Contacts of the helix formed by residues 214 - 224 (chain D) in PDB entry 1A4Y
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 214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183D GLU* 2.9 42.0 + - - +
186D VAL* 3.5 20.4 - - + +
187D ARG* 3.6 10.5 - - - +
210D VAL* 3.5 19.4 - - + -
211D THR* 2.9 30.6 + - - +
213D ASP* 1.3 75.2 - - - +
215D CYS* 1.3 57.2 + - - +
216D ARG 3.1 0.2 - - - -
217D ASP* 3.0 23.0 + - - +
218D LEU* 2.9 30.7 + - + +
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Residues in contact with CYS 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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211D THR 3.9 0.9 - - - -
212D SER 3.0 17.0 - - - +
213D ASP 2.8 0.6 - - - -
214D ASN* 1.3 80.2 - - - +
216D ARG* 1.3 55.6 + - - +
218D LEU* 4.0 10.4 - - - -
219D CYS* 3.1 25.1 + - - +
238D LEU* 3.8 35.7 - - - -
242D GLY* 3.5 38.6 - - - +
245D GLU* 3.9 9.1 - - + +
246D LEU* 4.0 15.1 - - - +
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Residues in contact with ARG 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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187D ARG* 6.0 0.2 - - - +
213D ASP* 3.0 14.4 + - - +
215D CYS* 1.3 76.4 - - - +
217D ASP* 1.3 70.4 + - - +
219D CYS* 3.2 19.9 + - - +
220D GLY* 3.2 4.7 + - - -
245D GLU* 3.9 18.6 + - + +
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Residues in contact with ASP 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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187D ARG* 2.9 49.8 + - - -
190D CYS* 3.6 29.4 - - + -
191D GLN* 5.2 4.5 + - - -
213D ASP 4.6 0.4 - - - -
214D ASN* 3.0 19.5 + - - +
216D ARG* 1.3 79.1 - - - +
218D LEU* 1.3 52.2 - - - +
220D GLY* 2.8 24.0 + - - -
221D ILE* 3.2 13.5 + - - +
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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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186D VAL* 4.9 2.2 - - + -
190D CYS* 3.8 21.1 - - - -
203D LEU* 4.6 13.0 - - + -
205D LEU* 4.4 15.7 - - + -
210D VAL* 4.0 20.0 - - + -
214D ASN* 2.9 21.4 + - + +
215D CYS* 4.0 7.4 - - - +
217D ASP* 1.3 77.2 - - - +
219D CYS* 1.3 63.6 + - - +
221D ILE* 3.2 9.7 + - + +
222D VAL* 2.9 31.8 + - + +
231D LEU* 4.9 7.2 - - + -
233D LEU* 3.9 33.2 - - + -
246D LEU* 4.0 13.9 - - + -
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Residues in contact with CYS 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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215D CYS 3.1 16.8 + - - +
216D ARG* 3.2 13.5 - - - +
217D ASP 3.1 0.4 - - - -
218D LEU* 1.3 77.0 - - - +
220D GLY* 1.3 57.7 + - - +
222D VAL* 3.6 2.6 + - - -
223D ALA* 2.9 32.0 + - - +
245D GLU 3.3 19.5 - - - +
246D LEU* 4.0 9.8 - - - +
248D PRO* 4.1 6.3 - - - -
249D GLY* 3.1 35.2 - - - -
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Residues in contact with GLY 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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194D LYS* 5.9 1.1 - - - -
216D ARG 3.2 4.5 + - - -
217D ASP* 2.8 11.5 + - - -
219D CYS* 1.3 77.7 - - - +
221D ILE* 1.3 64.1 + - - -
223D ALA* 3.3 5.6 + - - +
224D SER* 2.8 29.7 + - - -
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Residues in contact with ILE 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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190D CYS* 3.4 37.2 - - + +
193D LEU* 3.7 29.8 - - + -
194D LYS* 3.5 29.8 - - + +
203D LEU* 5.0 5.8 - - + -
217D ASP 3.2 11.6 + - - +
218D LEU* 3.2 10.7 + - + +
220D GLY* 1.3 77.0 - - - +
222D VAL* 1.3 60.7 + - + +
224D SER* 3.2 3.8 + - - +
225D LYS* 2.8 46.6 + - + +
228D LEU* 4.6 11.9 - - + -
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Residues in contact with VAL 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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218D LEU* 2.9 24.0 + - + +
219D CYS* 3.8 4.3 - - - +
221D ILE* 1.3 79.8 - - + +
223D ALA* 1.3 63.9 + - - +
224D SER 3.3 0.2 + - - -
225D LYS 3.7 11.4 + - - +
228D LEU* 4.2 17.9 - - + +
231D LEU* 3.7 30.1 - - + -
246D LEU* 4.3 8.7 - - + -
249D GLY 3.5 23.1 - - - +
250D LEU* 3.9 16.8 - - + -
255D SER* 3.7 25.5 + - - +
257D LEU* 5.1 2.7 - - + -
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Residues in contact with ALA 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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219D CYS* 2.9 21.0 + - - +
220D GLY* 3.6 6.1 - - - +
222D VAL* 1.3 78.6 - - - +
224D SER* 1.3 57.7 + - - +
249D GLY* 3.8 17.5 + - - -
252D HIS* 3.0 35.1 + - + +
254D SER* 2.9 24.6 + - - -
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Residues in contact with SER 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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194D LYS* 5.0 9.4 + - - +
220D GLY 2.8 23.0 + - - -
221D ILE* 3.6 8.1 + - - +
223D ALA* 1.3 78.9 - - - +
225D LYS* 1.3 66.0 + - - +
226D ALA* 3.3 6.9 + - - +
254D SER* 4.9 1.8 + - - -
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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