Contacts of the helix formed by residues 202 - 215 (chain A) in PDB entry 1MRA
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 VAL 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A ASP* 1.3 70.4 - - - +
203A PRO* 1.3 78.1 - - + +
205A ALA* 3.1 3.8 + - - +
206A ILE* 3.0 33.6 + - + +
224A THR* 4.3 9.2 + - + +
228A ASP* 4.4 5.8 - - - +
231A GLY* 3.8 31.2 - - - +
234A ARG* 3.8 41.3 - - + +
235A ILE* 3.9 22.6 - - + +
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Residues in contact with PRO 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ASP* 3.2 19.1 - - + +
202A VAL* 1.3 100.4 - - + +
204A ALA* 1.3 60.6 + - - +
206A ILE* 3.1 21.6 + - + +
207A LYS* 3.1 12.1 + - - +
234A ARG* 5.9 0.7 - - - +
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Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 4.4 15.5 - - + -
201A ASP* 2.7 34.8 + - - +
203A PRO* 1.3 73.7 - - - +
205A ALA* 1.3 57.2 + - - +
207A LYS* 3.3 8.0 + - - +
208A ARG* 2.9 36.3 + - + +
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 4.0 17.4 - - + +
201A ASP 2.9 20.0 + - - +
202A VAL 3.1 4.9 + - - +
204A ALA* 1.3 75.8 - - - +
206A ILE* 1.3 58.0 + - - +
208A ARG* 4.8 0.2 - - - -
209A SER* 2.6 36.5 + - - +
223A PRO* 3.9 21.1 - - + +
235A ILE* 3.8 25.6 - - + -
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A VAL* 3.0 31.0 + - + +
203A PRO* 3.1 11.4 + - + +
205A ALA* 1.3 75.1 - - - +
207A LYS* 1.3 64.6 + - - +
209A SER* 4.9 1.8 - - - -
210A GLN* 3.1 44.4 + - - +
234A ARG* 4.3 7.0 - - + +
235A ILE* 4.1 19.1 - - + -
238A LYS* 3.7 35.0 - - + -
239A LEU* 5.5 1.8 - - - -
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Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU* 4.5 18.7 - - + +
203A PRO 3.1 11.3 + - - +
204A ALA* 3.7 10.5 - - - +
206A ILE* 1.3 78.9 - - - +
208A ARG* 1.3 64.6 + - + +
210A GLN* 3.9 5.8 - - - +
211A ALA* 3.3 21.3 + - - +
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Residues in contact with ARG 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLY* 4.1 3.2 - - - -
169A TYR 2.9 30.7 + - - +
170A PRO* 3.3 18.8 + - - +
172A LEU* 3.4 40.4 - - + +
175A ASP* 2.4 42.7 + - - -
196A TYR* 3.3 23.6 - - + +
200A LEU* 4.1 23.5 - - + +
204A ALA* 2.9 20.6 + - + +
205A ALA 4.3 1.6 - - - +
207A LYS* 1.3 82.9 - - + +
209A SER* 1.3 63.1 + - - +
211A ALA* 3.4 2.3 + - - +
212A LEU* 3.1 29.0 + - - +
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Residues in contact with SER 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A TYR* 4.6 5.2 - - - -
205A ALA* 2.6 29.0 + - - +
206A ILE* 4.9 0.2 - - - -
208A ARG* 1.3 73.8 - - - +
210A GLN* 1.3 65.6 + - - +
212A LEU* 3.4 1.6 + - - +
213A GLN* 2.9 24.6 + - - +
220A ILE* 3.0 42.8 - - - +
235A ILE* 4.6 2.9 - - - +
239A LEU* 3.5 25.6 - - - +
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Residues in contact with GLN 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ILE* 3.1 30.3 + - - +
207A LYS* 3.9 5.9 - - - +
209A SER* 1.3 77.8 - - - +
211A ALA* 1.3 63.4 + - - +
213A GLN* 3.0 29.6 - - - +
214A GLN* 3.1 18.2 + - - +
238A LYS* 3.1 35.9 + - - +
239A LEU* 3.9 13.7 - - + -
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU* 3.9 26.9 - - + -
176A LEU* 4.3 13.9 - - + +
207A LYS 3.3 11.4 + - - +
208A ARG 3.7 7.2 - - - +
209A SER 3.3 0.2 - - - -
210A GLN* 1.3 78.1 - - - +
212A LEU* 1.3 63.6 + - - +
214A GLN* 2.9 29.5 + - - +
215A GLU* 3.4 5.9 + - - +
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Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ILE* 3.7 19.5 - - + -
172A LEU* 5.1 1.3 - - + -
175A ASP* 4.8 5.2 - - + -
176A LEU* 3.5 33.2 - - + +
179A VAL* 4.7 18.2 - - + -
194A VAL* 4.2 12.1 - - + -
196A TYR* 3.5 28.7 - - + +
208A ARG 3.1 14.4 + - - +
209A SER 3.8 3.8 - - - +
211A ALA* 1.3 77.1 - - + +
213A GLN* 1.3 55.9 + - - +
215A GLU* 2.7 26.4 + - + +
216A GLY 2.9 9.7 + - - -
217A VAL* 3.7 20.9 + - + +
220A ILE* 4.4 5.8 - - + -
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Residues in contact with GLN 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A SER 2.9 12.3 + - - +
210A GLN* 3.0 29.5 - - - +
212A LEU* 1.3 74.8 - - - +
214A GLN* 1.3 71.6 + - - +
216A GLY* 3.3 12.5 + - - +
217A VAL* 4.9 4.7 - - - +
238A LYS 4.8 1.6 + - - -
239A LEU* 3.0 21.7 - - - +
240A ASN* 2.5 52.1 + - + +
241A VAL* 3.2 25.4 + - + +
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Residues in contact with GLN 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A GLN* 3.1 27.3 + - - +
211A ALA* 2.9 17.5 + - - +
213A GLN* 1.3 96.3 + - - +
215A GLU* 1.3 65.6 + - - +
216A GLY* 3.3 1.2 + - - -
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Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 3.7 26.2 - - + +
179A VAL* 4.1 21.4 - - + +
180A ARG* 2.3 56.6 + - + +
183A ARG* 4.6 12.6 + - - +
211A ALA 4.3 2.4 - - - +
212A LEU* 2.7 14.3 + - - +
214A GLN* 1.3 81.9 - - - +
216A GLY* 1.3 61.2 + - - +
217A VAL* 5.1 0.9 - - + -
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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