Contacts of the helix formed by residues 212 - 219 (chain i) 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 i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185i LEU* 5.7 8.5 - - + -
189i ALA* 5.6 6.1 - - + -
199i THR* 3.8 8.5 - - - -
210i ASN* 3.3 5.1 - - + +
211i GLN* 1.3 77.0 - - - +
213i ASN* 1.3 54.0 + - - +
214i LEU 3.1 2.5 - - - -
215i ALA* 2.8 13.3 + - + -
216i SER* 2.8 40.4 + - - +
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Residues in contact with ASN 213 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199i THR 3.6 3.0 + - - +
200i GLN 4.5 2.5 - - - +
202i GLY* 3.7 22.4 - - - +
203i LEU 4.5 0.2 + - - -
204i LYS* 5.6 3.5 + - + +
207i ASN 4.7 13.5 - - - +
208i GLN* 5.6 2.0 - - - -
210i ASN* 3.8 24.6 + - + +
211i GLN 3.3 3.0 - - - -
212i PHE* 1.3 74.8 - - - +
214i LEU* 1.3 58.0 + - - +
216i SER* 3.8 7.6 - - - -
217i ASP* 2.9 30.8 + - - +
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Residues in contact with LEU 214 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192i VAL* 5.6 5.6 - - + -
198i MET 4.4 2.5 - - - +
199i THR* 3.4 20.7 + - - +
201i ILE 3.2 22.2 - - - +
202i GLY* 3.8 5.2 - - - -
203i LEU* 4.6 5.3 - - - +
212i PHE 2.9 1.4 + - - -
213i ASN* 1.3 78.1 - - - +
215i ALA* 1.3 59.2 + - - +
217i ASP* 3.2 4.6 + - - +
218i ILE* 2.9 27.9 + - - +
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Residues in contact with ALA 215 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185i LEU* 4.5 5.4 - - - +
188i PHE* 3.9 8.8 - - + +
189i ALA* 3.6 41.5 - - + +
192i VAL* 4.8 8.2 - - + +
199i THR* 5.1 4.6 - - - -
212i PHE* 2.8 15.0 + - + +
214i LEU* 1.3 75.9 - - - +
216i SER* 1.3 57.7 + - - +
218i ILE* 3.1 7.7 + - - +
219i MET* 2.9 33.2 + - - +
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Residues in contact with SER 216 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185i LEU* 5.7 7.8 - - - +
210i ASN* 5.9 3.4 - - - -
212i PHE* 2.8 27.3 + - - +
213i ASN* 3.9 9.9 - - - -
215i ALA* 1.3 73.4 - - - +
217i ASP* 1.3 58.8 + - - +
219i MET* 3.9 9.8 + - - +
220i GLU* 3.9 11.1 + - - +
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Residues in contact with ASP 217 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109i ILE* 4.1 16.2 - - + +
203i LEU* 4.0 25.8 - - + +
204i LYS* 5.0 6.5 - - + +
213i ASN 2.9 19.0 + - - +
214i LEU 3.2 4.7 + - - +
216i SER* 1.3 75.5 - - - +
218i ILE* 1.3 64.6 + - - +
220i GLU* 3.7 15.7 + - - +
221i PRO 5.3 0.2 - - - -
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Residues in contact with ILE 218 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109i ILE* 5.8 1.8 - - - +
188i PHE* 5.1 7.0 - - + -
214i LEU 2.9 16.1 + - - +
215i ALA* 3.1 7.8 + - - +
217i ASP* 1.3 78.0 - - - +
219i MET* 1.3 60.9 + - - +
220i GLU 3.2 1.9 + - - -
221i PRO* 4.3 8.8 - - - +
222i PHE 5.4 0.2 + - - -
270i THR* 6.2 5.2 - - - -
273i VAL* 5.9 6.7 - - + -
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Residues in contact with MET 219 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184i LEU* 4.3 23.3 - - + +
185i LEU* 5.0 2.9 - - - +
188i PHE* 4.1 17.7 - - + +
215i ALA 2.9 16.3 + - - +
216i SER* 3.9 5.8 + - - +
217i ASP 3.4 0.2 - - - -
218i ILE* 1.3 76.0 - - - +
220i GLU* 1.3 63.8 + - - +
221i PRO 3.4 0.9 - - - -
222i PHE* 3.3 18.6 + - + +
223i ARG* 3.5 9.5 + - - +
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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