Contacts of the helix formed by residues 212 - 219 (chain B) in PDB entry 2AG1
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 GLY 212 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU* 1.3 74.5 - - - +
213B SER* 1.3 66.4 + - - -
214B GLU 3.1 3.9 + - - -
215B ALA* 3.1 15.8 + - - +
216B SER 3.8 2.1 + - - -
238B ASP* 3.6 19.7 - - - -
241B GLY* 4.1 6.2 - - - -
276B LEU 3.1 10.9 + - - -
277B GLY 3.6 17.3 - - - -
278B ALA* 3.8 2.6 - - - +
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Residues in contact with SER 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASP 4.0 11.2 - - - -
92B ARG* 3.5 30.5 + - - +
212B GLY* 1.3 71.6 - - - -
214B GLU* 1.3 63.4 + - - +
216B SER* 2.9 21.4 + - - -
217B ARG* 3.0 18.1 + - - +
238B ASP* 4.1 5.6 + - - -
240B GLU* 3.6 31.4 - - - -
277B GLY 3.9 5.9 + - - -
279B ARG* 5.3 4.0 + - - -
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Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ARG* 3.9 30.3 - - - +
152B ALA* 3.5 13.2 - - - +
153B PRO* 3.5 12.2 - - - +
154B ARG* 2.8 58.6 + - - +
212B GLY 3.1 1.4 + - - -
213B SER* 1.3 79.8 + - - +
215B ALA* 1.3 64.4 + - - +
216B SER 3.1 0.2 - - - -
217B ARG* 3.8 5.9 - - - +
218B THR* 2.9 29.7 + - + +
277B GLY* 4.6 3.7 + - - -
303B PRO* 4.1 7.1 - - + +
321B ASP* 4.2 1.2 - - - +
322B VAL* 3.8 25.9 + - + +
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Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 4.2 23.1 - - + -
212B GLY 3.1 12.5 + - - +
214B GLU* 1.3 77.5 - - - +
216B SER* 1.3 57.7 - - - +
218B THR* 3.2 5.8 + - - -
219B ALA* 3.0 26.2 + - - -
220B ARG 4.3 0.2 + - - -
244B MSE 3.9 17.9 - - + +
276B LEU 4.4 1.5 + - - +
322B VAL* 3.7 23.0 - - + +
326B ILE* 4.2 14.3 - - + +
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Residues in contact with SER 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ARG 4.7 7.4 + - - -
65B ALA* 4.0 8.1 - - - +
212B GLY 3.8 1.3 + - - -
213B SER 2.9 12.4 + - - -
215B ALA* 1.3 77.9 - - - +
217B ARG* 1.3 75.4 + - - +
218B THR 3.2 1.0 + - - -
219B ALA* 3.3 14.7 + - - +
240B GLU* 3.4 27.1 + - - -
241B GLY* 4.6 0.6 - - - -
243B SER* 4.4 9.2 + - - -
244B MSE 3.8 17.4 - - - +
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Residues in contact with ARG 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ALA 5.3 4.9 - - - -
62B ARG* 3.8 17.9 + - - +
65B ALA* 3.9 24.4 - - - +
91B ASP* 2.9 26.7 + - - +
92B ARG 2.9 16.5 + - - +
93B THR* 3.5 15.9 - - - +
94B PRO* 3.7 26.3 - - + +
154B ARG* 3.7 33.7 + - + +
213B SER* 3.0 19.3 + - - +
214B GLU* 3.5 11.2 + - - +
215B ALA 3.5 0.2 - - - -
216B SER* 1.3 86.7 + - - +
218B THR* 1.3 60.2 + - - +
240B GLU* 3.0 41.8 + - - +
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Residues in contact with THR 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ARG* 3.5 35.2 - - - +
184B ALA 6.1 0.9 - - - +
214B GLU* 2.9 19.0 + - + +
215B ALA* 3.2 8.7 + - - -
217B ARG* 1.3 75.5 - - - +
219B ALA* 1.3 70.3 + - - +
220B ARG* 2.9 22.2 + - - +
321B ASP* 3.9 18.8 - - - +
322B VAL 5.4 0.2 - - - +
323B GLY* 3.3 24.3 + - - +
326B ILE* 5.4 0.5 - - - +
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Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ALA* 4.5 14.4 - - + -
215B ALA 3.0 14.6 + - - -
216B SER 3.3 10.4 + - - +
218B THR* 1.3 78.2 - - - +
220B ARG* 1.3 51.0 + - - +
221B LYS* 2.7 40.3 + - - +
244B MSE 3.8 12.3 - - - -
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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