Contacts of the helix formed by residues 208 - 220 (chain E) in PDB entry 4P9U
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 208 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80E LEU* 3.4 34.5 - - + +
83E LEU* 3.6 26.9 - - + -
101E LEU* 3.9 17.9 - - + -
104E ALA* 5.7 1.3 - - + -
204E ILE* 3.1 33.3 + - + +
205E PHE* 3.2 8.2 + - + +
207E GLY* 1.3 75.5 - - - +
209E LYS* 1.3 57.9 + - - +
210E LYS 3.3 2.5 - - - -
211E LEU* 3.3 15.2 + - + +
212E TYR* 2.8 30.9 + - + +
200F ILE* 3.8 23.8 - - + -
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Residues in contact with LYS 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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155E GLU* 5.4 12.7 - - - +
183E PHE* 6.3 1.2 - - - -
186E TYR* 3.5 44.2 - - + +
205E PHE 3.1 4.9 + - - -
206E ASN* 3.6 15.5 - - - +
207E GLY 3.3 3.6 + - - -
208E LEU* 1.3 78.4 - - - +
210E LYS* 1.3 60.6 + - + +
212E TYR* 3.4 6.7 - - - +
213E ASP* 2.4 65.2 + - - +
76F GLU 5.4 7.9 - - - +
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Residues in contact with LYS 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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81E HIS* 5.9 4.0 - - + +
84E ASP* 3.3 35.2 - - + +
207E GLY 4.9 4.4 + - - +
208E LEU 3.3 0.4 - - - -
209E LYS* 1.3 77.9 - - + +
211E LEU* 1.3 58.3 + - - +
213E ASP* 3.9 5.4 - - - +
214E ARG* 2.9 27.2 + - - +
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Residues in contact with LEU 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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83E LEU* 3.8 32.5 - - + +
84E ASP* 3.3 19.7 + - + +
87E MET* 3.7 33.4 - - + -
97E ILE* 3.9 14.8 - - + -
98E VAL* 5.2 0.7 - - + -
101E LEU* 3.6 33.2 - - + -
208E LEU* 3.3 14.4 + - + +
210E LYS* 1.3 76.7 - - - +
212E TYR* 1.3 57.9 + - - +
214E ARG* 3.8 3.9 - - + +
215E VAL* 2.9 47.7 + - + +
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Residues in contact with TYR 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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101E LEU* 4.1 27.4 - - + -
105E ARG* 3.0 28.4 + - + -
182E ASN* 3.2 13.6 - - - +
185E ASP* 2.6 29.5 + - - -
186E TYR* 3.5 42.6 - + + -
189E PHE* 3.1 17.3 - - - -
205E PHE* 3.8 27.1 - + - -
208E LEU* 2.8 18.2 + - + +
209E LYS* 3.4 10.5 - - - +
211E LEU* 1.3 78.3 - - - +
213E ASP* 1.3 56.2 + - - +
215E VAL* 3.9 1.6 - - - +
216E GLY* 2.9 23.6 + - - -
220E PHE* 6.1 0.4 - + - -
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Residues in contact with ASP 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E ASN* 2.8 26.8 + - - +
183E PHE* 5.3 1.0 - - - -
186E TYR* 4.2 14.6 - - - +
209E LYS* 2.4 52.0 + - - +
210E LYS* 3.9 5.2 - - - +
212E TYR* 1.3 76.0 - - - +
214E ARG* 1.3 58.3 + - - +
217E SER* 2.7 39.9 + - - +
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Residues in contact with ARG 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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84E ASP* 3.0 35.7 + - - +
87E MET* 3.4 41.4 - - + +
88E THR* 4.3 7.3 - - - +
210E LYS 2.9 17.3 + - - +
211E LEU* 3.8 5.4 - - - +
213E ASP* 1.3 78.7 - - - +
215E VAL* 1.3 63.1 + - + +
