Contacts of the helix formed by residues 201 - 211 (chain A) in PDB entry 1NUS
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 SER 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ARG* 5.8 2.9 - - - +
199A GLU 3.7 2.6 + - - -
200A ILE* 1.3 74.0 - - - +
202A ALA* 1.3 66.4 + - - +
203A THR* 3.7 5.6 + - - -
204A TYR* 3.0 37.9 + - - +
205A ILE* 3.0 16.3 + - - +
501A APC 4.1 14.4 - - - -
140B LYS* 5.9 1.6 - - - -
169B SER* 3.6 24.6 + - - -
170B HIS 4.7 0.5 - - - -
171B ASP* 3.7 13.3 + - - +
175B TYR* 5.6 1.3 - - - -
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Residues in contact with ALA 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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16A ASN 4.0 11.4 - - - +
17A PRO* 4.1 16.2 - - + +
19A THR* 4.3 8.7 - - + +
22A HIS* 4.5 2.9 - - + -
200A ILE 4.1 1.0 + - - -
201A SER* 1.3 73.5 - - - +
203A THR* 1.3 56.7 + - - +
205A ILE* 3.1 12.7 + - - +
206A ARG* 2.8 47.7 + - - +
501A APC 3.3 27.7 + - - +
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Residues in contact with THR 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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56A LYS* 4.7 2.3 + - - -
201A SER* 3.0 7.6 - - - -
202A ALA* 1.3 78.7 - - - +
204A TYR* 1.3 64.0 + - - +
206A ARG* 3.2 20.8 + - - +
207A ARG* 3.1 21.1 + - - +
501A APC 2.5 26.3 + - - -
140B LYS* 5.2 0.2 - - - -
143B GLN* 5.4 0.3 + - - -
171B ASP* 3.7 14.8 - - + +
174B GLY* 3.7 34.1 - - - +
175B TYR* 3.6 22.4 - - + -
178B GLU* 4.3 7.6 - - - +
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Residues in contact with TYR 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* 5.8 3.1 - - + -
201A SER* 3.0 24.0 + - - +
203A THR* 1.3 79.0 - - - +
205A ILE* 1.3 69.9 + - + +
207A ARG* 3.3 31.1 + - - -
208A ALA* 2.8 48.3 + - + +
213A GLN* 4.4 9.9 + - - +
214A SER 5.4 3.1 + - - -
215A VAL* 5.5 0.2 - - + -
218A LEU* 4.1 21.1 - - + -
171B ASP* 3.6 17.5 + - + +
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Residues in contact with ILE 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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17A PRO* 4.0 20.6 - - + -
19A THR* 4.2 5.8 - - + -
200A ILE* 5.0 7.0 - - + -
201A SER 3.0 15.3 + - - +
202A ALA* 3.1 14.8 + - - +
204A TYR* 1.3 80.8 - - + +
206A ARG* 1.3 57.4 + - - +
208A ALA* 3.3 1.9 + - - +
209A LEU* 2.9 50.6 + - + +
215A VAL* 3.8 14.8 - - + +
218A LEU* 3.8 41.1 - - + -
219A ILE* 4.1 20.6 - - + -
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Residues in contact with ARG 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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16A ASN* 2.8 53.9 + - - +
17A PRO* 4.2 4.5 - - + -
56A LYS* 3.6 17.6 - - - +
57A ASP 4.9 4.2 + - - -
202A ALA* 2.8 24.3 + - - +
203A THR* 3.4 26.0 + - - +
205A ILE* 1.3 73.6 - - - +
207A ARG* 1.3 57.5 + - - +
209A LEU* 3.3 10.1 + - - +
210A GLY* 2.8 26.2 + - - -
233A TYR* 3.4 36.8 - - + +
501A APC 3.5 14.8 + - - -
178B GLU* 2.7 46.3 + - - +
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Residues in contact with ARG 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 THR 3.1 16.3 + - - +
204A TYR* 3.6 24.6 - - - +
206A ARG* 1.3 72.3 - - - +
208A ALA* 1.3 68.7 + - - +
210A GLY* 3.1 3.3 + - - +
211A GLN* 2.9 57.7 + - + +
213A GLN* 5.5 2.2 + - - -
171B ASP* 2.8 39.6 + - - +
173B LYS* 3.5 50.9 - - - +
174B GLY* 3.8 11.7 - - - +
177B ALA* 5.6 5.6 - - + -
178B GLU* 5.4 0.4 + - - -
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Residues in contact with ALA 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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204A TYR* 2.8 43.4 + - + +
205A ILE 3.6 3.4 - - - +
207A ARG* 1.3 72.9 - - - +
209A LEU* 1.3 64.7 + - - +
211A GLN* 3.0 7.9 + - - -
213A GLN* 2.9 47.8 + - + +
214A SER 4.6 2.2 - - - +
215A VAL* 3.8 17.5 - - + -
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Residues in contact with LEU 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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205A ILE* 2.9 35.9 + - + +
206A ARG* 3.6 4.3 - - - +
208A ALA* 1.3 76.5 - - - +
210A GLY* 1.3 63.2 + - - +
212A GLY* 3.0 14.8 + - - -
213A GLN 4.3 9.6 - - - +
215A VAL* 3.7 26.7 - - + -
224A ILE* 5.8 5.6 - - + -
227A ILE* 3.8 40.4 - - + -
232A LEU 5.2 0.7 - - - +
233A TYR* 3.9 29.0 - - + +
234A THR* 5.6 0.7 - - - -
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Residues in contact with GLY 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 ARG 2.8 14.4 + - - -
207A ARG* 3.1 5.3 + - - -
209A LEU* 1.3 77.1 - - - +
211A GLN* 1.3 60.1 + - - +
212A GLY 3.3 0.8 + - - -
233A TYR 3.4 15.6 + - - -
234A THR* 4.7 12.4 - - - +
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Residues in contact with GLN 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 ARG* 2.9 57.7 + - + +
208A ALA 3.0 4.9 + - - +
210A GLY* 1.3 78.0 - - - +
212A GLY* 1.3 62.0 + - - +
213A GLN* 3.4 29.1 + - + +
173B LYS* 5.6 0.4 - - - +
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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