Contacts of the helix formed by residues 213 - 220 (chain D) in PDB entry 5E6J
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 213 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211D THR* 3.2 8.8 + - - -
212D LEU* 1.3 77.5 - - - +
214D TYR* 1.3 63.9 + - - +
215D ASP* 3.6 9.2 + - - +
216D ASN* 3.2 42.7 + - - -
217D LEU* 3.4 17.5 + - - +
245D MET* 4.2 4.1 - - - +
252D TYR* 3.5 20.8 + - - -
306D TYR* 3.6 4.9 - - - -
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Residues in contact with TYR 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ARG* 5.6 0.7 - - - -
212D LEU 3.5 1.0 + - - -
213D SER* 1.3 69.1 + - - +
215D ASP* 1.3 64.7 + - - +
217D LEU* 2.9 16.1 + - + +
218D LYS* 2.8 54.9 + - + +
235D LEU* 4.0 18.1 - - + +
238D GLN* 3.4 26.4 - - + +
243D VAL* 3.5 21.6 - - + +
245D MET* 4.1 19.1 - - + -
306D TYR* 3.4 54.9 + + + -
307D LYS 5.2 2.0 - - - -
308D GLU* 3.2 27.8 + - + -
311D TYR* 4.6 0.9 - - - +
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Residues in contact with ASP 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D SER* 3.4 8.1 + - - +
214D TYR* 1.3 79.9 - - - +
216D ASN* 1.3 61.1 + - - +
218D LYS* 3.1 25.6 + - - +
219D THR* 2.8 37.6 + - + +
258D THR* 5.7 6.2 - - - +
306D TYR* 6.0 2.0 - - - -
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Residues in contact with ASN 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D THR* 4.5 11.1 + - + +
213D SER* 3.2 31.9 + - - +
214D TYR 3.2 0.6 - - - -
215D ASP* 1.3 79.7 - - - +
217D LEU* 1.3 57.1 + - - +
219D THR* 3.4 7.7 + - - +
220D GLY 2.8 39.2 + - - +
221D VAL* 5.5 2.0 - - + -
252D TYR* 6.0 1.0 - - - -
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Residues in contact with LEU 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ARG* 4.7 11.9 - - - +
186D LEU* 4.3 20.6 - - + -
208D TYR* 4.3 31.6 - - + -
211D THR* 4.8 5.5 - - + +
213D SER 3.4 8.9 + - - +
214D TYR* 2.9 19.8 + - + +
216D ASN* 1.3 78.1 - - - +
218D LYS* 1.3 67.2 + - - +
220D GLY* 3.9 3.1 + - - -
221D VAL* 4.5 15.9 - - + -
233D GLN* 5.1 1.6 - - - +
234D TYR* 3.7 7.9 - - - +
235D LEU* 3.3 24.1 + - + +
245D MET* 3.7 33.2 - - + -
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Residues in contact with LYS 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D TYR* 2.8 49.4 + - + +
215D ASP* 3.3 25.8 + - - +
217D LEU* 1.3 79.0 - - - +
219D THR* 1.3 64.3 + - + +
234D TYR* 4.0 2.3 - - - +
235D LEU* 3.9 31.8 + - + +
308D GLU* 5.1 2.2 + - - -
311D TYR* 3.5 48.7 - - + +
313D THR* 4.8 2.4 - - - +
315D ILE* 4.1 10.5 - - - +
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Residues in contact with THR 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D ASP* 2.8 23.9 + - + +
216D ASN* 2.9 16.9 + - - +
218D LYS* 1.3 78.3 - - + +
220D GLY* 1.3 67.4 + - - +
234D TYR* 3.4 11.7 - - - +
315D ILE* 4.1 18.8 - - + +
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Residues in contact with GLY 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D ASN* 2.8 23.0 + - - +
217D LEU 4.3 1.6 - - - -
218D LYS 3.7 0.4 - - - -
219D THR* 1.3 87.2 + - - +
221D VAL* 1.3 58.6 + - - +
232D THR* 5.4 4.3 - - - -
233D GLN 3.2 13.0 - - - -
234D TYR* 4.1 1.8 - - - -
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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