Contacts of the helix formed by residues 201 - 215 (chain E) in PDB entry 5JLH
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 201 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A MET* 5.9 2.1 - - - +
269A GLU* 3.2 44.0 + - + +
270A SER* 4.4 4.9 + - - -
285D ASP* 4.7 9.9 - - - +
38E ARG* 4.8 0.7 - - - +
189E MET* 5.9 0.3 - - - +
199E PHE 3.6 1.3 + - - -
200E THR* 1.3 91.9 + - - +
202E THR* 1.3 70.8 - - - +
203E ALA* 3.2 8.7 - - + +
204E GLU* 3.1 21.8 + - - +
205E ARG* 2.8 30.6 + - - +
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Residues in contact with THR 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLU* 3.0 19.5 + - - -
65E THR* 4.0 3.0 + - - -
66E LEU* 3.5 49.8 + - + +
68E TYR* 5.8 5.2 - - + -
201E THR* 1.3 75.7 - - - +
203E ALA* 1.3 66.9 + - - +
205E ARG* 3.1 37.2 + - + +
206E GLU* 3.2 10.9 + - + +
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Residues in contact with ALA 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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269A GLU* 5.1 1.6 + - - +
285D ASP* 4.8 7.6 - - + +
286D VAL* 5.6 2.9 - - + -
287D ASP* 4.9 6.5 - - + -
61E ARG* 3.4 55.5 - - + +
62E GLY* 4.6 6.5 - - - +
64E LEU 5.2 2.8 + - - +
66E LEU* 4.6 3.9 - - - +
201E THR* 4.0 7.2 - - + +
202E THR* 1.3 81.9 - - - +
204E GLU* 1.3 64.3 + - + +
206E GLU* 3.1 14.6 + - - +
207E ILE* 3.5 3.4 + - - +
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Residues in contact with GLU 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D ASP* 5.7 2.1 - - - +
286D VAL* 3.9 30.6 + - + +
198E SER 4.6 1.9 - - - +
199E PHE* 3.5 35.5 - - + +
200E THR* 2.9 26.0 + - - -
201E THR* 3.1 32.7 + - - +
203E ALA* 1.3 74.6 - - - +
205E ARG* 1.3 64.3 + - - +
206E GLU 3.1 1.3 - - - -
207E ILE* 2.9 29.7 + - + +
208E VAL* 2.9 15.9 + - - +
241E LEU* 6.1 0.2 - - + -
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Residues in contact with ARG 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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68E TYR* 3.8 19.8 - - - -
182E ARG* 3.3 52.1 + - - +
185E THR* 3.9 14.1 - - + +
186E ASP* 3.3 34.9 + - - -
189E MET* 3.8 25.1 - - - -
199E PHE* 5.6 0.9 - - - -
201E THR 2.8 14.2 + - - +
202E THR* 3.1 27.7 - - - +
204E GLU* 1.3 78.1 - - - +
206E GLU* 1.3 60.0 + - + +
208E VAL* 2.9 26.9 - - - +
209E ARG* 2.9 11.3 + - - +
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Residues in contact with GLU 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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31E PRO* 4.9 1.4 - - - +
33E ILE* 3.9 6.9 - - - +
58E GLN* 2.3 42.5 + - - +
61E ARG* 4.4 8.0 + - - +
66E LEU* 3.6 22.3 - - + +
68E TYR* 2.8 35.9 + - + +
202E THR* 4.1 9.6 - - + +
203E ALA 3.1 11.0 + - - +
204E GLU 3.1 0.4 - - - -
205E ARG* 1.3 81.9 - - + +
207E ILE* 1.3 64.8 + - - +
209E ARG* 3.2 23.9 + - - +
210E ASP* 3.0 21.3 + - - +
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Residues in contact with ILE 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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286D VAL* 5.0 5.8 - - + -
287D ASP* 5.3 1.6 - - + +
61E ARG* 3.1 28.9 - - - +
199E PHE* 5.2 4.7 - - + -
203E ALA 4.1 1.1 - - - +
204E GLU* 2.9 29.4 + - + +
206E GLU* 1.3 74.3 - - - +
208E VAL* 1.3 63.4 + - - +
210E ASP* 3.0 18.0 + - + +
211E ILE* 3.0 15.8 + - + +
239E TYR* 4.4 15.3 - - + +
241E LEU* 4.1 30.5 - - + -
242E PRO* 3.7 29.8 - - + -
