Contacts of the helix formed by residues 212 - 220 (chain z) 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 z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185z LEU* 5.5 11.0 - - + +
210z ASN* 3.2 4.9 - - + +
211z GLN* 1.3 77.2 - - - +
213z ASN* 1.3 58.3 + - - +
214z LEU 3.4 2.0 - - - -
215z ALA* 3.5 10.5 + - + +
216z SER* 2.8 32.3 + - - -
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Residues in contact with ASN 213 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200z GLN 4.5 2.9 - - - +
202z GLY* 4.3 17.7 - - - +
208z GLN* 5.3 8.3 - - + +
210z ASN* 3.4 28.8 + - + +
211z GLN 3.4 2.6 - - - -
212z PHE* 1.3 76.3 - - - +
214z LEU* 1.3 59.7 + - - +
216z SER* 3.2 7.5 + - - -
217z ASP* 2.9 28.4 + - - +
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Residues in contact with LEU 214 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192z VAL* 5.8 4.3 - - + -
198z MET 4.5 2.7 - - - +
199z THR* 3.4 21.8 + - - +
201z ILE 3.3 24.4 + - - +
202z GLY* 4.4 4.5 - - - -
203z LEU 5.3 1.1 - - - +
212z PHE 3.4 0.4 - - - -
213z ASN* 1.3 79.1 - - - +
215z ALA* 1.3 59.8 + - - +
217z ASP* 3.1 8.6 + - - +
218z ILE* 2.9 28.3 + - - +
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Residues in contact with ALA 215 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185z LEU* 4.1 9.4 - - + +
188z PHE* 3.8 9.3 - - + +
189z ALA* 3.7 39.7 - - + +
192z VAL* 5.2 6.6 - - + +
199z THR* 4.7 3.6 + - - -
211z GLN 5.2 1.5 + - - +
212z PHE* 3.5 13.9 + - + +
213z ASN 3.4 0.2 - - - -
214z LEU* 1.3 78.4 - - - +
216z SER* 1.3 57.1 + - - +
218z ILE* 3.5 6.1 + - - +
219z MET* 2.9 30.5 + - - +
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Residues in contact with SER 216 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185z LEU* 5.8 5.8 - - - +
212z PHE* 2.8 20.8 + - - -
213z ASN* 3.5 6.7 - - - -
214z LEU 3.2 0.2 - - - -
215z ALA* 1.3 75.0 - - - +
217z ASP* 1.3 60.6 + - - +
219z MET* 3.1 6.7 + - - +
220z GLU* 2.9 30.5 + - - +
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Residues in contact with ASP 217 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106z TRP* 5.8 6.5 - - + -
109z ILE* 4.3 16.7 - - + +
203z LEU* 5.1 17.7 - - + +
204z LYS* 5.9 5.4 - - + +
213z ASN 2.9 13.1 + - - +
214z LEU* 3.1 11.0 + - - +
216z SER* 1.3 76.3 - - - +
218z ILE* 1.3 59.9 + - - +
220z GLU* 3.7 15.7 + - - +
221z PRO 5.2 0.2 - - - -
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Residues in contact with ILE 218 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109z ILE* 6.1 0.4 - - - -
188z PHE* 5.1 7.9 - - + +
214z LEU 2.9 14.9 + - - +
215z ALA* 3.9 7.6 - - - +
216z SER 3.2 0.2 - - - -
217z ASP* 1.3 77.8 - - - +
219z MET* 1.3 58.8 + - - +
220z GLU 3.3 1.8 + - - -
221z PRO* 4.5 7.1 - - - +
222z PHE* 5.5 0.7 + - - +
270z THR* 5.9 8.3 - - - -
273z VAL* 6.0 6.1 - - + -
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Residues in contact with MET 219 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184z LEU* 4.5 19.0 - - + +
185z LEU* 5.1 3.6 - - + +
188z PHE* 4.2 14.6 - - + -
215z ALA 2.9 19.0 + - - +
216z SER* 3.1 7.6 + - - +
218z ILE* 1.3 74.3 - - - +
220z GLU* 1.3 64.3 + - - +
221z PRO 3.4 2.0 - - - -
222z PHE* 3.4 18.3 + - + +
223z ARG* 3.9 8.3 + - - +
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Residues in contact with GLU 220 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109z ILE* 5.2 7.0 - - + +
110z ILE* 5.7 2.2 - - - -
113z LYS* 3.7 18.9 - - + +
216z SER 2.9 13.5 + - - +
217z ASP* 3.8 13.2 - - - +
218z ILE 3.3 2.2 - - - -
219z MET* 1.3 78.2 - - - +
221z PRO* 1.3 64.0 - - - +
222z PHE 3.2 0.9 + - - -
223z ARG* 3.5 16.8 + - - +
224z PRO 5.2 0.2 - - - -
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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