Contacts of the helix formed by residues 204 - 216 (chain E) in PDB entry 6O81
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 HIS 204 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200E SER* 4.1 0.7 - - - -
203E ILE* 1.3 78.6 - - - +
205E PRO* 1.3 75.1 - - + +
206E ALA* 3.2 31.5 + - + +
207E MET* 3.1 14.8 + - + -
208E VAL* 2.8 28.2 + - - +
235E GLN* 3.7 21.2 + - + -
236E VAL* 3.5 25.9 - - + +
239E ASP* 3.5 34.2 + - + +
255E LYS* 5.9 2.9 - - - -
259E TYR* 3.4 21.8 - - + -
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Residues in contact with PRO 205 (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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200E SER* 3.6 22.2 - - - +
204E HIS* 1.3 102.8 - - + +
206E ALA* 1.3 54.9 + - - +
208E VAL* 3.3 12.5 - - + +
209E ARG* 2.9 32.4 + - - +
1I MET* 5.0 4.0 - - - +
2I GLU* 3.6 48.9 - - + +
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Residues in contact with ALA 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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204E HIS* 3.2 17.7 + - + +
205E PRO* 1.3 77.9 - - - +
207E MET* 1.3 58.0 + - - +
209E ARG* 3.4 10.4 + - - +
210E LEU* 2.9 28.8 + - - +
232E ALA* 4.0 18.3 - - + +
235E GLN* 3.8 29.6 - - + -
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Residues in contact with MET 207 (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 ILE* 3.9 13.2 - - + -
204E HIS* 3.1 20.5 + - + +
206E ALA* 1.3 80.7 - - - +
208E VAL* 1.3 57.7 + - - +
210E LEU* 3.3 13.1 + - - +
211E GLY* 2.9 24.3 + - - -
229E LEU* 5.2 0.7 - - - -
232E ALA* 4.7 6.7 - - + +
233E LEU* 4.2 11.7 - - + -
236E VAL* 3.8 24.7 - - + -
259E TYR* 3.7 39.9 - - + +
260E MET* 4.0 11.0 - - + -
262E PHE* 3.9 5.6 - - + -
263E LEU* 3.7 31.5 - - + +
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Residues in contact with VAL 208 (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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193E THR* 3.7 23.3 - - + -
196E MET* 4.1 11.2 - - + -
200E SER* 3.3 22.9 - - - +
203E ILE* 4.2 5.1 - - + +
204E HIS 2.8 16.7 + - - +
205E PRO* 3.3 13.5 - - + +
207E MET* 1.3 70.1 - - - +
209E ARG* 1.3 62.9 + - - +
211E GLY 3.8 0.2 - - - -
212E LEU* 2.9 32.0 + - + +
262E PHE* 3.6 28.5 - - + -
122I ARG* 4.0 22.0 - - - +
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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 PRO 2.9 19.8 + - - +
206E ALA* 3.6 9.8 - - - +
208E VAL* 1.3 74.8 - - - +
210E LEU* 1.3 60.1 + - - +
212E LEU* 3.4 6.2 + - - +
213E GLN* 2.9 39.9 + - - +
2I GLU* 4.1 17.0 + - - +
100I ASP* 4.7 6.5 + - - -
121I PHE* 3.7 16.8 + - - -
122I ARG* 3.0 50.7 + - + +
125I ASP* 3.0 38.9 + - - +
126I ALA 5.5 0.2 + - - -
208I LYS* 5.2 6.8 - - - +
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Residues in contact with LEU 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 ALA 2.9 17.8 + - - +
207E MET* 3.5 8.1 - - - +
209E ARG* 1.3 77.2 - - - +
211E GLY* 1.3 56.3 + - - +
213E GLN* 3.4 25.7 - - - +
214E TYR* 2.9 61.6 + - + -
228E ALA* 3.5 24.9 - - + +
229E LEU* 3.7 21.8 - - + -
232E ALA* 3.9 13.0 - - + -
263E LEU* 3.8 30.1 - - + -
