Contacts of the helix formed by residues 202 - 222 (chain C) in PDB entry 4U0Q
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 202 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C ILE* 3.3 25.4 - - + -
198C SER 5.7 0.2 - - - +
199C THR* 3.1 41.3 + - + +
201C GLY* 1.4 73.5 - - - +
203C TYR* 1.4 62.4 + - - +
204C ILE 3.2 0.9 - - - -
205C ALA* 3.2 20.7 + - + +
206C VAL* 3.3 15.9 + - + +
339C LEU* 4.7 8.6 - - + +
342C GLN* 3.6 31.1 + - - +
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Residues in contact with TYR 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C TYR* 4.6 2.9 - - + -
193C ILE* 4.0 7.3 - - + +
194C TYR* 3.4 31.4 - - + +
200C TYR 3.3 24.4 + - - +
201C GLY 3.1 3.8 - - - -
202C LYS* 1.4 76.6 - - - +
204C ILE* 1.4 87.9 - - + +
206C VAL* 3.3 7.2 + - - +
207C ASP* 3.0 53.6 + - - +
363C TYR* 4.9 2.2 - - - -
130D SER 4.4 2.8 + - - -
131D VAL* 3.3 28.3 - - + -
133D PRO* 3.1 46.8 - - + +
164D GLN* 4.4 7.1 + - - +
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Residues in contact with ILE 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C GLY* 3.9 14.4 - - - +
202C LYS 3.2 0.8 - - - -
203C TYR* 1.4 107.8 - - + +
205C ALA* 1.4 56.9 + - - +
207C ASP* 3.4 6.4 + - + +
208C ALA* 3.0 29.9 + - + +
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Residues in contact with ALA 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C GLY 4.9 0.4 + - - -
202C LYS* 3.2 14.5 + - + +
204C ILE* 1.4 73.1 - - - +
206C VAL* 1.3 60.6 + - - +
208C ALA* 3.5 7.9 - - - +
209C PHE* 2.9 30.0 + - - +
335C TYR* 3.5 9.4 + - - +
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Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C SER* 3.8 19.1 - - - -
190C TYR* 3.6 29.2 - - + -
193C ILE* 3.6 28.7 - - + -
202C LYS* 3.3 16.3 + - + +
203C TYR* 3.7 7.9 - - - +
204C ILE 3.3 0.4 - - - -
205C ALA* 1.3 72.8 - - - +
207C ASP* 1.4 54.4 + - - +
209C PHE* 3.2 2.6 + - - +
210C ILE* 2.8 45.9 + - + +
335C TYR* 3.4 25.4 - - + +
339C LEU* 4.3 1.1 - - + -
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Residues in contact with ASP 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C TYR* 2.4 35.9 + - - -
203C TYR* 3.0 41.8 + - - +
204C ILE* 3.5 7.6 - - + +
206C VAL* 1.4 72.6 - - - +
208C ALA* 1.4 57.1 + - - +
210C ILE* 3.5 4.8 + - - +
211C LYS* 3.0 30.4 + - - +
363C TYR* 4.4 2.6 + - - -
164D GLN* 4.3 9.7 + - - +
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Residues in contact with ALA 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C ILE* 3.0 20.0 + - + +
205C ALA* 3.5 10.3 - - - +
206C VAL 3.3 0.2 - - - -
207C ASP* 1.4 73.0 - - - +
209C PHE* 1.3 59.6 + - - +
211C LYS* 3.5 8.0 + - - +
212C LYS* 3.1 33.9 + - + +
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Residues in contact with PHE 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C ALA 2.9 18.8 + - - +
206C VAL 3.2 3.8 + - - +
208C ALA* 1.3 72.6 - - - +
210C ILE* 1.3 60.6 + - - +
212C LYS* 3.2 13.7 + - + +
213C ILE* 2.9 55.6 + - + +
331C ASP* 3.8 11.9 - - + -
332C MET* 3.7 14.1 - - + -
335C TYR* 3.5 59.7 - + + -
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Residues in contact with ILE 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C LYS* 3.8 36.6 - - + +
189C SER* 5.2 1.1 - - - -
190C TYR* 3.6 37.7 - - + +
206C VAL* 2.8 26.9 + - + +
207C ASP* 3.8 5.2 - - - +
209C PHE* 1.3 71.9 - - + +
211C LYS* 1.4 56.1 + - - +
213C ILE* 3.2 2.8 + - + +
214C ASN* 2.9 57.9 + - - +
332C MET* 3.8 26.2 - - + -
335C TYR* 6.0 0.7 - - + -
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Residues in contact with LYS 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C ASP 3.0 18.3 + - - +
208C ALA* 3.6 9.4 - - - +
210C ILE* 1.4 74.6 - - - +
212C LYS* 1.4 57.3 + - + +
214C ASN* 3.2 9.7 + - - +
215C GLU* 2.9 61.2 + - + +
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Residues in contact with LYS 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ALA* 3.1 19.6 + - - +
