Contacts of the helix formed by residues 212 - 219 (chain l) 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 l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185l LEU* 5.7 8.7 - - + -
189l ALA* 5.6 5.8 - - + -
199l THR* 3.8 8.7 - - - -
210l ASN* 3.3 4.9 - - + +
211l GLN* 1.3 76.3 - - - +
213l ASN* 1.3 55.7 + - - +
214l LEU 3.1 2.9 - - - -
215l ALA* 2.8 13.7 + - + -
216l SER* 2.7 41.0 + - - +
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Residues in contact with ASN 213 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199l THR 4.5 1.8 - - - +
200l GLN 4.6 2.2 - - - +
202l GLY* 3.7 22.4 - - - +
203l LEU 4.5 0.4 + - - +
204l LYS* 5.6 2.6 + - + +
207l ASN 4.7 15.0 - - - +
208l GLN* 5.6 1.8 - - - -
210l ASN* 3.7 23.7 + - + +
211l GLN 3.3 2.6 + - - -
212l PHE* 1.3 75.8 - - - +
214l LEU* 1.3 57.5 + - - +
216l SER* 3.8 8.6 - - - -
217l ASP* 2.9 31.0 + - - +
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Residues in contact with LEU 214 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192l VAL* 5.6 5.6 - - + -
198l MET 4.4 2.2 - - - +
199l THR* 3.4 20.9 + - - +
201l ILE 3.2 22.7 - - - +
202l GLY* 3.8 6.3 - - - -
203l LEU* 4.6 4.4 - - - +
212l PHE 2.9 1.8 + - - -
213l ASN* 1.3 77.2 - - - +
215l ALA* 1.3 58.0 + - - +
217l ASP* 3.2 5.2 + - - +
218l ILE* 2.9 28.2 + - - +
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Residues in contact with ALA 215 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185l LEU* 4.5 4.7 - - - +
188l PHE* 3.9 9.1 - - + +
189l ALA* 3.6 41.3 - - + +
192l VAL* 4.8 7.8 - - + +
199l THR* 5.1 4.0 - - - -
212l PHE* 2.8 14.4 + - + +
214l LEU* 1.3 77.1 - - - +
216l SER* 1.3 58.2 + - - +
218l ILE* 3.7 6.9 - - - +
219l MET* 2.9 34.0 + - - +
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Residues in contact with SER 216 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185l LEU* 5.7 8.0 - - - +
210l ASN* 5.9 2.9 - - - -
212l PHE* 2.7 27.4 + - - +
213l ASN* 3.9 9.9 - - - -
215l ALA* 1.3 73.3 - - - +
217l ASP* 1.3 60.0 + - - +
219l MET* 3.8 9.6 + - - +
220l GLU* 3.9 10.9 + - - +
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Residues in contact with ASP 217 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106l TRP* 6.4 0.4 - - + -
109l ILE* 4.1 16.0 - - + +
203l LEU* 4.0 26.5 - - + +
204l LYS* 5.0 6.5 - - + +
213l ASN 2.9 19.2 + - - +
214l LEU 3.2 4.0 + - - +
216l SER* 1.3 75.6 - - - +
218l ILE* 1.3 64.0 + - - +
220l GLU* 3.7 15.6 + - - +
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Residues in contact with ILE 218 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109l ILE* 5.8 2.3 - - - +
188l PHE* 5.1 6.1 - - + -
214l LEU 2.9 15.3 + - - +
215l ALA* 3.1 8.5 + - - +
217l ASP* 1.3 78.0 - - - +
219l MET* 1.3 61.0 + - - +
220l GLU 3.2 1.8 + - - -
221l PRO* 4.3 8.5 - - - +
222l PHE 5.4 0.2 + - - -
270l THR* 6.2 5.4 - - - -
273l VAL* 5.9 6.5 - - + -
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Residues in contact with MET 219 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184l LEU* 4.3 23.4 - - + +
185l LEU* 5.0 2.9 - - + +
188l PHE* 4.0 17.9 - - + +
215l ALA 2.9 16.0 + - - +
216l SER* 4.4 6.1 - - - +
217l ASP 3.4 0.2 - - - -
218l ILE* 1.3 76.0 - - - +
220l GLU* 1.3 63.9 + - - +
221l PRO 3.4 0.9 - - - -
222l PHE* 3.4 18.2 + - + +
223l ARG* 3.5 9.7 + - - +
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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