Contacts of the helix formed by residues 215 - 227 (chain O) in PDB entry 2EIN
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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146O MET* 3.9 20.6 - - + -
214O VAL* 1.4 89.8 - - + +
216O LEU* 1.3 68.3 + - - +
217O LYS* 3.1 5.1 + - + +
218O TYR* 3.1 15.5 + - + -
219O PHE* 3.1 16.9 + - - +
57V MET* 3.4 33.4 - - + -
60V PHE* 3.5 34.5 - - + -
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Residues in contact with LEU 216 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145O PRO* 4.2 16.7 - - + +
146O MET 5.0 2.4 + - - +
148O MET* 4.7 24.2 - - + -
214O VAL 3.9 0.8 + - - -
215O PRO* 1.3 70.9 - - - +
217O LYS* 1.3 66.4 + - + +
219O PHE* 2.9 22.5 + - + +
220O GLU* 2.9 46.4 + - + +
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Residues in contact with LYS 217 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215O PRO* 4.6 2.9 - - + +
216O LEU* 1.3 78.1 - - + +
218O TYR* 1.3 77.4 + - + +
220O GLU* 2.9 43.5 + - - +
221O LYS* 3.1 33.3 + - - +
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Residues in contact with TYR 218 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214O VAL* 4.0 13.5 - - + -
215O PRO* 3.1 19.0 + - + +
217O LYS* 1.3 90.7 - - + +
219O PHE* 1.3 63.5 + - - +
221O LYS* 3.3 30.2 + - + +
222O TRP* 2.8 26.2 + - - +
57V MET* 5.0 7.5 - - + +
60V PHE* 3.6 21.9 - + - -
61V GLU* 3.7 18.4 + - - -
64V ARG* 3.9 22.9 + - - -
71V SER* 4.6 7.5 - - - +
72V ALA* 3.4 26.5 - - + -
73V LYS 5.7 0.4 - - - -
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Residues in contact with PHE 219 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95O LEU* 3.8 27.4 - - + -
110O TYR* 3.6 21.3 - + - -
143O VAL* 3.3 31.6 - - + -
144O LEU* 3.9 6.5 - - - -
145O PRO* 3.7 19.5 - - + -
214O VAL* 3.7 11.6 - - + +
215O PRO 3.1 10.7 + - - +
216O LEU* 2.9 25.0 + - + +
218O TYR* 1.3 78.3 - - - +
220O GLU* 1.3 54.3 - - + +
222O TRP* 3.3 26.7 + + - +
223O SER* 2.7 45.0 + - - -
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Residues in contact with GLU 220 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216O LEU* 2.9 37.4 + - + +
217O LYS* 2.9 41.5 + - - +
219O PHE* 1.3 77.2 - - + +
221O LYS* 1.3 67.7 + - + +
223O SER* 3.0 11.2 + - - +
224O ALA* 3.0 23.8 + - - +
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Residues in contact with LYS 221 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217O LYS* 3.1 33.0 + - - +
218O TYR* 3.6 35.7 - - + +
220O GLU* 1.3 78.9 - - + +
222O TRP* 1.3 53.4 + - - +
224O ALA* 3.2 6.9 + - - +
225O SER* 2.7 36.2 + - - -
71V SER 5.7 2.5 - - - +
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Residues in contact with TRP 222 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110O TYR* 3.5 34.8 - + - -
116O LEU* 4.0 11.9 - - + -
118O PHE* 4.0 13.7 - + - -
141O ARG 4.7 1.9 + - - -
143O VAL* 3.3 24.9 - - + +
218O TYR 2.8 17.7 + - - +
219O PHE* 3.3 36.6 - + - +
221O LYS* 1.3 74.2 - - - +
223O SER* 1.3 80.6 + - - +
225O SER* 3.1 11.0 + - - -
226O MET* 2.8 68.8 + - + +
70V GLN* 5.5 4.1 + - + -
71V SER* 3.4 38.3 + - - +
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Residues in contact with SER 223 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110O TYR* 6.3 0.2 - - - -
114O GLU* 6.2 5.2 - - - -
116O LEU* 3.8 15.6 - - - +
219O PHE* 2.7 37.9 + - - -
220O GLU* 3.0 14.5 + - - -
222O TRP* 1.3 86.6 - - - +
224O ALA* 1.3 67.4 + - - +
226O MET* 3.1 16.5 + - - +
227O LEU* 3.4 8.2 + - - +
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Residues in contact with ALA 224 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114O GLU* 6.1 1.6 - - - -
220O GLU 3.0 7.7 + - - +
221O LYS* 3.2 12.1 - - - +
223O SER* 1.3 79.9 - - - +
225O SER* 1.3 61.4 + - - +
227O LEU* 2.7 44.4 + - + +
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Residues in contact with SER 225 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221O LYS 2.7 21.0 + - - -
222O TRP* 3.1 17.0 + - - -
224O ALA* 1.3 73.1 - - - +
226O MET* 1.3 60.4 + - - +
227O LEU* 3.2 6.6 + - - +
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Residues in contact with MET 226 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O LEU* 3.6 29.1 - - + +
118O PHE* 4.7 13.9 - - + -
140O ASN* 4.5 18.4 - - - +
222O TRP* 2.8 54.6 + - + +
223O SER 3.1 8.0 + - - +
225O SER* 1.3 74.0 - - - +
227O LEU* 1.3 68.3 + - - +
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Residues in contact with LEU 227 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114O GLU* 3.5 43.7 - - + +
116O LEU* 5.2 8.7 - - + +
223O SER 3.4 7.6 + - - +
224O ALA* 2.7 34.7 + - + +
225O SER 3.2 5.4 - - - +
226O MET* 1.3 82.4 - - - +
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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