Contacts of the helix formed by residues 191 - 205 (chain E) in PDB entry 5A0Q
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 LEU 191 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42E THR* 3.9 11.5 - - - +
44E GLU* 3.2 31.1 + - + +
45E GLY* 3.9 19.1 - - - +
46E VAL 5.2 2.7 - - - +
47E CYS* 5.5 0.6 - - + +
190E THR* 1.3 79.5 - - + +
192E LYS* 1.3 70.3 + - + +
194E ALA* 3.3 3.3 + - - +
195E ILE* 3.2 44.9 + - + +
219E THR* 5.7 2.9 - - - +
220E VAL 4.5 1.6 - - - +
221E GLN* 3.2 59.2 - - + +
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Residues in contact with LYS 192 (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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190E THR* 3.5 6.7 - - + +
191E LEU* 1.3 84.3 - - + +
193E GLU* 1.3 64.6 + - + +
195E ILE* 3.3 16.7 + - + +
196E LYS* 3.1 25.1 + - - +
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Residues in contact with GLU 193 (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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189E MET* 5.6 4.7 - - + +
190E THR* 3.2 37.2 + - + +
191E LEU 3.3 0.6 - - - -
192E LYS* 1.3 84.1 - - + +
194E ALA* 1.3 56.5 + - - +
196E LYS* 3.4 8.6 + - - +
197E SER* 3.2 23.4 + - - -
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Residues in contact with ALA 194 (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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40E ILE* 3.5 23.6 - - + +
42E THR* 2.1 47.6 - - + -
47E CYS* 5.3 0.4 - - + -
189E MET* 3.9 14.5 - - - -
190E THR 3.1 6.7 + - - +
191E LEU 3.4 1.6 - - - +
193E GLU* 1.3 74.0 - - - +
195E ILE* 1.4 64.3 + - + +
197E SER* 3.3 18.7 - - - -
198E SER 3.5 4.5 + - - -
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Residues in contact with ILE 195 (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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47E CYS* 3.4 28.0 - - + -
191E LEU* 3.2 42.1 + - + +
192E LYS* 3.4 13.7 - - + +
193E GLU 3.3 0.2 - - - -
194E ALA* 1.4 73.6 - - - +
196E LYS* 1.3 64.2 + - - +
198E SER* 2.7 20.3 + - - -
199E LEU* 3.1 21.0 + - + +
217E LEU* 3.8 23.6 - - + -
219E THR* 4.0 18.2 - - + +
229E PHE* 5.2 11.4 - - + -
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Residues in contact with LYS 196 (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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192E LYS 3.1 14.1 + - - +
193E GLU* 3.4 11.6 + - - +
195E ILE* 1.3 75.4 - - - +
197E SER* 1.4 62.0 + - - +
199E LEU* 3.2 16.0 + - + +
200E ILE* 3.1 46.3 + - + +
236E GLU 6.2 4.9 - - - -
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Residues in contact with SER 197 (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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40E ILE* 4.2 11.5 - - - +
181E LEU* 4.4 1.7 - - - +
184E VAL* 4.1 19.7 - - - +
189E MET* 5.5 7.6 - - - +
193E GLU 3.2 12.4 + - - -
194E ALA* 3.3 14.4 - - - -
195E ILE 3.1 0.4 - - - -
196E LYS* 1.4 76.1 - - - +
198E SER* 1.4 56.7 + - - +
200E ILE* 3.4 6.1 + - - +
201E ILE* 3.0 48.8 + - - +
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Residues in contact with SER 198 (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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38E ILE* 3.6 16.2 - - - -
40E ILE* 3.9 15.8 - - - +
47E CYS* 3.5 19.2 - - - -
49E ALA* 3.8 23.8 - - - -
194E ALA 3.5 1.6 + - - -
195E ILE* 2.7 18.2 + - - -
197E SER* 1.4 78.2 - - - +
199E LEU* 1.3 55.6 + - - +
202E LEU* 3.0 37.0 + - - +
217E LEU* 3.8 7.7 - - - +
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Residues in contact with LEU 199 (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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195E ILE* 3.1 31.7 + - + +
196E LYS* 3.2 17.5 + - + +
198E SER* 1.3 76.3 - - - +
200E ILE* 1.4 60.0 + - + +
202E LEU* 5.0 0.2 - - - -
203E LYS* 3.8 21.1 + - - +
210E LEU* 3.9 17.7 - - + +
215E ILE* 3.7 27.6 - - + -
217E LEU* 4.7 7.0 - - + -
233E GLU 5.0 1.6 - - - +
234E LEU* 3.8 43.7 - - + +
236E GLU 4.6 14.6 - - - -
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Residues in contact with ILE 200 (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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196E LYS* 3.1 46.3 + - + +
197E SER* 3.9 5.4 - - - +
199E LEU* 1.4 76.9 - - + +
201E ILE* 1.3 69.3 + - + +
202E LEU 3.2 0.4 - - - -
203E LYS* 3.2 24.7 + - + +
204E GLN* 3.7 18.7 + - + +
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Residues in contact with ILE 201 (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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38E ILE* 3.6 19.5 - - + -
177E ALA* 4.0 8.1 - - + -
180E SER* 3.7 19.7 - - - +
181E LEU* 3.8 24.9 - - + -
184E VAL* 4.4 10.3 - - + -
197E SER* 3.0 37.4 + - - +
200E ILE* 1.3 79.6 - - + +
202E LEU* 1.4 57.4 + - - +
204E GLN* 3.0 41.5 + - - +
205E VAL* 3.2 24.3 + - + +
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Residues in contact with LEU 202 (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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36E THR* 4.2 11.0 - - + +
38E ILE* 3.9 17.0 - - + -
49E ALA* 3.9 18.8 - - + -
50E VAL* 4.3 4.3 - - - +
51E GLU* 4.0 23.1 - - + +
198E SER 3.0 21.2 + - - +
200E ILE 3.2 0.2 - - - -
201E ILE* 1.4 77.9 - - - +
203E LYS* 1.4 56.0 + - - +
205E VAL* 3.5 18.1 - - + +
206E MET* 3.1 30.0 + - - +
210E LEU* 3.9 21.5 - - + +
215E ILE* 3.4 37.0 - - + -
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Residues in contact with LYS 203 (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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199E LEU 3.8 15.8 + - - +
200E ILE* 3.2 14.1 + - + +
202E LEU* 1.4 76.0 - - - +
204E GLN* 1.4 62.2 + - + +
206E MET* 3.5 12.6 - - - +
208E GLU 4.2 6.2 - - - +
209E LYS* 3.8 37.5 - - + +
210E LEU* 3.1 47.4 + - + +
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Residues in contact with GLN 204 (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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176E GLY 4.9 1.4 - - - +
180E SER* 3.6 28.8 + - - -
200E ILE* 3.7 21.4 - - + +
201E ILE* 3.0 23.5 + - - +
203E LYS* 1.4 75.7 - - + +
205E VAL* 1.3 67.9 + - + +
206E MET 3.3 7.4 - - - +
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Residues in contact with VAL 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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36E THR* 3.5 31.2 - - + +
38E ILE* 5.8 0.4 - - + -
173E ALA* 3.3 38.9 - - + +
176E GLY 5.0 1.1 - - - -
177E ALA* 3.7 33.2 - - + +
201E ILE* 3.4 19.1 - - + +
202E LEU* 3.5 22.0 - - + +
204E GLN* 1.3 77.5 - - + +
206E MET* 1.3 64.6 + - - +
207E GLU 4.0 0.2 + - - -
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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