Contacts of the helix formed by residues 215 - 220 (chain B) in PDB entry 2QNJ
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 SER 215 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ASP* 3.8 22.6 + - - -
179B LEU 4.4 4.2 - - - +
180B LYS* 3.4 25.0 - - - +
211B THR 3.5 10.9 + - - -
212B PHE* 3.9 10.9 - - - +
213B CYS 3.4 0.2 - - - -
214B GLY* 1.3 74.9 - - - +
216B PRO* 1.4 73.4 - - - +
218B TYR* 2.8 17.0 + - - +
219B ALA* 3.0 14.0 + - - +
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Residues in contact with PRO 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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212B PHE* 3.3 23.1 - - + +
213B CYS 3.8 3.1 - - - +
214B GLY 3.7 0.7 - - - -
215B SER* 1.4 90.9 - - - +
217B PRO* 1.4 72.4 - - + +
218B TYR 2.9 1.9 + - - -
219B ALA* 3.0 24.0 + - + +
224B PHE* 4.8 3.7 - - + -
258B LEU* 4.0 21.1 - - + -
261B LEU* 3.6 30.7 - - + +
265B VAL* 5.0 0.9 - - - +
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Residues in contact with PRO 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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213B CYS 4.5 4.5 - - - +
214B GLY* 3.3 19.5 - - - +
216B PRO* 1.4 96.1 - - + +
218B TYR* 1.3 66.1 + - + +
219B ALA 3.5 1.8 - - - +
237B TRP* 5.2 0.2 + - - -
241B VAL* 3.8 19.3 - - - +
251B LEU* 3.8 34.0 - - + +
252B PRO* 5.6 0.5 - - - +
253B PHE* 4.3 17.0 - - - +
254B ASP* 5.6 0.7 - - - +
261B LEU* 4.1 15.4 - - + +
265B VAL* 5.3 0.9 - - - +
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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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141B PHE* 4.2 14.2 - - - +
179B LEU 3.3 26.7 - - - +
180B LYS* 4.2 2.2 - - - -
181B ALA* 4.0 32.3 - - + +
214B GLY* 3.4 21.8 - - - -
215B SER 2.8 4.4 + - - +
217B PRO* 1.3 90.1 - - + +
219B ALA* 1.3 63.9 + - - +
237B TRP* 3.6 9.4 - - - -
238B SER* 2.9 33.7 + - - +
241B VAL* 3.8 24.7 - - + -
242B ILE* 3.8 33.2 - - + -
245B THR* 4.4 3.4 + - + +
251B LEU* 3.9 17.7 - - + +
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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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215B SER* 3.0 12.9 + - - +
216B PRO* 3.0 21.1 + - + +
217B PRO 4.8 0.7 - - - +
218B TYR* 1.3 78.4 - - - +
220B ALA* 1.3 62.1 + - - +
221B PRO 4.1 0.3 - - - -
223B LEU* 4.1 23.6 - - + -
224B PHE* 4.6 5.5 - - + -
229B TYR* 3.3 16.4 - - - +
237B TRP* 3.3 13.4 + - - -
265B VAL* 4.2 11.3 - - - +
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Residues in contact with ALA 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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218B TYR 3.7 1.0 + - - -
219B ALA* 1.3 73.9 - - - +
221B PRO* 1.3 70.4 - - + +
222B GLU* 2.8 31.9 + - - +
223B LEU* 2.9 21.1 + - - +
224B PHE* 4.2 2.1 + - - -
229B TYR* 3.2 15.9 + - + +
234B VAL* 4.4 8.0 - - + +
237B TRP* 3.5 25.8 - - + -
265B VAL* 4.5 0.7 - - - -
295B ARG* 3.9 0.4 - - - +
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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