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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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185E THR* 3.7 20.2 - - + +
188E LEU* 3.9 13.6 - - + +
189E MET* 4.3 20.0 - - + -
192E LEU* 4.1 12.8 - - + -
199E PHE* 3.3 37.9 - - + -
204E GLU 2.9 8.6 + - - +
205E ARG* 2.9 30.7 - - - +
207E ILE* 1.3 73.4 - - - +
209E ARG* 1.3 66.2 + - - +
211E ILE* 3.1 12.9 + - + +
212E LYS* 2.9 24.3 + - - +
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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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15E MET* 5.8 7.5 - - - +
31E PRO* 4.9 9.2 - - - +
58E GLN* 3.9 20.2 + - - +
68E TYR* 3.6 22.5 + - - -
156E ASP* 5.0 2.7 - - - -
185E THR* 4.1 20.4 - - + +
205E ARG 2.9 14.3 + - - +
206E GLU* 3.2 31.7 + - - +
208E VAL* 1.3 77.3 - - - +
210E ASP* 1.3 57.2 + - - +
212E LYS* 3.3 5.1 + - - +
213E GLU* 2.5 72.2 + - - +
401E ADP 3.7 27.4 + - - +
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Residues in contact with ASP 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 GLU 3.0 12.0 + - - +
207E ILE* 3.0 15.0 + - + +
209E ARG* 1.3 76.6 - - - +
211E ILE* 1.3 65.8 + - - +
213E GLU* 3.2 28.0 + - - +
214E LYS* 3.3 27.7 + - - +
239E TYR* 3.1 19.0 + - - +
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Residues in contact with ILE 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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188E LEU* 4.4 11.4 - - + -
192E LEU* 4.9 8.3 - - + -
199E PHE* 4.8 8.1 - - + -
207E ILE* 3.0 14.7 + - + +
208E VAL* 3.1 29.6 + - + +
210E ASP* 1.3 75.3 - - - +
212E LYS* 1.3 64.4 + - - +
214E LYS* 3.0 3.4 + - - -
215E LEU* 2.8 46.6 + - + +
216E CYS* 5.0 2.2 - - - -
239E TYR* 3.5 47.8 - - + -
241E LEU* 5.0 2.2 - - + -
247E ILE* 5.3 7.0 - - + -
249E ILE* 4.1 16.2 - - + -
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Residues in contact with LYS 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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181E GLY* 2.5 24.0 + - - -
184E LEU* 4.0 13.2 - - + -
185E THR* 2.5 35.3 + - - +
188E LEU* 3.8 7.6 - - + -
208E VAL 2.9 13.8 + - - +
209E ARG* 3.6 10.0 - - - +
211E ILE* 1.3 78.0 - - - +
213E GLU* 1.3 60.7 + - - +
214E LYS* 3.0 2.6 + - - +
216E CYS* 3.5 42.9 + - - +
256E CYS* 4.3 5.4 - - - -
305E TYR* 3.1 33.2 - - + +
401E ADP 2.6 31.8 + - - -
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Residues in contact with GLU 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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15E MET* 5.8 1.6 - - - +
209E ARG* 2.5 56.5 + - - +
210E ASP* 3.2 23.3 + - - +
212E LYS* 1.3 74.7 - - - +
214E LYS* 1.3 57.9 + - - +
335E LYS* 5.3 1.7 + - - -
401E ADP 3.0 77.9 + - + +
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Residues in contact with LYS 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 ASP* 3.3 37.4 + - - +
211E ILE 3.0 8.0 + - - +
212E LYS 3.8 0.2 - - - -
213E GLU* 1.3 79.6 - - - +
215E LEU* 1.3 83.9 - - + +
216E CYS 3.3 10.5 + - - +
237E LYS* 5.9 0.3 + - - -
239E TYR* 3.4 31.6 + - - -
306E PRO* 5.2 5.9 - - - +
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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 ILE* 2.8 23.1 + - + +
214E LYS* 1.3 91.1 - - + +
216E CYS* 1.3 54.4 + - - +
217E TYR* 4.1 1.4 - - - +
237E LYS* 3.8 36.7 + - + +
238E SER 4.7 3.4 - - - +
239E TYR* 3.7 36.6 - - + -
249E ILE* 3.5 36.8 - - + -
253E ARG* 2.7 36.1 + - + +
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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