217E SER* 3.7 9.7 + - - -
218E TYR* 3.9 5.5 + - - +
274E PHE* 3.2 44.2 + - + +
275E THR* 4.3 0.4 - - - +
276E GLU 2.8 33.9 + - - +
277E ASP* 4.8 3.6 - - - +
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Residues in contact with VAL 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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87E MET* 5.5 0.4 - - + -
98E VAL* 3.7 43.7 - - + -
101E LEU* 3.9 17.0 - - + -
102E LEU* 4.9 9.9 - - + -
211E LEU* 2.9 29.5 + - + +
212E TYR 3.9 2.9 - - - +
214E ARG* 1.3 78.6 - - + +
216E GLY* 1.3 60.6 + - - +
218E TYR* 3.3 5.4 + - - +
219E TYR* 2.9 33.4 + - + +
263E TRP* 4.7 8.9 - - + -
274E PHE* 4.6 10.5 - - + -
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Residues in contact with GLY 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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182E ASN* 3.2 24.6 - - - +
212E TYR* 2.9 12.3 + - - -
213E ASP 3.4 0.2 + - - -
215E VAL* 1.3 74.3 - - - +
217E SER* 1.3 56.0 + - - +
218E TYR 3.1 5.4 - - - -
219E TYR* 4.3 5.2 - - - -
220E PHE* 2.9 46.5 + - - +
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Residues in contact with SER 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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175E ILE* 4.9 7.3 - - - +
178E ALA* 3.1 30.8 - - - +
179E LYS* 3.8 29.3 - - - +
182E ASN* 4.0 9.2 + - - +
213E ASP* 2.7 26.0 + - - +
214E ARG* 4.1 6.5 - - - -
215E VAL 3.3 0.6 - - - -
216E GLY* 1.3 74.1 - - - +
218E TYR* 1.3 57.4 + - - +
221E SER* 4.3 2.1 - - - -
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Residues in contact with TYR 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 ARG 3.9 2.5 + - - +
215E VAL 3.3 4.4 + - - +
216E GLY 3.1 0.2 - - - -
217E SER* 1.3 80.4 - - - +
219E TYR* 1.3 64.9 + - - +
220E PHE 3.1 1.6 - - - -
221E SER* 2.5 34.7 + - - -
263E TRP* 3.9 16.6 - + - -
266E MET* 2.7 60.1 + - + +
269E THR* 2.7 22.4 + - - -
270E LEU* 3.7 16.6 - - + -
271E PRO* 3.5 29.4 - - + -
274E PHE* 4.1 20.4 - + + -
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Residues in contact with TYR 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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105E ARG* 6.3 0.7 - - - -
215E VAL* 2.9 27.8 + - + +
216E GLY* 4.2 2.5 - - - +
218E TYR* 1.3 80.0 - - - +
220E PHE* 1.3 93.4 + + - +
221E SER 3.2 2.5 + - - -
222E ASN* 3.7 5.2 + - - +
225E ALA* 3.4 32.8 + - + +
228E LEU* 5.6 0.7 - - - +
255E TYR* 4.3 10.1 + - - -
259E SER* 3.2 41.0 - - - -
262E ILE* 3.5 25.7 - - + +
263E TRP* 4.4 20.4 - + + -
266E MET* 3.7 21.2 - - - +
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Residues in contact with PHE 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E ARG* 6.1 0.7 - - - -
178E ALA* 3.2 24.5 - - - +
181E PHE* 3.5 34.1 - + + -
182E ASN* 3.5 22.0 - - + -
185E ASP* 3.6 42.0 - - + -
212E TYR* 6.1 0.4 - + - -
216E GLY* 2.9 29.6 + - - +
219E TYR* 1.3 107.2 - + - +
221E SER* 1.3 55.5 + - - +
222E ASN 3.1 5.8 - - - +
225E ALA 4.4 1.6 - - - -
226E ARG* 2.8 35.4 + - + -
229E ALA* 4.0 11.7 - - + -
255E TYR* 4.7 2.5 - - - -
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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