Contacts of the helix formed by residues 212 - 220 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185M LEU* 5.5 10.8 - - + +
189M ALA* 6.1 3.6 - - + -
210M ASN* 3.2 4.7 - - + +
211M GLN* 1.3 76.1 - - + +
213M ASN* 1.3 58.5 + - - +
214M LEU 3.4 2.2 - - - -
215M ALA* 3.5 10.8 + - + -
216M SER* 2.8 33.4 + - - -
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Residues in contact with ASN 213 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200M GLN 4.5 2.9 - - - +
202M GLY* 4.3 17.7 - - - +
208M GLN* 5.3 7.9 - - + +
210M ASN* 3.4 28.8 + - + +
211M GLN 3.4 2.0 - - - -
212M PHE* 1.3 77.3 - - - +
214M LEU* 1.3 58.1 + - - +
216M SER* 3.2 7.4 + - - -
217M ASP* 2.9 28.2 + - - +
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Residues in contact with LEU 214 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198M MET 4.5 2.5 - - - +
199M THR* 3.4 21.4 + - - +
201M ILE 3.3 24.4 + - - +
202M GLY* 4.5 3.8 - - - -
203M LEU 5.3 1.1 - - - +
212M PHE 3.4 0.2 - - - -
213M ASN* 1.3 78.4 - - - +
215M ALA* 1.3 59.5 + - - +
217M ASP* 3.1 8.9 + - - +
218M ILE* 2.9 28.3 + - - +
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Residues in contact with ALA 215 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185M LEU* 4.1 8.7 - - + +
188M PHE* 3.8 9.9 - - + +
189M ALA* 3.7 40.2 - - + +
192M VAL* 5.2 5.6 - - + -
199M THR* 4.7 4.1 + - - -
211M GLN 5.5 1.1 - - - +
212M PHE* 3.5 12.8 + - + +
213M ASN 3.4 0.4 - - - -
214M LEU* 1.3 78.1 - - - +
216M SER* 1.3 56.5 + - - +
218M ILE* 3.5 6.3 + - - +
219M MET* 2.9 30.5 + - - +
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Residues in contact with SER 216 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185M LEU* 5.8 5.6 - - - +
212M PHE* 2.8 21.0 + - - -
213M ASN* 3.5 6.7 - - - -
215M ALA* 1.3 75.4 - - - +
217M ASP* 1.3 60.9 + - - +
219M MET* 3.1 6.0 + - - +
220M GLU* 2.9 29.8 + - - +
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Residues in contact with ASP 217 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106M TRP* 5.8 6.5 - - + -
109M ILE* 4.3 16.9 - - + +
203M LEU* 5.1 17.5 - - + +
204M LYS* 5.9 5.6 - - + +
213M ASN 2.9 14.0 + - - +
214M LEU* 3.1 10.5 + - - +
216M SER* 1.3 76.8 - - - +
218M ILE* 1.3 60.8 + - - +
220M GLU* 3.7 15.5 + - - +
221M PRO 5.2 0.3 - - - -
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Residues in contact with ILE 218 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109M ILE* 6.1 0.4 - - - -
188M PHE* 5.1 7.2 - - + -
214M LEU 2.9 14.9 + - - +
215M ALA* 3.9 7.6 - - - +
217M ASP* 1.3 78.1 - - - +
219M MET* 1.3 58.6 + - - +
220M GLU 3.3 1.7 + - - -
221M PRO* 4.5 6.6 - - - +
222M PHE* 5.5 0.7 + - - +
270M THR* 5.9 8.5 - - - -
273M VAL* 6.0 6.1 - - + -
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Residues in contact with MET 219 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184M LEU* 4.5 19.2 - - + +
185M LEU* 5.1 3.4 - - + +
188M PHE* 4.2 14.8 - - + -
215M ALA 2.9 19.6 + - - +
216M SER* 3.1 7.1 + - - +
218M ILE* 1.3 74.9 - - - +
220M GLU* 1.3 64.0 + - - +
221M PRO 3.4 1.8 - - - -
222M PHE* 3.4 18.0 + - + +
223M ARG* 3.9 8.1 + - - +
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Residues in contact with GLU 220 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109M ILE* 5.2 7.0 - - + +
110M ILE* 5.7 1.8 - - - -
113M LYS* 3.7 18.5 - - + +
216M SER 2.9 13.9 + - - +
217M ASP* 3.8 12.8 - - - +
218M ILE 3.3 1.8 - - - -
219M MET* 1.3 77.8 - - - +
221M PRO* 1.3 62.6 - - - +
222M PHE 3.2 0.9 + - - -
223M ARG* 3.5 17.3 + - - +
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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