Contacts of the helix formed by residues 212 - 222 (chain F) in PDB entry 3MQ6
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 THR 212 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44F ALA* 4.5 9.0 - - - +
48F GLY* 3.4 23.7 + - - +
209F ALA* 6.5 0.2 - - + -
210F GLY* 3.1 5.4 + - - +
211F LEU* 1.3 82.4 - - - +
213F ARG* 1.3 61.6 + - - +
214F PRO* 3.3 18.2 - - - +
215F ASN* 3.1 21.6 + - - +
216F GLN* 2.8 21.7 + - - +
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Residues in contact with ARG 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F GLN* 2.8 45.6 + - + +
41F ASN* 5.8 3.6 - - - +
44F ALA* 4.5 8.2 - - + +
211F LEU 3.8 0.2 + - - -
212F THR* 1.3 71.4 - - - +
214F PRO* 1.4 72.3 - - + +
216F GLN* 3.3 42.5 + - - +
217F ILE* 3.1 51.5 + - + +
220F SER* 5.4 2.6 + - - -
15O A 3.3 15.0 + - - -
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Residues in contact with PRO 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F THR* 3.3 15.0 - - - +
213F ARG* 1.4 95.7 - - + +
215F ASN* 1.3 59.4 + - - +
217F ILE* 3.4 11.7 + - + +
218F LEU* 3.0 26.3 + - - +
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Residues in contact with ASN 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F ILE* 3.7 33.2 - - + +
209F ALA* 4.2 5.5 - - - +
210F GLY 2.9 33.5 + - - +
211F LEU* 4.4 2.9 - - - -
212F THR* 3.1 18.8 + - - +
214F PRO* 1.3 80.2 - - - +
216F GLN* 1.3 66.5 + - - +
218F LEU* 3.2 12.1 + - - +
219F LEU* 3.1 26.9 + - - +
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Residues in contact with GLN 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F GLN* 3.0 41.7 + - - +
43F LEU* 3.6 19.9 - - + +
44F ALA* 3.7 4.4 - - - +
104F ILE* 5.5 5.1 - - + +
211F LEU* 2.9 39.9 + - + +
212F THR 2.8 20.3 + - - +
213F ARG* 3.3 36.9 + - - +
215F ASN* 1.3 71.9 - - - +
217F ILE* 1.3 59.8 + - - +
219F LEU* 3.3 3.3 + - - +
220F SER* 2.9 32.1 + - - -
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Residues in contact with ILE 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F ARG* 3.1 44.0 + - + +
214F PRO* 3.6 11.0 - - + +
215F ASN 3.2 0.2 - - - -
216F GLN* 1.3 73.4 - - - +
218F LEU* 1.3 67.6 + - - +
220F SER* 3.6 8.4 + - - +
221F GLY* 2.8 24.9 + - - -
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Residues in contact with LEU 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F TRP* 3.9 26.0 - - + +
203F MET* 4.2 18.2 - - + +
206F GLU 6.1 0.2 - - - +
208F ILE* 4.7 11.2 - - + -
214F PRO 3.0 14.3 + - - +
215F ASN* 3.2 16.1 + - - +
217F ILE* 1.3 77.1 - - - +
219F LEU* 1.3 69.4 + - + +
221F GLY 3.8 0.9 - - - -
222F ALA* 3.1 23.6 + - - +
225F ARG* 3.9 24.7 + - - +
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Residues in contact with LEU 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F ILE* 5.5 1.3 - - + +
107F SER* 5.0 1.8 - - - +
108F ALA* 3.8 27.8 - - + +
111F TRP* 3.5 54.6 - - + +
149F ASN* 4.4 20.5 + - + +
208F ILE* 3.5 30.3 - - + -
211F LEU* 4.2 9.2 - - + -
215F ASN 3.1 9.6 + - - +
216F GLN* 3.7 6.3 - - - +
218F LEU* 1.3 89.3 - - + +
220F SER* 1.3 61.8 + - - +
222F ALA* 3.2 16.6 + - - +
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Residues in contact with SER 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F ASN* 4.0 21.6 - - - +
151F PRO* 5.3 2.6 - - - +
213F ARG* 5.4 2.8 + - - -
216F GLN 2.9 21.9 + - - -
217F ILE* 3.6 10.4 + - - +
219F LEU* 1.3 72.6 - - - +
221F GLY* 1.3 59.1 + - - +
223F TYR* 3.2 25.6 - - - -
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Residues in contact with GLY 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F ILE* 2.8 18.9 + - - -
218F LEU 3.8 1.6 - - - -
220F SER* 1.3 76.4 + - - +
222F ALA* 1.3 63.2 + - - +
223F TYR* 3.2 8.1 - - - -
224F GLN* 3.1 32.7 + - - +
225F ARG* 4.3 6.4 + - - +
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Residues in contact with ALA 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F TRP* 3.6 27.4 - - + -
147F VAL 4.6 1.1 - - - +
148F LEU* 3.9 13.0 - - + -
204F TRP* 4.4 6.5 - - + -
218F LEU 3.1 12.7 + - - +
219F LEU 3.2 15.6 + - - +
221F GLY* 1.3 78.2 - - - +
223F TYR* 1.3 61.6 + - - +
224F GLN 3.2 0.9 + - - -
225F ARG* 3.2 31.7 + - - +
226F LEU* 3.9 9.0 - - - +
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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