Contacts of the helix formed by residues 201 - 211 (chain A) in PDB entry 1IN4
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 GLU 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A ILE* 1.3 76.6 - - - +
202A ASP* 1.3 67.2 + - - +
203A ALA* 4.4 10.1 - - + +
204A ALA* 2.9 18.0 + - + +
205A ALA* 3.1 9.9 + - - +
237A ARG* 3.1 41.4 + - - +
238A ILE 3.0 12.1 + - - +
239A ASN* 4.0 21.8 - - - +
240A THR* 5.1 1.6 + - - +
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Residues in contact with ASP 202 (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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186A LYS* 2.8 31.6 + - - +
190A LYS* 2.9 34.0 + - - +
200A ILE 3.8 2.6 + - - -
201A GLU* 1.3 71.3 - - - +
203A ALA* 1.3 66.3 + - - +
205A ALA* 3.1 3.3 + - - +
206A GLU* 2.9 23.6 + - - +
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Residues in contact with ALA 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 GLU* 3.2 9.1 - - + +
202A ASP* 1.3 82.0 + - - +
204A ALA* 1.3 58.5 + - - +
206A GLU* 3.4 8.1 + - - +
207A MET* 3.1 26.9 + - - +
240A THR* 3.8 21.1 - - + +
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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 ILE* 3.9 3.6 - - + -
201A GLU* 2.9 10.9 + - + +
203A ALA* 1.3 76.8 - - - +
205A ALA* 1.3 66.4 + - - +
207A MET* 3.3 4.5 + - - +
208A ILE* 3.1 27.5 + - - +
238A ILE* 3.6 18.4 - - + +
239A ASN* 3.6 32.3 - - - +
240A THR* 4.1 7.1 - - - +
243A VAL* 3.8 11.2 - - + +
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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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186A LYS* 3.5 18.5 - - + +
189A ILE* 3.6 15.4 - - + +
190A LYS* 3.9 22.4 - - + -
200A ILE* 3.7 20.8 - - + +
201A GLU 3.1 9.0 + - - +
202A ASP 3.1 7.8 + - - +
204A ALA* 1.3 77.1 - - - +
206A GLU* 1.3 62.0 + - - +
208A ILE* 3.4 1.3 + - - -
209A ALA* 3.0 24.6 + - - +
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Residues in contact with GLU 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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182A VAL* 3.8 20.4 - - - +
183A LYS* 5.4 0.5 - - - -
186A LYS* 3.1 33.8 + - - +
202A ASP* 2.9 13.9 + - - +
203A ALA* 3.4 13.2 - - - +
205A ALA* 1.3 76.9 - - - +
207A MET* 1.3 62.1 + - - +
209A ALA* 3.3 3.5 + - - +
210A LYS* 3.0 51.7 + - + +
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Residues in contact with MET 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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203A ALA 3.1 12.1 + - - +
204A ALA* 3.3 10.3 + - - +
206A GLU* 1.3 78.7 - - - +
208A ILE* 1.3 60.6 + - - +
210A LYS* 3.4 6.1 + - - -
211A ARG* 3.0 58.7 + - - +
240A THR* 3.9 27.8 - - + +
243A VAL* 3.6 25.4 - - + -
244A LEU* 3.6 36.3 - - + -
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Residues in contact with ILE 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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189A ILE* 3.5 21.1 - - + -
200A ILE* 4.2 17.9 - - + -
204A ALA 3.1 15.4 + - - +
205A ALA 3.8 2.5 - - - +
206A GLU 3.3 0.2 - - - -
207A MET* 1.3 75.9 - - - +
209A ALA* 1.3 54.6 + - - +
211A ARG* 2.9 16.8 + - - +
212A SER* 2.8 24.6 + - - +
219A ALA 4.1 6.5 - - - +
222A LEU* 3.8 27.5 - - + +
223A THR* 4.2 13.0 - - + +
226A VAL* 3.8 28.7 - - + -
243A VAL* 3.8 22.7 - - + -
247A MET* 4.6 8.5 - - + -
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Residues in contact with ALA 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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182A VAL* 3.5 33.1 - - + +
185A LEU* 3.8 16.1 - - + +
186A LYS* 3.6 15.9 - - + +
189A ILE* 3.4 9.8 - - + +
205A ALA 3.0 17.5 + - - +
206A GLU 3.3 4.9 + - - +
208A ILE* 1.3 76.6 - - - +
210A LYS* 1.3 62.4 + - - +
211A ARG 3.2 0.9 + - - -
212A SER* 3.2 17.3 + - - -
213A ARG 4.7 0.3 + - - -
214A GLY 5.2 0.3 + - - -
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Residues in contact with LYS 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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182A VAL* 4.0 26.1 - - + +
206A GLU* 3.0 45.8 + - + +
207A MET* 3.7 9.6 - - - +
208A ILE 3.2 0.4 - - - -
209A ALA* 1.3 75.8 - - - +
211A ARG* 1.3 67.5 + - - +
212A SER 3.5 0.4 + - - -
213A ARG 4.9 2.1 + - - -
254A ASP 4.4 5.4 - - - +
255A GLU* 4.3 12.3 - - - +
300A TYR* 5.0 5.2 + - - -
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Residues in contact with ARG 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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207A MET* 3.0 45.0 + - - +
208A ILE 2.9 10.5 + - - +
210A LYS* 1.3 87.1 - - - +
212A SER* 1.3 57.6 + - - +
213A ARG 3.4 5.1 + - - -
218A ILE* 4.4 2.4 - - - +
222A LEU* 3.5 12.5 - - + +
244A LEU* 4.3 17.1 - - - +
247A MET* 3.4 44.0 - - + +
252A ILE* 4.2 6.4 - - + +
253A ASP 3.5 20.3 + - - +
254A ASP* 3.7 31.3 + - - +
256A GLY* 3.5 28.3 - - - +
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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