Contacts of the helix formed by residues 201 - 209 (chain C) in PDB entry 1P5Q
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 PRO 201 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199C ASP 4.1 2.0 - - - +
200C LEU* 1.3 88.3 - - + +
202C TYR* 1.3 62.7 + - - +
203C GLY 3.0 3.6 + - - +
204C LEU* 3.2 15.4 + - + +
205C GLU* 3.4 7.8 + - - +
221C LEU* 4.3 4.0 - - + -
225C TYR 3.7 2.7 - - - +
226C ALA* 3.5 39.3 - - + +
227C PHE* 3.8 22.1 - - + -
243C LEU* 5.1 0.4 - - + -
245C TYR* 2.9 42.8 - - + +
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Residues in contact with TYR 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C GLU* 6.2 5.4 - - + +
200C LEU 3.5 1.2 + - - +
201C PRO* 1.3 69.2 - - - +
203C GLY* 1.3 61.3 + - - +
204C LEU 3.2 0.2 - - - -
205C GLU* 3.5 21.5 - - + +
206C ARG* 2.8 55.5 + - + +
224C SER 3.3 27.8 + - - -
225C TYR* 3.7 33.6 + + - -
226C ALA 4.5 5.2 - - - -
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Residues in contact with GLY 203 (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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150C ILE* 3.9 15.5 - - - +
201C PRO 3.0 0.2 - - - -
202C TYR* 1.3 77.1 - - - +
204C LEU* 1.3 54.0 + - - +
206C ARG* 2.9 5.4 + - - +
207C ALA* 2.7 34.5 + - - +
221C LEU* 3.5 17.3 - - - -
225C TYR* 2.8 27.8 + - - -
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Residues in contact with LEU 204 (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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174C LEU* 4.1 19.7 - - + -
200C LEU* 4.1 16.2 - - + -
201C PRO* 3.2 17.0 + - + +
203C GLY* 1.3 77.4 - - - +
205C GLU* 1.3 61.6 + - - +
207C ALA* 3.7 4.0 - - - +
208C ILE* 3.0 41.2 + - + +
219C VAL* 4.4 9.4 - - + -
221C LEU* 3.8 10.3 - - + +
245C TYR* 3.6 55.0 - - + -
247C LEU* 3.5 25.4 - - + -
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Residues in contact with GLU 205 (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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190C PHE* 3.5 21.2 - - + -
192C ILE* 3.5 12.7 - - + +
193C GLY* 2.6 37.3 + - - -
195C GLY* 3.2 31.2 + - - -
196C GLU* 3.9 6.2 + - - +
200C LEU* 4.9 3.6 - - + -
201C PRO 3.4 7.5 + - - +
202C TYR* 3.3 21.9 + - + +
203C GLY 3.1 1.0 - - - -
204C LEU* 1.3 76.8 - - - +
206C ARG* 1.3 77.8 + - - +
208C ILE* 3.1 18.8 + - + +
209C GLN* 3.1 16.6 + - - +
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Residues in contact with ARG 206 (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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145C GLU* 4.9 7.0 - - - +
150C ILE* 3.8 20.9 - - + -
166C GLU* 3.9 26.9 + - - -
192C ILE* 5.3 0.2 - - - +
202C TYR* 2.8 45.0 + - + +
203C GLY 3.3 7.6 - - - +
205C GLU* 1.3 85.1 + - - +
207C ALA* 1.3 63.1 + - - +
209C GLN* 3.2 43.8 + - - +
210C ARG* 3.9 9.7 - - - +
225C TYR* 5.7 1.1 - - + -
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Residues in contact with ALA 207 (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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150C ILE* 3.7 15.6 - - + +
152C ARG* 4.8 7.7 - - - +
203C GLY 2.7 17.9 + - - +
204C LEU 3.7 5.6 - - - +
206C ARG* 1.3 72.5 - - - +
208C ILE* 1.3 53.2 + - + +
210C ARG* 2.8 39.6 + - - +
211C MSE 3.8 9.4 + - + +
219C VAL* 3.4 34.3 - - + -
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Residues in contact with ILE 208 (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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164C PRO* 3.8 10.1 - - + +
170C VAL* 4.2 19.1 - - + -
172C VAL* 4.5 15.3 - - + -
174C LEU* 5.8 0.7 - - + -
190C PHE* 3.9 26.9 - - + -
192C ILE* 3.9 18.6 - - + -
200C LEU* 5.5 0.2 - - + -
204C LEU* 3.0 39.4 + - + +
205C GLU* 3.1 5.6 + - + +
207C ALA* 1.3 76.1 - - - +
209C GLN* 1.3 56.3 + - - +
210C ARG 2.9 5.9 + - - -
211C MSE 3.2 21.0 + - - +
247C LEU* 3.3 31.2 - - + -
249C LEU* 4.7 7.2 - - + -
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Residues in contact with GLN 209 (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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163C LYS* 3.8 10.2 - - - +
164C PRO* 3.2 43.7 - - + +
165C ASN* 4.1 4.1 - - - +
166C GLU* 3.6 28.4 + - - +
192C ILE* 3.6 23.2 - - + +
205C GLU 3.1 10.2 + - - +
206C ARG* 3.3 38.2 + - - +
207C ALA 3.0 1.0 + - - -
208C ILE* 1.3 74.3 - - - +
210C ARG* 1.3 61.2 + - + +
211C MSE 3.7 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