Contacts of the helix formed by residues 212 - 219 (chain r) in PDB entry 6QXT
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 r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185r LEU* 5.7 8.5 - - + -
189r ALA* 5.6 5.4 - - + -
199r THR* 3.8 8.1 - - - -
210r ASN* 3.3 4.9 - - + +
211r GLN* 1.3 76.1 - - - +
213r ASN* 1.3 54.3 + - - +
214r LEU 3.1 2.9 - - - -
215r ALA* 2.8 14.2 + - + -
216r SER* 2.8 40.4 + - - +
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Residues in contact with ASN 213 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199r THR 3.6 2.0 + - - +
200r GLN 4.6 2.5 - - - +
202r GLY* 3.7 22.2 - - - +
203r LEU 4.6 0.2 + - - -
204r LYS* 5.6 3.5 + - + +
207r ASN 4.7 14.4 - - - +
208r GLN* 5.6 1.6 - - - -
210r ASN* 3.8 22.9 + - + +
211r GLN 3.3 3.4 + - - -
212r PHE* 1.3 75.8 - - - +
214r LEU* 1.3 57.6 + - - +
216r SER* 3.8 7.7 - - - -
217r ASP* 2.9 30.8 + - - +
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Residues in contact with LEU 214 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192r VAL* 5.6 5.6 - - + -
198r MET 4.5 2.2 - - - +
199r THR* 3.4 20.5 + - - +
201r ILE 3.2 21.8 - - - +
202r GLY* 3.8 5.5 - - - -
203r LEU* 4.6 5.1 - - - +
212r PHE 2.9 1.8 + - - -
213r ASN* 1.3 78.9 - - - +
215r ALA* 1.3 57.2 + - - +
217r ASP* 3.2 5.1 + - - +
218r ILE* 2.9 28.0 + - - +
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Residues in contact with ALA 215 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185r LEU* 4.5 5.2 - - - +
188r PHE* 3.9 8.7 - - + +
189r ALA* 3.6 41.5 - - + +
192r VAL* 4.8 8.2 - - + +
199r THR* 5.1 4.4 - - - -
212r PHE* 2.8 13.9 + - + +
214r LEU* 1.3 76.1 - - - +
216r SER* 1.3 58.6 + - - +
218r ILE* 3.1 7.8 + - - +
219r MET* 2.9 33.4 + - - +
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Residues in contact with SER 216 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185r LEU* 5.7 7.8 - - - +
210r ASN* 5.9 3.1 - - - -
212r PHE* 2.8 25.4 + - - +
213r ASN* 3.9 9.9 - - - -
215r ALA* 1.3 72.4 - - - +
217r ASP* 1.3 60.4 + - - +
219r MET* 3.9 9.8 + - - +
220r GLU* 3.9 11.1 + - - +
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Residues in contact with ASP 217 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106r TRP* 6.4 0.4 - - + -
109r ILE* 4.1 16.6 - - + +
203r LEU* 4.0 26.2 - - + +
204r LYS* 5.0 6.3 - - + +
213r ASN 2.9 19.4 + - - +
214r LEU 3.6 3.6 - - - +
216r SER* 1.3 75.3 - - - +
218r ILE* 1.3 64.3 + - - +
219r MET 3.4 0.4 + - - -
220r GLU* 3.7 15.4 + - - +
221r PRO 5.3 0.2 - - - -
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Residues in contact with ILE 218 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109r ILE* 5.8 1.9 - - - +
188r PHE* 5.1 6.7 - - + -
214r LEU 2.9 15.9 + - - +
215r ALA* 3.1 8.7 + - - +
217r ASP* 1.3 77.4 - - - +
219r MET* 1.3 59.7 + - - +
220r GLU 3.2 2.0 + - - -
221r PRO* 4.3 8.5 - - - +
270r THR* 6.2 5.4 - - - -
273r VAL* 5.9 6.7 - - + -
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Residues in contact with MET 219 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184r LEU* 4.3 23.9 - - + +
185r LEU* 5.0 2.2 - - - +
188r PHE* 4.1 16.8 - - + +
215r ALA 2.9 16.9 + - - +
216r SER* 3.9 6.5 + - - +
217r ASP 3.4 0.6 - - - -
218r ILE* 1.3 75.8 - - - +
220r GLU* 1.3 63.3 + - - +
221r PRO 3.4 0.7 - - - -
222r PHE* 3.3 18.1 + - + +
223r 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