Contacts of the helix formed by residues 219 - 225 (chain D) in PDB entry 3Q37
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 219 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181D PRO* 6.3 1.6 - - + -
214D SER* 3.1 24.5 + - - -
215D VAL* 3.6 0.7 - - - -
216D THR* 2.8 41.0 + - - +
218D LYS* 1.3 77.5 - - + +
220D ALA* 1.3 66.4 + - - +
221D ARG 3.4 2.5 - - - -
222D THR* 3.3 10.7 + - + -
223D LEU* 3.0 38.7 + - + +
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Residues in contact with ALA 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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215D VAL* 4.2 13.2 - - + -
216D THR 3.0 15.8 + - - +
217D ALA 4.6 3.8 - - - +
218D LYS 3.6 1.4 - - - -
219D ASN* 1.3 83.3 + - - +
221D ARG* 1.3 62.8 + - - +
223D LEU* 4.7 0.4 - - - -
224D TYR* 3.0 20.4 + - - +
232D PHE* 3.3 18.5 - - + -
246D ILE* 4.2 14.4 - - + -
249D ALA* 3.3 23.8 - - + -
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Residues in contact with ARG 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 ALA 5.1 1.8 + - - -
218D LYS 5.1 2.5 + - - +
219D ASN 3.4 0.6 - - - -
220D ALA* 1.3 77.8 - - - +
222D THR* 1.3 64.1 + - - +
224D TYR* 3.2 4.0 + - + +
225D GLN* 3.0 34.2 + - + +
248D GLU* 4.5 17.2 + - - +
249D ALA* 3.7 25.8 + - + +
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Residues in contact with THR 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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181D PRO* 3.6 25.4 - - + -
182D GLN* 6.1 1.1 - - - +
218D LYS 5.0 4.4 + - - -
219D ASN* 3.3 15.1 + - + +
220D ALA 3.3 0.4 - - - -
221D ARG* 1.3 79.2 - - - +
223D LEU* 1.3 62.2 + - - +
225D GLN* 3.1 37.8 + - - +
226D MET* 4.0 7.9 + - - +
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Residues in contact with LEU 223 (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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180D THR 5.1 0.4 - - - +
181D PRO* 3.8 33.7 - - + -
184D ALA* 4.3 4.0 - - + -
211D TYR* 3.9 38.6 - - + -
214D SER 4.2 1.8 - - - +
215D VAL* 4.6 2.7 - - + -
219D ASN* 3.0 47.9 + - + +
220D ALA* 3.7 0.4 - - - +
222D THR* 1.3 75.9 - - - +
224D TYR* 1.3 63.7 + - - +
226D MET* 3.0 22.0 + - - +
229D ILE* 3.5 24.2 - - + +
232D PHE* 3.7 20.6 - - + -
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Residues in contact with TYR 224 (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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4D LYS* 2.6 57.9 + - + +
5D PRO 4.6 0.7 + - - -
7D PRO* 3.4 32.1 - - + +
220D ALA 3.0 18.0 + - - +
221D ARG* 3.2 4.2 + - + +
223D LEU* 1.3 76.0 - - - +
225D GLN* 1.3 56.0 + - - +
226D MET 3.1 0.4 - - - -
229D ILE* 3.8 12.3 - - - -
230D ASN* 3.8 8.0 - - - -
231D GLY* 3.7 31.2 - - - -
232D PHE* 4.1 6.4 - + + -
249D ALA 3.7 20.4 - - - +
250D THR* 3.9 23.0 + - + -
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Residues in contact with GLN 225 (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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4D LYS* 4.6 1.0 + - - -
221D ARG* 3.0 29.0 + - + +
222D THR* 3.1 33.5 + - - +
223D LEU 3.1 0.4 - - - -
224D TYR* 1.3 78.2 - - - +
226D MET* 1.3 65.3 + - - +
227D ARG* 3.5 2.8 + - - -
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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