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Residues in contact with GLY 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 MET 2.9 15.5 + - - -
208E VAL 3.4 2.4 + - - -
209E ARG 3.3 0.2 - - - -
210E LEU* 1.3 76.5 - - - +
212E LEU* 1.3 56.9 + - - +
214E TYR* 3.7 3.2 - - - +
215E SER* 2.9 31.9 + - - -
262E PHE* 4.4 2.0 - - - -
263E LEU* 4.0 12.8 - - - +
266E CYS* 3.6 27.7 - - - -
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Residues in contact with LEU 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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191E SER* 5.7 7.0 - - - +
192E LEU 6.1 0.7 - - - +
193E THR* 3.7 28.9 - - + +
208E VAL* 2.9 25.0 + - + +
209E ARG* 3.8 4.7 - - - +
210E LEU 3.3 0.2 - - - -
211E GLY* 1.3 79.5 - - - +
213E GLN* 1.3 60.4 + - - +
215E SER* 4.3 3.1 - - - -
216E GLN* 3.3 36.3 + - + +
262E PHE* 5.2 2.7 - - + -
266E CYS* 5.5 2.2 - - - -
119I ASP* 3.7 43.1 - - + +
122I ARG* 3.8 25.8 - - + -
123I ALA* 4.0 13.0 - - + -
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Residues in contact with GLN 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 30.2 + - - +
210E LEU* 3.4 34.7 - - - +
212E LEU* 1.3 75.5 - - - +
214E TYR* 1.3 61.2 + - + +
216E GLN 4.4 0.9 - - - -
218E LEU* 3.4 18.4 + - + -
219E VAL* 3.4 40.5 + - + +
228E ALA* 3.8 15.4 - - - +
122I ARG 5.3 0.2 - - - +
123I ALA* 3.8 22.6 - - - +
125I ASP* 5.7 4.0 - - - +
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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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188E ARG* 5.8 0.2 + - - -
210E LEU* 2.9 45.3 + - + +
211E GLY* 3.7 5.6 - - - +
212E LEU 3.2 0.4 - - - -
213E GLN* 1.3 83.0 - - + +
215E SER* 1.3 64.7 + - - +
216E GLN 3.3 0.4 - - - -
217E GLY* 3.4 11.3 + - - -
219E VAL* 4.1 21.9 - - + +
225E ARG* 2.4 69.3 + - + +
228E ALA* 4.7 0.7 - - + -
229E LEU* 3.4 13.5 + - - +
263E LEU* 4.1 15.7 - - + -
266E CYS* 5.2 2.0 - - + -
267E ARG* 3.3 32.3 - - + +
269E LEU* 5.6 0.4 - - + -
273E MET* 3.6 26.2 - - + -
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Residues in contact with SER 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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170E ARG* 3.9 18.9 + - - -
187E SER 5.0 2.6 + - - -
188E ARG* 3.3 26.0 + - - +
190E ASN 5.0 2.9 + - - -
191E SER* 5.9 1.4 - - - -
211E GLY 2.9 17.7 + - - -
212E LEU* 4.3 3.8 - - - -
214E TYR* 1.3 77.7 - - - +
216E GLN* 1.3 63.2 + - - +
217E GLY 3.4 0.9 + - - -
266E CYS* 3.8 26.4 + - - -
267E ARG* 4.9 2.9 - - - +
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Residues in contact with GLN 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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188E ARG* 3.6 30.8 + - + +
212E LEU* 3.3 18.8 + - - +
213E GLN 4.4 0.2 - - - -
215E SER* 1.3 78.5 - - - +
217E GLY* 1.3 60.4 + - - +
218E LEU* 3.8 20.0 + - + +
119I ASP* 4.7 10.3 + - - +
120I LEU* 6.1 0.6 - - - +
123I ALA* 3.4 32.9 - - - +
124I TYR* 3.9 22.3 + - - -
165I LYS* 5.6 4.9 - - - +
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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