Contacts of the helix formed by residues 215 - 226 (chain B) in PDB entry 3AG2
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 PRO 215 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B MET* 4.1 28.9 - - + -
189B PRO* 5.4 2.5 - - + -
214B VAL* 1.3 92.9 - - + +
216B LEU* 1.3 66.2 + - - +
217B LYS* 4.5 3.6 - - + +
218B TYR* 3.0 34.2 + - + +
219B PHE 3.0 17.2 + - - -
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Residues in contact with LEU 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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145B PRO* 3.9 28.3 - - + +
146B MET* 5.0 2.8 + - - +
148B MET* 4.1 22.4 - - + -
214B VAL 3.6 1.2 + - - -
215B PRO* 1.3 71.7 - - - +
217B LYS* 1.3 61.5 + - + +
219B PHE* 3.0 11.8 + - + +
220B GLU* 2.8 56.5 + - + +
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Residues in contact with LYS 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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215B PRO* 3.2 3.5 + - + +
216B LEU* 1.3 79.4 - - + +
218B TYR* 1.3 64.9 + - + +
220B GLU* 3.4 21.0 + - - +
221B LYS* 3.2 39.1 + - + +
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Residues in contact with TYR 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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214B VAL* 3.8 17.3 - - + -
215B PRO* 3.0 34.4 + - + +
217B LYS* 1.3 79.7 - - + +
219B PHE* 1.3 63.4 + - - +
221B LYS* 3.3 8.7 + - + +
222B TRP* 3.0 24.8 + - - +
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Residues in contact with PHE 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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95B LEU* 3.9 23.1 - - + -
110B TYR* 3.6 25.6 - + - -
113B TYR* 6.4 2.0 - + - -
143B VAL* 3.4 30.7 - - + -
144B LEU* 3.9 2.0 - - - -
145B PRO* 3.7 34.3 - - + -
214B VAL* 3.7 10.2 - - + +
215B PRO 3.0 11.5 + - - +
216B LEU* 3.0 21.3 + - + +
218B TYR* 1.3 76.2 - - - +
220B GLU* 1.3 70.8 + - + +
222B TRP* 3.4 11.2 + + - +
223B SER* 2.9 49.3 + - - -
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Residues in contact with GLU 220 (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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216B LEU* 2.8 48.9 + - + +
217B LYS* 3.5 27.1 - - - +
219B PHE* 1.3 79.2 - - + +
221B LYS* 1.3 60.0 + - + +
223B SER* 3.3 6.6 + - - -
224B ALA* 3.0 27.4 + - - +
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Residues in contact with LYS 221 (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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217B LYS* 3.2 25.5 + - - +
218B TYR* 3.9 7.6 - - + +
219B PHE 3.3 0.2 - - - -
220B GLU* 1.3 75.8 - - + +
222B TRP* 1.3 66.1 + - - +
224B ALA* 3.3 7.5 + - - +
225B SER* 2.9 25.5 + - - -
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Residues in contact with TRP 222 (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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110B TYR* 3.5 33.0 - + - -
116B LEU* 4.2 8.3 - - + -
118B PHE* 3.6 31.4 - + - -
141B ARG 4.0 3.6 + - - -
143B VAL* 3.3 45.0 - - + +
212B GLU* 5.8 0.7 - - - -
218B TYR 3.0 17.9 + - - +
219B PHE* 3.6 13.9 - + - +
221B LYS* 1.3 75.9 - - - +
223B SER* 1.3 93.2 + - - +
225B SER* 2.7 25.6 + - - -
226B MET* 3.0 41.0 + - + +
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Residues in contact with SER 223 (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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116B LEU* 3.8 18.9 - - - +
219B PHE* 2.9 38.2 + - - -
220B GLU* 3.5 7.0 - - - -
222B TRP* 1.3 94.3 - - - +
224B ALA* 1.3 64.2 + - - +
226B MET* 3.1 12.1 + - - +
227B LEU* 3.6 14.2 + - - +
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Residues in contact with ALA 224 (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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220B GLU 3.0 13.6 + - - +
221B LYS* 3.6 11.4 - - - +
223B SER* 1.3 76.5 - - - +
225B SER* 1.3 61.8 + - - +
226B MET 3.3 0.9 + - - -
227B LEU* 3.4 27.7 + - + +
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Residues in contact with SER 225 (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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221B LYS 2.9 14.1 + - - -
222B TRP* 2.7 26.0 + - - -
224B ALA* 1.3 75.2 - - - +
226B MET* 1.3 63.6 + - - +
227B LEU* 3.4 4.0 + - - +
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Residues in contact with MET 226 (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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116B LEU* 3.4 32.0 - - + +
117B SER 5.2 2.4 - - - +
118B PHE* 3.5 44.0 - - + -
140B ASN* 4.9 11.9 - - + +
222B TRP* 3.0 49.4 + - + +
223B SER 3.1 4.8 + - - +
225B SER* 1.3 79.0 - - - +
227B LEU* 1.3 66.1 + - - +
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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