Contacts of the helix formed by residues 213 - 218 (chain D) in PDB entry 3CMT
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 ASN 213 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168D ALA* 5.3 0.8 + - - +
212D GLY* 1.3 77.5 - - - -
214D ALA* 1.3 68.4 + - - +
215D LEU 3.3 2.8 + - - -
216D LYS* 2.9 44.2 + - - +
217D PHE* 3.2 28.1 - - + -
1002E T 5.6 7.3 - - - +
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Residues in contact with ALA 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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168D ALA 5.1 0.7 - - - +
171D MET* 4.2 4.9 - - + +
172D SER* 3.5 43.3 - - - +
175D MET* 3.8 13.7 - - + -
212D GLY 3.7 0.8 - - - -
213D ASN* 1.3 77.0 - - - +
215D LEU* 1.3 64.5 + - - +
217D PHE* 3.1 17.1 + - - +
218D TYR* 3.2 26.4 + - + -
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Residues in contact with LEU 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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61D ILE* 3.7 30.5 - - + -
63D GLU* 3.5 41.3 - - + +
146D VAL* 4.2 13.2 - - + -
171D MET* 5.6 8.0 - - + +
175D MET* 3.9 19.5 - - + +
191D PHE* 3.7 28.5 - - + -
193D ASN* 4.5 2.7 - - - +
209D THR* 5.9 2.7 - - + -
210D THR 5.7 1.6 - - - +
211D GLY 5.3 5.5 + - - +
212D GLY 5.1 3.5 + - - +
213D ASN 3.3 1.0 - - - -
214D ALA* 1.3 77.1 - - - +
216D LYS* 1.3 66.5 + - - +
218D TYR 4.5 0.4 - - - +
219D ALA* 2.9 32.2 + - + +
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Residues in contact with LYS 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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63D GLU* 4.6 0.8 + - - -
208D THR* 4.3 21.6 - - - +
209D THR* 4.8 12.5 + - + +
212D GLY 4.2 10.5 + - - +
213D ASN* 2.9 42.5 + - + +
214D ALA 3.3 0.4 - - - -
215D LEU* 1.3 77.3 - - - +
217D PHE* 1.3 61.3 + - + +
219D ALA 4.0 1.2 + - - -
222D ARG* 4.1 39.7 + - - +
248D LYS* 2.7 35.5 + - - +
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Residues in contact with PHE 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 ASN* 3.2 35.4 - - + -
214D ALA* 3.1 9.4 + - - +
216D LYS* 1.3 88.3 - - + +
218D TYR* 1.3 70.2 + - + +
219D ALA 3.6 1.0 - - - +
248D LYS* 2.8 20.0 + - - +
250D LYS* 3.8 11.8 + - - -
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Residues in contact with TYR 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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61D ILE* 4.1 25.2 + - + +
172D SER* 5.1 2.5 - - - -
175D MET* 3.4 46.0 - - + -
176D ARG* 3.6 24.2 - - - +
179D ALA* 4.0 22.0 - - + -
214D ALA* 3.2 30.9 + - + +
215D LEU 4.3 0.7 - - - +
217D PHE* 1.3 84.9 - - + +
219D ALA* 1.3 65.4 + - - +
220D SER* 3.4 7.4 + - - -
250D LYS* 4.7 5.6 + - - +
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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