Contacts of the helix formed by residues 213 - 225 (chain D) in PDB entry 5ON2
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 PRO 213 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212D TRP* 1.3 87.9 - - + +
214D ASP* 1.3 64.1 + - - +
215D THR* 3.3 11.1 + - + +
216D VAL* 3.8 22.0 - - + -
217D LYS* 3.3 21.9 + - - +
563D LEU* 3.8 31.4 - - + +
565D CYS* 5.1 8.5 - - + +
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Residues in contact with ASP 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 TRP 4.0 0.6 + - - -
213D PRO* 1.3 70.6 - - - +
215D THR* 1.3 61.4 + - - +
217D LYS* 3.6 25.4 + - - +
218D THR* 2.6 40.3 + - - +
221D ARG* 5.7 1.2 + - - -
4E C 5.2 0.2 - - - +
5E G 5.3 4.9 - - - +
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Residues in contact with THR 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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213D PRO* 3.9 14.4 - - + +
214D ASP* 1.3 77.5 - - + +
216D VAL* 1.3 66.5 + - - +
219D MET* 3.2 39.9 + - - +
531D ILE* 4.2 8.6 - - - +
4E C 3.5 29.1 + - - +
5E G 3.8 31.2 - - - +
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Residues in contact with VAL 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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212D TRP* 4.0 17.9 - - + -
213D PRO* 3.4 23.6 + - + +
215D THR* 1.3 78.6 + - - +
217D LYS* 1.3 60.1 + - - +
219D MET* 3.5 7.8 + - - +
220D GLN* 3.0 39.6 + - - +
531D ILE* 3.8 26.0 - - + -
534D ALA* 3.7 27.6 - - + +
538D LEU* 4.2 0.9 - - + -
563D LEU* 4.0 5.2 - - + -
565D CYS* 3.8 19.1 - - - -
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Residues in contact with LYS 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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206D LEU* 3.4 45.6 + - + +
207D ASP 5.6 1.0 + - - -
209D LEU* 3.1 24.2 + - + +
210D ASP* 4.3 7.7 + - - +
212D TRP* 3.5 32.6 + - + -
213D PRO 3.3 11.2 + - - +
214D ASP* 3.6 26.9 + - - +
216D VAL* 1.3 77.2 - - - +
218D THR* 1.3 57.6 + - - +
220D GLN* 3.2 3.8 + - - +
221D ARG* 2.9 50.1 + - - +
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Residues in contact with THR 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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214D ASP* 2.6 28.3 + - - +
215D THR* 4.3 0.7 - - - -
217D LYS* 1.3 72.5 - - - +
219D MET* 1.3 61.1 + - - +
221D ARG* 3.3 17.2 + - + +
222D ASN* 3.0 51.5 + - - +
4E C 3.8 26.0 - - - +
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Residues in contact with MET 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 THR 3.2 34.4 + - - +
216D VAL* 3.7 4.5 - - - +
217D LYS 3.3 0.2 - - - -
218D THR* 1.3 76.5 - - - +
220D GLN* 1.3 57.2 + - - +
222D ASN* 3.7 1.7 + - - +
223D TRP* 3.1 26.9 + - - +
531D ILE* 3.9 20.4 - - + +
534D ALA* 3.7 26.0 - - + -
535D ILE* 4.0 28.3 - - + +
3E C 4.1 13.0 + - - +
4E C 3.3 35.0 - - - +
70E G 3.8 25.6 - - - +
71E G 5.9 0.9 - - - -
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Residues in contact with GLN 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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206D LEU* 3.6 19.3 - - + +
212D TRP* 3.7 25.3 - - - -
216D VAL* 3.0 19.9 + - - +
217D LYS 3.6 4.0 - - - +
219D MET* 1.3 75.5 - - - +
221D ARG* 1.3 59.1 + - - +
223D TRP* 3.5 6.1 - - + +
224D ILE* 2.9 39.1 + - + +
534D ALA 3.1 26.3 + - - +
535D ILE* 4.6 8.3 - - - +
538D LEU* 3.7 13.1 - - - +
539D LEU* 3.8 17.0 - - + +
542D ARG* 3.3 27.2 + - - -
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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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203D LEU* 4.0 25.6 + - + +
206D LEU* 3.7 24.6 + - + +
207D ASP* 2.7 40.6 + - - +
214D ASP* 5.7 1.6 + - - -
217D LYS* 2.9 43.9 + - - +
218D THR* 3.3 16.0 + - + +
220D GLN* 1.3 76.3 - - - +
222D ASN* 1.3 60.3 + - - +
224D ILE* 3.5 1.7 + - - +
225D GLY* 3.0 25.5 + - - -
226D ARG 4.6 0.7 + - - -
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Residues in contact with ASN 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 THR* 3.0 37.4 + - - +
219D MET 4.2 0.9 - - - +
221D ARG* 1.3 75.4 - - - +
223D TRP* 1.3 64.7 + - - +
225D GLY* 3.8 7.8 + - - -
416D ARG* 3.9 14.2 + - - -
3E C 3.0 51.2 + - - +
4E C 3.8 1.6 + - - -
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Residues in contact with TRP 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 MET 3.1 19.6 + - - +
220D GLN* 3.5 7.9 - - - +
221D ARG 3.3 0.2 - - - -
222D ASN* 1.3 74.8 - - - +
224D ILE* 1.3 65.7 + - - +
292D GLU* 5.2 0.2 - - - -
416D ARG* 3.0 46.6 + - - +
417D LEU* 3.8 25.2 + - + +
535D ILE* 3.3 39.8 - - + +
536D MET* 4.7 9.3 - - + +
539D LEU* 3.6 28.0 - - + +
71E G 6.1 1.8 - - - -
72E U 3.9 34.3 - - - -
73E A 3.4 53.6 - + - -
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Residues in contact with ILE 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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199D ALA 4.1 12.1 - - - +
202D LEU* 4.0 11.2 - - + +
203D LEU* 4.0 40.8 - - + +
206D LEU* 4.6 4.3 - - + -
220D GLN* 2.9 25.4 + - + +
221D ARG 4.0 2.9 - - - +
223D TRP* 1.3 73.9 - - - +
225D GLY* 1.3 64.0 + - - +
226D ARG 4.9 0.4 - - - +
415D TYR* 3.8 24.9 - - + -
416D ARG 3.1 16.8 + - - -
417D LEU* 3.1 28.6 + - + +
539D LEU* 4.1 28.7 - - + -
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Residues in contact with GLY 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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221D ARG 3.0 16.3 + - - -
222D ASN* 3.9 10.1 - - - -
223D TRP 3.3 0.2 - - - -
224D ILE* 1.3 75.5 - - - +
226D ARG* 1.3 65.0 + - - +
227D SER* 4.5 2.8 - - - -
330D TYR* 5.3 1.6 + - - -
414D ASN 3.7 0.9 - - - +
415D TYR* 3.6 3.6 - - - -
416D ARG* 2.9 35.7 + - - +
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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