4 - - + +
293E ALA* 3.6 32.5 - - + +
294E ILE* 6.2 0.2 - - + -
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Residues in contact with TYR 214 (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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210E ILE 3.2 12.8 + - - +
211E TYR* 3.4 9.4 - + - +
213E ALA* 1.3 75.1 - - - +
215E LEU* 1.3 77.2 + - + +
216E LYS 3.1 0.2 - - - -
218E PHE* 3.1 61.6 + + + +
220E MET 5.3 1.3 + - - -
221E ASN* 4.6 12.1 - - + -
222E LYS 4.8 3.1 + - - -
290E PHE* 3.6 13.0 - + + -
320E MET* 4.0 19.9 - - - +
323E SER* 5.1 2.1 + - - -
372E ASP* 3.3 44.2 + - + -
375E ILE* 3.6 30.6 - - + +
376E SER* 3.7 21.3 - - - -
379E VAL* 4.8 3.6 - - + -
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Residues in contact with LEU 215 (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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211E TYR* 3.2 51.8 + - + +
212E GLU* 3.4 6.9 + - - +
214E TYR* 1.3 92.3 - - + +
216E LYS* 1.3 61.8 + - - +
218E PHE 3.5 14.2 - - - +
221E ASN* 3.8 27.4 - - + +
372E ASP* 4.7 4.5 - - + +
216G LYS* 3.7 27.8 + - + +
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Residues in contact with LYS 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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212E GLU 2.9 19.1 + - - +
213E ALA* 3.5 6.7 - - - +
214E TYR 3.1 0.2 - - - -
215E LEU* 1.3 79.6 - - - +
217E ASN* 1.3 74.3 + - - +
218E PHE 3.9 0.9 + - - +
219E ASN* 5.5 3.3 + - - -
215G LEU 3.4 17.8 + - - -
216G LYS* 3.5 41.2 - - + +
218G PHE 4.7 7.3 + - - -
219G ASN* 5.5 9.2 - - - +
224G LYS* 5.1 10.3 - - - +
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Residues in contact with ASN 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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213E ALA* 2.7 35.3 + - - +
216E LYS* 1.3 86.9 - - - +
218E PHE* 1.3 60.8 + - + +
219E ASN* 5.4 1.2 + - - -
286E GLU* 3.2 42.1 - - + +
289E GLU* 3.1 38.2 - - - +
290E PHE* 3.8 16.2 - - + +
293E ALA* 4.8 2.9 - - - +
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Residues in contact with PHE 218 (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 TYR* 3.1 60.4 + + + +
215E LEU* 3.5 15.6 - - - +
216E LYS 3.6 0.4 - - - +
217E ASN* 1.3 77.9 - - + +
219E ASN* 1.3 68.8 + - - +
220E MET 4.4 13.3 - - - +
221E ASN* 5.3 4.4 - - + +
283E THR* 4.5 4.9 - - + -
286E GLU* 3.4 35.7 - - + +
287E LEU* 3.4 37.9 - - + -
290E PHE* 3.9 30.1 - + + -
320E MET* 4.0 17.9 - - + -
379E VAL* 5.5 0.4 - - + -
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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