Contacts of the helix formed by residues 211 - 219 (chain A) in PDB entry 2ILU
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 THR 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ASP* 5.3 0.3 + - - -
41A GLY 3.3 17.7 + - - -
42A GLN* 3.8 23.1 - - - +
43A ALA* 4.3 9.8 + - - +
208A ARG* 3.0 50.9 + - - +
210A GLU* 1.3 81.3 - - + +
212A VAL* 1.3 69.1 + - - +
213A GLY 3.3 0.7 - - - -
214A GLN* 3.6 1.6 + - - +
215A GLU* 3.4 21.1 + - - +
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Residues in contact with VAL 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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41A GLY* 3.3 33.0 - - - +
42A GLN* 3.9 7.2 - - - +
45A ASP* 5.4 2.5 - - + -
46A ALA* 4.3 9.2 - - + +
176A LYS* 3.6 22.9 - - + -
205A VAL* 3.4 35.9 - - + +
206A LEU 3.6 15.3 - - - +
207A GLY* 3.8 6.3 - - - -
208A ARG 2.9 2.3 + - - +
211A THR* 1.3 79.0 + - - +
213A GLY* 1.3 64.0 + - - +
215A GLU* 3.6 6.2 + - - +
216A LEU* 3.1 22.7 + - + +
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Residues in contact with GLY 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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149A ILE* 3.7 14.3 - - - +
176A LYS* 3.7 8.8 - - - +
208A ARG 3.3 4.8 + - - -
209A GLY* 3.0 18.2 + - - -
212A VAL* 1.3 75.4 - - - +
214A GLN* 1.3 63.5 + - - +
216A LEU* 3.0 15.5 + - - +
217A ALA* 3.1 10.6 + - - +
482A NDP 3.7 16.4 - - - -
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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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209A GLY 2.9 8.1 + - - +
210A GLU* 3.4 26.9 - - - +
211A THR 3.6 2.6 + - - +
212A VAL 3.5 0.2 - - - -
213A GLY* 1.3 75.2 - - - +
215A GLU* 1.3 57.2 + - - +
217A ALA* 3.3 3.6 + - - +
218A GLY* 2.8 27.9 + - - -
236A LYS* 3.7 21.3 + - - +
237A ILE* 4.3 2.2 - - - +
240A THR* 2.5 32.1 + - - +
482A NDP 2.7 39.4 + - - +
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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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43A ALA* 3.4 26.9 - - + +
46A ALA* 3.4 28.7 - - + -
47A ARG* 3.2 26.5 + - + +
50A ILE* 4.2 1.2 - - + +
211A THR 3.4 14.2 + - - +
212A VAL 3.8 0.9 - - - +
213A GLY 3.1 0.8 - - - -
214A GLN* 1.3 76.2 - - - +
216A LEU* 1.3 62.8 + - - +
217A ALA 3.0 6.0 + - - -
218A GLY* 5.1 0.8 - - - -
219A ASN* 2.8 66.1 + - - +
220A PRO* 5.6 0.2 - - - +
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Residues in contact with LEU 216 (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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46A ALA* 4.2 15.5 - - + -
50A ILE* 4.6 7.6 - - + -
147A THR* 2.8 46.1 + - + +
148A GLY 3.8 7.9 - - - +
149A ILE* 4.1 11.0 - - + -
174A VAL* 3.6 41.1 - - + +
176A LYS* 3.4 33.9 - - + +
205A VAL* 4.4 3.8 - - + -
212A VAL* 3.1 18.6 + - + +
213A GLY 3.0 9.5 + - - +
215A GLU* 1.3 75.4 - - - +
217A ALA* 1.3 58.1 + - - +
222A VAL* 3.8 8.1 - - - +
225A VAL* 3.8 2.6 - - - +
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Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A GLY 3.1 12.3 + - - +
214A GLN* 3.8 4.7 - - - +
215A GLU 3.0 0.4 - - - -
216A LEU* 1.3 80.4 - - - +
218A GLY* 1.3 60.9 - - - +
219A ASN 3.5 1.9 + - - +
222A VAL* 5.4 0.6 - - - +
225A VAL* 4.1 12.8 - - + -
237A ILE* 3.9 39.9 - - + +
240A THR* 4.0 7.6 - - + -
241A ALA* 3.6 19.2 - - - +
244A ASN* 5.0 0.2 + - - -
246A THR* 4.4 12.5 + - - +
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Residues in contact with GLY 218 (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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214A GLN 2.8 17.2 + - - -
215A GLU* 4.1 2.9 - - - -
217A ALA* 1.3 73.2 - - - +
219A ASN* 1.3 60.0 + - - +
220A PRO* 3.4 4.3 - - - +
240A THR* 3.3 23.1 - - - +
243A LYS* 5.7 2.0 - - - +
244A ASN* 2.8 24.9 + - - -
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Residues in contact with ASN 219 (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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47A ARG* 3.5 16.2 - - - +
50A ILE* 3.4 28.9 - - + +
51A ASP* 5.6 1.2 + - - -
215A GLU* 2.8 41.7 + - - +
216A LEU 4.8 0.4 - - - -
217A ALA 3.5 1.5 - - - +
218A GLY* 1.3 76.6 - - - +
220A PRO* 1.3 75.3 - - - +
221A LYS* 2.9 42.3 + - - +
222A VAL* 3.0 23.8 + - + +
244A ASN* 4.0 2.1 + - - -
246A THR* 4.5 2.9 + - - -
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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