209C PHE* 3.2 17.5 + - + +
211C LYS* 1.4 76.3 - - + +
213C ILE* 1.3 56.0 + - - +
215C GLU* 3.5 13.0 + - - +
216C ALA* 3.0 28.8 + - - +
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Residues in contact with ILE 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C LEU* 3.9 21.5 - - + -
209C PHE* 2.9 47.7 + - + +
210C ILE* 3.2 5.3 + - + +
212C LYS* 1.3 74.1 - - - +
214C ASN* 1.4 67.0 + - - +
216C ALA* 3.3 6.3 + - + +
217C TYR* 2.9 30.2 + - + +
328C ILE* 3.7 25.0 - - + +
331C ASP* 3.8 8.7 - - + +
332C MET* 3.5 42.2 - - + +
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Residues in contact with ASN 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C LEU* 5.4 8.8 - - - +
186C LYS* 6.0 0.8 - - - +
210C ILE* 2.9 43.2 + - - +
211C LYS* 3.7 7.3 - - - +
213C ILE* 1.4 78.9 - - - +
215C GLU* 1.4 57.6 + - + +
217C TYR* 3.5 6.1 + - - +
218C ASP* 3.0 42.5 + - - +
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Residues in contact with GLU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C LYS* 2.9 51.7 + - + +
212C LYS* 3.8 14.3 - - - +
214C ASN* 1.4 76.0 - - + +
216C ALA* 1.4 50.8 + - - +
218C ASP* 3.4 7.4 + - - +
219C LYS* 2.8 36.5 + - - +
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Residues in contact with ALA 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C LYS 3.0 19.0 + - - +
213C ILE* 3.5 8.7 - - + +
215C GLU* 1.4 72.5 - - - +
217C TYR* 1.3 63.1 + - - +
219C LYS* 3.3 10.0 + - - +
220C VAL* 3.1 26.7 + - - +
328C ILE* 3.7 19.7 - - + +
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Residues in contact with TYR 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C ILE* 3.3 19.9 + - + +
178C HIS* 2.8 44.6 + - + +
182C LEU* 4.1 22.2 - - + -
213C ILE* 2.9 17.5 + - + +
214C ASN* 3.8 6.7 - - - +
216C ALA* 1.3 74.8 - - - +
218C ASP* 1.4 61.8 + - - +
220C VAL* 3.2 4.7 + - - +
221C LYS* 2.9 43.4 + - + +
325C PHE* 3.4 34.0 - + + -
328C ILE* 3.8 27.1 - - + +
329C CYS* 4.2 5.4 - - - -
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Residues in contact with ASP 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C ASN* 3.0 31.0 + - - +
215C GLU* 3.8 6.0 + - - +
217C TYR* 1.4 77.5 - - - +
219C LYS* 1.4 60.2 + - - +
221C LYS* 3.6 30.7 + - + +
222C SER* 3.0 28.9 + - - -
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Residues in contact with LYS 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C GLU 2.8 17.9 + - - +
216C ALA* 3.3 11.0 + - - +
218C ASP* 1.4 74.0 - - - +
220C VAL* 1.4 62.2 + - + +
222C SER* 2.6 23.8 + - - +
223C LYS* 3.8 10.4 - - - +
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Residues in contact with VAL 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ALA 3.1 14.6 + - - +
217C TYR 3.2 7.8 + - - +
219C LYS* 1.4 73.1 - - + +
221C LYS* 1.3 55.5 + - - +
222C SER 3.1 3.8 - - - -
223C LYS* 3.0 33.3 + - + +
224C CYS* 4.4 1.6 + - - -
321C HIS* 3.8 16.4 + - + +
324C ASP* 3.7 33.0 - - + +
325C PHE* 3.6 27.0 - - + -
328C ILE* 3.7 17.0 - - + -
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Residues in contact with LYS 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C ASP* 3.0 33.2 + - - -
173C PHE* 3.1 55.0 + - + +
174C VAL* 4.5 8.9 - - - +
175C ILE* 6.0 0.2 - - + -
217C TYR* 2.9 34.2 + - + +
218C ASP* 3.5 30.3 + - + +
220C VAL* 1.3 74.5 - - - +
222C SER* 1.4 57.5 + - - +
223C LYS 3.3 0.4 + - - -
224C CYS* 3.7 11.5 + - - +
225C ASN* 3.9 6.9 - - - +
228C LYS* 5.8 0.2 - - - +
325C PHE* 3.9 11.0 - - + -
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Residues in contact with SER 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C ASP 3.0 14.4 + - - -
219C LYS* 2.6 29.1 + - - +
221C LYS* 1.4 73.7 - - - +
223C LYS* 1.3 59.2 + - - +
224C CYS 3.1 5.4 - - - -
225C ASN* 3.2 39.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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