Contacts of the helix formed by residues 212 - 219 (chain y) in PDB entry 6QY3
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 PHE 212 (chain y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185y LEU* 5.7 8.7 - - + -
189y ALA* 5.6 6.1 - - + -
199y THR* 3.8 8.3 - - - -
210y ASN* 3.3 5.0 - - + +
211y GLN* 1.3 76.3 - - - +
213y ASN* 1.3 54.3 + - - +
214y LEU 3.1 3.1 - - - -
215y ALA* 2.8 13.7 + - + -
216y SER* 2.7 40.0 + - - +
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Residues in contact with ASN 213 (chain y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199y THR 3.6 2.0 + - - +
200y GLN 4.6 2.9 - - - +
202y GLY* 3.7 22.1 - - - +
204y LYS* 5.6 3.5 + - + +
207y ASN 4.7 13.9 - - - +
208y GLN* 5.6 1.6 - - - -
210y ASN* 3.7 24.8 + - + +
211y GLN 3.3 2.8 + - - -
212y PHE* 1.3 75.8 - - - +
214y LEU* 1.3 57.4 + - - +
216y SER* 3.8 8.4 - - - -
217y ASP* 2.9 31.0 + - - +
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Residues in contact with LEU 214 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192y VAL* 5.6 6.3 - - + -
198y MET 4.4 2.2 - - - +
199y THR* 3.4 21.8 + - - +
201y ILE 3.2 22.9 - - - +
202y GLY* 3.8 6.0 - - - -
203y LEU* 4.6 4.6 - - - +
212y PHE 2.9 2.2 + - - -
213y ASN* 1.3 77.7 - - - +
215y ALA* 1.3 56.9 + - - +
217y ASP* 3.2 5.2 + - - +
218y ILE* 2.9 27.5 + - - +
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Residues in contact with ALA 215 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185y LEU* 4.5 6.3 - - + +
188y PHE* 3.9 8.0 - - + +
189y ALA* 3.6 41.7 - - + +
192y VAL* 4.8 8.2 - - + +
199y THR* 5.1 3.7 - - - -
212y PHE* 2.8 13.5 + - + +
214y LEU* 1.3 76.7 - - - +
216y SER* 1.3 58.3 + - - +
218y ILE* 3.1 7.5 + - - +
219y MET* 2.9 33.3 + - - +
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Residues in contact with SER 216 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185y LEU* 5.7 8.2 - - - +
210y ASN* 5.9 3.4 - - - -
212y PHE* 2.7 27.1 + - - +
213y ASN* 3.9 9.4 - - - -
215y ALA* 1.3 73.4 - - - +
217y ASP* 1.3 60.5 - - - +
219y MET* 3.9 9.8 + - - +
220y GLU* 3.9 11.6 + - - +
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Residues in contact with ASP 217 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106y TRP* 6.4 0.7 - - + -
109y ILE* 4.1 15.8 - - + +
203y LEU* 4.0 26.5 - - + +
204y LYS* 5.0 6.3 - - + +
213y ASN 2.9 19.4 + - - +
214y LEU 3.6 4.0 - - - +
216y SER* 1.3 74.8 - - - +
218y ILE* 1.3 63.3 + - - +
220y GLU* 3.7 15.9 + - - +
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Residues in contact with ILE 218 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109y ILE* 5.8 1.8 - - - +
188y PHE* 5.1 6.5 - - + -
214y LEU 2.9 15.9 + - - +
215y ALA* 3.1 8.3 + - - +
217y ASP* 1.3 77.6 - - - +
219y MET* 1.3 59.7 + - - +
220y GLU 3.3 2.0 + - - -
221y PRO* 4.3 9.0 - - - +
222y PHE 5.4 0.2 + - - -
270y THR* 6.2 5.6 - - - -
273y VAL* 5.9 7.2 - - + -
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Residues in contact with MET 219 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184y LEU* 4.3 23.2 - - + +
185y LEU* 5.0 2.5 - - - +
188y PHE* 4.0 17.9 - - + -
215y ALA 2.9 16.7 + - - +
216y SER* 3.9 6.0 + - - +
217y ASP 3.4 0.4 - - - -
218y ILE* 1.3 76.4 - - - +
220y GLU* 1.3 64.2 + - - +
221y PRO 3.4 1.1 - - - -
222y PHE* 3.4 17.0 + - + +
223y ARG* 3.5 10.0 + - - +
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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