Contacts of the helix formed by residues 216 - 230 (chain B) in PDB entry 2YEV
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 216 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B ALA* 4.4 7.2 - - + -
190B PRO* 4.4 20.6 - - + -
215B LEU* 1.3 88.4 - - + +
217B LYS* 1.3 67.5 + - - +
218B GLU* 4.5 6.1 - - + +
219B GLU* 2.8 38.4 + - + +
220B PHE 3.0 10.0 + - - -
334B LEU* 5.5 2.9 - - + -
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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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146B PRO* 4.0 17.1 - - + +
147B ALA* 3.8 17.1 + - - +
149B VAL* 3.9 25.5 - - + +
215B LEU 3.4 2.6 + - - -
216B PRO* 1.3 68.8 - - - +
218B GLU* 1.3 64.2 + - - +
220B PHE* 3.1 2.3 + - - +
221B ASP* 3.0 49.5 + - - +
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Residues in contact with GLU 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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216B PRO* 3.0 6.8 + - + +
217B LYS* 1.3 80.2 - - - +
219B GLU* 1.3 65.9 + - - +
221B ASP* 3.5 8.1 + - - +
222B ARG* 3.0 59.7 + - - +
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Residues in contact with GLU 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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215B LEU* 3.9 24.3 - - + +
216B PRO* 2.8 30.4 + - + +
218B GLU* 1.3 79.9 + - - +
220B PHE* 1.3 65.0 + - - +
222B ARG* 3.3 26.9 + - - +
223B PHE* 3.0 22.0 + - - +
328B GLY 4.9 1.4 - - - +
329B PHE* 3.5 34.1 - - + +
330B ASP 5.0 2.8 + - - -
331B PHE* 4.7 2.6 - - - -
334B LEU* 5.6 2.1 - - - +
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Residues in contact with PHE 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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117B MET* 4.0 23.3 - - + -
132B TYR* 4.3 5.8 - + - -
135B LEU* 4.2 8.7 - - + -
144B VAL* 3.4 36.1 - - + -
145B LEU* 3.7 9.9 - - - +
146B PRO* 3.5 49.6 - - + -
215B LEU* 4.1 11.5 - - + +
216B PRO 3.0 8.0 + - - +
217B LYS 3.1 6.3 + - - +
219B GLU* 1.3 77.2 - - - +
221B ASP* 1.3 78.6 + - - +
223B PHE* 3.0 13.2 + - - +
224B VAL* 3.0 41.4 + - + +
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Residues in contact with ASP 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* 3.0 50.2 + - - +
218B GLU* 3.8 6.7 - - - +
220B PHE* 1.3 93.6 - - - +
222B ARG* 1.3 56.9 + - - +
224B VAL* 3.7 3.8 + - - +
225B GLU* 3.0 44.7 + - - +
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Residues in contact with ARG 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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218B GLU* 3.0 45.6 + - - +
219B GLU* 3.4 32.9 + - - +
221B ASP* 1.3 78.0 - - - +
223B PHE* 1.3 62.0 + - - +
225B GLU* 3.5 12.4 + - - +
226B ALA* 3.1 23.6 + - - +
328B GLY 4.7 12.5 + - - -
329B PHE* 3.9 13.1 - - + -
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Residues in contact with PHE 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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137B LEU* 5.2 5.4 - - + -
139B ASN* 5.3 2.5 - - - -
144B VAL* 4.1 28.0 - - + -
215B LEU* 4.6 3.6 - - + -
219B GLU 3.0 13.3 + - - +
220B PHE* 3.0 11.2 + - - +
222B ARG* 1.3 75.7 - - - +
224B VAL* 1.3 74.8 + - + +
226B ALA* 3.3 4.2 + - - +
227B ALA* 3.0 22.8 + - + +
268B LEU* 4.2 27.8 - - + -
271B ASN* 4.1 14.6 - - + -
326B VAL* 3.6 21.4 - - + +
329B PHE* 3.2 33.4 - + + -
331B PHE* 3.6 33.7 - + - -
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Residues in contact with VAL 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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135B LEU* 3.4 42.6 - - + -
137B LEU* 4.3 16.6 - - + -
220B PHE* 3.0 47.6 + - + +
221B ASP* 4.1 4.7 - - - +
223B PHE* 1.3 77.3 - - + +
225B GLU* 1.3 68.2 + - + +
227B ALA* 3.3 7.9 + - - +
228B LYS* 3.1 28.2 + - + +
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Residues in contact with GLU 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 ASP* 3.0 36.7 + - + +
222B ARG* 3.5 10.8 + - - +
224B VAL* 1.3 78.1 - - - +
226B ALA* 1.3 56.5 + - - +
228B LYS* 3.3 2.6 + - - +
229B ALA* 3.0 30.3 + - - +
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Residues in contact with ALA 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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222B ARG 3.1 12.9 + - - +
223B PHE* 3.3 4.2 + - - +
225B GLU* 1.3 79.2 - - - +
227B ALA* 1.3 63.5 + - - +
229B ALA* 3.3 18.2 + - - +
230B SER* 3.9 8.1 + - - +
255B ARG* 4.0 1.9 + - - -
326B VAL* 3.5 30.3 - - + +
327B GLU 5.5 1.8 - - - +
329B PHE* 4.9 5.2 - - + -
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Residues in contact with ALA 227 (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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137B LEU* 4.0 25.8 - - + -
223B PHE* 3.0 16.1 + - + +
224B VAL* 3.5 12.6 - - - +
225B GLU 3.3 0.2 - - - -
226B ALA* 1.3 77.9 - - - +
228B LYS* 1.3 61.3 + - - +
230B SER 3.7 4.5 - - - +
255B ARG* 3.0 34.1 + - - +
268B LEU* 4.4 17.3 - - + -
326B VAL* 3.7 4.2 - - + +
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Residues in contact with LYS 228 (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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135B LEU 4.0 16.6 - - - +
136B GLY* 3.0 26.4 + - - +
137B LEU* 3.9 23.6 - - + -
224B VAL* 3.1 23.9 + - + +
225B GLU* 3.8 2.5 - - - +
227B ALA* 1.3 78.3 - - + +
229B ALA* 1.3 64.1 + - - +
230B SER 3.5 1.7 - - - -
254B ALA 4.5 4.6 + - - -
255B ARG* 3.6 14.6 + - + +
256B SER* 4.0 9.5 - - - -
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Residues in contact with ALA 229 (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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225B GLU 3.0 17.7 + - - +
226B ALA* 3.3 12.9 + - - +
228B LYS* 1.3 80.8 - - - +
230B SER* 1.3 66.1 + - - +
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Residues in contact with SER 230 (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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226B ALA 3.9 4.7 + - - -
227B ALA 3.7 5.5 - - - +
228B LYS 4.7 1.5 - - - -
229B ALA* 1.3 83.0 - - - +
231B PRO* 1.3 83.2 + - - +
255B ARG* 3.3 18.0 + - - -
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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