Contacts of the helix formed by residues 212 - 222 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44D ALA* 4.6 7.9 - - - +
48D GLY* 3.5 23.9 + - - +
210D GLY* 3.1 3.9 + - - +
211D LEU* 1.3 83.5 - - - +
213D ARG* 1.3 60.6 + - - +
214D PRO* 3.3 18.0 - - - +
215D ASN* 3.2 20.2 + - - +
216D GLN* 2.9 21.1 + - - +
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Residues in contact with ARG 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D GLN* 3.0 41.9 + - - +
44D ALA* 4.5 8.3 - - + +
211D LEU 3.8 0.2 + - - -
212D THR* 1.3 70.2 - - - +
214D PRO* 1.3 74.1 - - + +
216D GLN* 3.3 39.1 + - - +
217D ILE* 3.0 52.5 + - + +
220D SER* 5.3 4.2 + - - -
15N A 3.5 18.8 + - - -
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Residues in contact with PRO 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D THR* 3.3 17.0 - - - +
213D ARG* 1.3 93.8 - - + +
215D ASN* 1.3 57.9 + - - +
217D ILE* 3.2 13.0 + - + +
218D LEU* 3.0 27.2 + - - +
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Residues in contact with ASN 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D ILE* 3.4 37.8 - - + +
209D ALA* 4.0 7.3 - - - +
210D GLY 2.8 30.5 + - - +
211D LEU* 4.4 2.5 - - - -
212D THR* 3.2 18.6 + - - +
214D PRO* 1.3 79.5 - - - +
216D GLN* 1.3 66.8 + - - +
218D LEU* 3.2 11.8 + - - +
219D LEU* 3.0 27.3 + - - +
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Residues in contact with GLN 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D GLN* 3.1 42.6 + - - +
43D LEU* 3.8 17.2 - - + +
44D ALA* 3.8 4.4 - - - +
104D ILE* 5.5 3.8 - - + -
211D LEU* 3.0 42.1 + - + +
212D THR 2.9 16.0 + - - +
213D ARG* 3.3 41.6 + - - +
215D ASN* 1.3 76.7 - - - +
217D ILE* 1.3 58.7 + - - +
219D LEU* 3.2 3.0 + - - +
220D SER* 2.8 33.2 + - - -
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Residues in contact with ILE 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ARG* 3.0 59.1 + - + +
214D PRO* 3.6 10.5 - - + +
215D ASN 3.2 0.2 - - - -
216D GLN* 1.3 75.4 - - - +
218D LEU* 1.3 59.9 + - - +
220D SER* 3.6 8.4 + - - +
221D GLY* 2.9 28.6 + - - -
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Residues in contact with LEU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D TRP* 4.2 11.4 - - + +
203D MET* 4.1 24.5 - - + +
208D ILE* 4.2 16.8 - - + -
214D PRO 3.0 13.8 + - - +
215D ASN* 3.2 13.0 + - - +
217D ILE* 1.3 77.8 - - - +
219D LEU* 1.3 76.7 + - + +
221D GLY 4.1 0.5 - - - -
222D ALA* 3.3 22.7 + - - +
225D ARG* 4.1 24.1 + - - +
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Residues in contact with LEU 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ILE* 5.5 0.9 - - + +
107D SER* 4.8 1.6 - - - +
108D ALA* 3.6 39.3 - - + +
111D TRP* 3.5 54.9 - - + +
147D VAL 5.2 0.2 - - - +
149D ASN* 4.2 23.5 + - + +
208D ILE* 3.9 20.2 - - + -
211D LEU* 4.2 8.1 - - + -
215D ASN 3.0 19.0 + - - +
216D GLN* 3.8 4.0 - - - +
218D LEU* 1.3 88.6 - - + +
220D SER* 1.3 59.9 + - - +
221D GLY 3.5 0.5 + - - -
222D ALA* 3.7 12.1 + - - +
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Residues in contact with SER 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D ASN* 4.0 21.7 - - - +
151D PRO* 5.1 2.6 - - - +
213D ARG* 5.3 3.5 + - - -
216D GLN* 2.8 19.3 + - - -
217D ILE* 3.6 10.7 + - - +
219D LEU* 1.3 77.2 - - - +
221D GLY* 1.3 59.2 + - - +
222D ALA 3.5 0.2 - - - -
223D TYR* 3.4 23.0 - - - -
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Residues in contact with GLY 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D ILE* 2.9 17.0 + - - -
218D LEU 4.1 1.1 - - - -
220D SER* 1.3 76.9 + - - +
222D ALA* 1.3 64.4 + - - +
223D TYR* 3.2 6.5 - - - -
224D GLN* 2.9 39.2 + - - +
225D ARG* 4.1 5.1 + - - +
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Residues in contact with ALA 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D TRP* 3.8 26.2 - - + -
147D VAL 4.7 0.9 - - - +
148D LEU* 4.1 13.5 - - + -
203D MET* 4.9 0.4 - - + -
204D TRP* 4.4 7.6 - - + -
218D LEU 3.3 17.6 + - - +
219D LEU 3.7 9.8 + - - +
220D SER 3.5 1.0 - - - -
221D GLY* 1.3 76.9 - - - +
223D TYR* 1.3 62.3 + - - +
225D ARG* 3.0 31.7 + - - +
226D LEU* 3.6 8.7 - - - +
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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