Contacts of the helix formed by residues 202 - 211 (chain C) in PDB entry 2R7D
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 TYR 202 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ILE* 3.5 36.4 + - + +
93C ASP* 3.0 23.3 + - - -
94C ASP* 3.1 40.4 - - - -
95C GLU* 5.2 1.2 - - - +
201C ALA* 1.3 71.7 - - - +
203C GLN* 1.3 58.5 + - + +
205C ALA* 3.2 3.5 + - - +
206C GLN* 2.8 29.1 + - - +
258C PRO* 6.0 0.9 - - + -
260C PRO* 4.0 18.3 - - + +
262C MSE 3.9 5.5 - - - +
263C ARG* 3.4 56.3 + - + +
266C VAL* 3.7 25.7 - - + +
267C GLN 5.5 0.3 + - - -
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Residues in contact with GLN 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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210B GLU 3.8 3.2 - - - +
95C GLU* 3.5 27.2 + - + +
201C ALA* 3.2 1.2 - - - +
202C TYR* 1.3 77.8 - - + +
204C GLU* 1.3 61.0 + - + +
206C GLN* 3.4 6.8 + - - +
207C ALA* 3.0 26.0 + - - +
258C PRO* 3.4 34.9 - - + +
260C PRO* 3.3 29.2 - - + +
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Residues in contact with GLU 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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209B LEU* 4.3 3.8 - - - +
210B GLU 3.2 20.0 - - - +
211B ALA 3.8 11.6 - - - +
212B GLY* 3.4 21.6 - - - +
217B VAL* 4.1 11.6 - - - +
95C GLU* 6.3 0.7 - - - -
199C ARG 4.7 0.3 - - - +
200C LEU* 3.5 16.3 - - + +
201C ALA* 2.8 41.6 + - + +
203C GLN* 1.3 76.5 - - + +
205C ALA* 1.3 66.1 + - - +
207C ALA* 3.3 3.6 + - - +
208C ARG* 3.2 26.7 + - - +
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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
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92C ILE* 3.6 30.3 - - + -
200C LEU* 4.3 6.4 - - + +
201C ALA 3.0 5.5 + - - +
202C TYR 3.5 7.6 - - - +
204C GLU* 1.3 74.0 - - - +
206C GLN* 1.3 61.2 + - - +
208C ARG* 3.1 4.7 + - - +
209C LEU* 2.9 27.9 + - - +
216C PHE* 4.0 27.4 - - + -
262C MSE 3.6 13.3 - - + +
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Residues in contact with GLN 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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202C TYR 2.8 16.8 + - - +
203C GLN* 3.5 10.5 - - - +
205C ALA* 1.3 77.6 - - - +
207C ALA* 1.3 62.4 + - - +
209C LEU* 3.2 16.2 + - - +
210C GLU* 2.9 65.3 + - - +
260C PRO* 3.6 18.6 - - + -
261C GLU* 3.2 18.4 + - - +
262C MSE 2.9 38.1 + - + +
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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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207A ALA* 5.3 1.4 - - - +
207B ALA 5.3 1.3 - - - +
210B GLU* 3.5 32.5 - - + +
211B ALA* 3.7 13.4 - - + +
203C GLN 3.0 9.5 + - - +
204C GLU 3.5 4.7 - - - +
205C ALA 3.3 0.2 - - - -
206C GLN* 1.3 77.0 - - - +
208C ARG* 1.3 60.2 + - - +
210C GLU* 3.4 14.3 + - - +
211C ALA* 3.3 19.6 + - - +
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Residues in contact with ARG 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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211B ALA* 2.8 33.5 + - + +
212B GLY 3.5 18.2 + - - -
213B GLU* 4.1 14.3 + - - +
90C PHE* 3.8 25.3 - - - -
198C GLN* 4.6 5.9 + - - -
200C LEU* 3.6 20.4 - - - +
204C GLU 3.2 9.1 + - - +
205C ALA 3.1 6.1 + - - +
207C ALA* 1.3 74.1 - - - +
209C LEU* 1.3 67.1 + - - +
211C ALA* 3.0 10.7 + - - +
213C GLU* 3.1 50.0 + - - +
216C PHE* 3.5 34.7 - - + -
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Residues in contact with LEU 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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204A GLU* 4.4 4.4 - - - +
205C ALA 2.9 13.6 + - - +
206C GLN* 3.5 27.1 - - - +
208C ARG* 1.3 75.8 - - - +
210C GLU* 1.3 63.9 + - + +
212C GLY* 3.0 18.6 + - - +
213C GLU 4.8 1.1 - - - -
216C PHE* 3.6 31.4 - - + +
217C VAL* 3.8 18.0 - - + +
220C ALA* 4.1 11.4 - - + -
224C ARG* 4.8 5.2 - - - +
261C GLU* 4.0 17.5 - - - +
262C MSE 3.9 22.0 - - + -
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Residues in contact with GLU 210 (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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203A GLN* 3.8 3.1 - - - +
204A GLU* 3.3 25.6 - - - +
207A ALA* 3.5 13.1 - - + +
206C GLN* 2.9 51.4 + - - +
207C ALA* 3.7 11.2 - - - +
208C ARG 3.2 0.4 - - - -
209C LEU* 1.3 80.5 - - + +
211C ALA* 1.3 55.8 + - - +
212C GLY 3.2 1.3 + - - -
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Residues in contact with ALA 211 (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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204A GLU* 3.9 10.6 - - - +
207A ALA* 3.7 18.8 - - + -
208A ARG* 2.9 43.8 + - + +
213A GLU* 5.7 1.8 - - - +
207C ALA 3.3 12.0 + - - +
208C ARG 3.0 10.3 + - - +
210C GLU* 1.3 77.5 - - - +
212C GLY* 1.3 58.7 + - - +
213C GLU* 3.4 19.1 - - + +
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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