Contacts of the helix formed by residues 212 - 219 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210C VAL 4.1 0.8 + - - -
211C LEU* 1.3 74.2 - - - +
213C SER* 1.3 66.0 + - - +
214C GLU 3.3 2.5 - - - -
215C ALA* 3.1 20.6 + - - +
216C SER 3.7 2.1 + - - -
238C ASP* 3.3 20.9 - - - -
241C GLY* 4.1 5.8 - - - -
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Residues in contact with SER 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C ASP 3.7 21.3 + - - -
92C ARG* 3.7 22.5 + - - +
212C GLY* 1.3 70.9 - - - -
214C GLU* 1.3 59.5 + - - +
216C SER* 2.9 22.5 + - - -
217C ARG* 3.0 19.5 + - - +
238C ASP* 4.1 5.4 + - - -
240C GLU* 3.6 32.1 - - - -
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Residues in contact with GLU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ARG* 3.9 35.7 - - - +
152C ALA* 3.4 14.1 - - - +
153C PRO* 3.4 13.0 - - + +
154C ARG* 2.8 59.6 + - - +
212C GLY 3.1 1.0 + - - -
213C SER* 1.3 76.8 + - - +
215C ALA* 1.3 61.6 + - - +
217C ARG* 3.5 4.4 + - - +
218C THR* 3.0 29.4 + - + +
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Residues in contact with ALA 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C LEU* 4.1 35.4 - - + -
212C GLY 3.1 14.2 + - - +
214C GLU* 1.3 76.4 - - - +
216C SER* 1.3 59.1 + - - +
218C THR* 3.3 7.2 + - - -
219C ALA* 2.9 27.4 + - - -
220C ARG 4.4 0.2 + - - -
224C LEU* 6.4 0.2 - - + -
241C GLY* 5.7 0.2 - - - -
244C MSE 3.9 16.5 - - + +
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Residues in contact with SER 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C ARG 4.7 8.0 + - - -
65C ALA* 4.0 8.1 - - - +
212C GLY 3.7 1.0 + - - -
213C SER* 2.9 13.2 + - - -
215C ALA* 1.3 80.6 - - - +
217C ARG* 1.3 73.5 + - - -
218C THR 3.3 0.9 + - - -
219C ALA* 3.4 15.6 + - - +
240C GLU* 3.4 27.5 + - - +
241C GLY* 4.6 0.6 - - - -
243C SER* 4.4 10.7 + - - -
244C MSE 3.8 15.5 - - - +
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Residues in contact with ARG 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C ALA 5.3 5.8 - - - -
62C ARG* 3.9 16.8 + - - +
65C ALA* 3.8 24.6 - - - +
91C ASP 2.9 26.7 + - - -
92C ARG 2.8 16.4 + - - +
93C THR* 3.4 18.4 - - - +
94C PRO* 3.7 22.3 - - + +
154C ARG* 3.8 33.6 + - + +
213C SER* 3.0 15.7 + - - +
214C GLU* 3.5 8.0 + - - +
215C ALA 3.4 0.2 - - - -
216C SER* 1.3 87.7 + - - +
218C THR* 1.3 59.8 + - - +
240C GLU* 3.0 41.5 + - - +
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Residues in contact with THR 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ARG* 3.5 35.7 - - - +
214C GLU* 3.0 18.9 + - + +
215C ALA* 3.3 9.7 + - - -
217C ARG* 1.3 74.1 - - - +
219C ALA* 1.3 71.0 + - - +
220C ARG* 2.9 34.4 + - - +
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Residues in contact with ALA 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ALA* 4.5 14.4 - - + -
215C ALA 2.9 14.5 + - - -
216C SER 3.4 10.9 + - - +
218C THR* 1.3 77.7 - - - +
220C ARG* 1.3 51.2 + - - +
221C LYS* 2.7 39.9 + - - +
244C 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