Contacts of the helix formed by residues 213 - 225 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A HIS 4.4 0.4 - - - +
212A TRP* 1.4 87.9 - - + +
214A ASP* 1.3 63.3 + - - +
215A THR* 3.2 12.8 - - + +
216A VAL* 3.3 22.1 + - + +
217A LYS* 3.3 20.7 + - - +
563A LEU* 3.6 33.4 - - + +
565A CYS* 5.1 7.9 - - + +
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Residues in contact with ASP 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A TRP 5.1 0.7 - - - -
213A PRO* 1.3 69.4 - - - +
215A THR* 1.3 65.0 + - - +
217A LYS* 3.5 27.1 + - - +
218A THR* 2.8 36.3 + - - +
221A ARG* 5.8 1.4 + - - -
5B G 5.6 2.0 + - - -
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Residues in contact with THR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A PRO* 3.7 17.9 - - + +
214A ASP* 1.3 78.2 - - - +
216A VAL* 1.3 68.2 + - - +
218A THR* 5.2 0.2 - - - -
219A MET* 3.3 34.5 + - - +
531A ILE* 4.3 8.8 - - - +
4B C 3.6 19.8 + - - +
5B G 3.6 35.9 - - - +
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Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A TRP* 4.1 13.5 - - + -
213A PRO* 3.3 20.7 + - + +
215A THR* 1.3 74.3 + - - +
217A LYS* 1.3 61.3 + - - +
219A MET* 3.3 9.0 + - - +
220A GLN* 3.0 29.1 + - - +
531A ILE* 3.8 16.4 - - + -
534A ALA* 3.5 30.3 - - + +
538A LEU* 4.2 0.7 - - + -
563A LEU* 3.8 20.4 - - + -
565A CYS* 3.7 28.7 - - - -
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Residues in contact with LYS 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU* 3.5 41.2 + - + +
207A ASP 5.4 1.0 + - - -
209A LEU* 2.7 33.2 + - + +
210A ASP* 4.1 8.1 + - - +
212A TRP* 3.4 35.9 + - + -
213A PRO 3.3 10.1 + - - +
214A ASP* 3.5 25.8 + - - +
215A THR 3.5 0.2 - - - -
216A VAL* 1.3 77.4 - - - +
218A THR* 1.3 56.6 + - - +
220A GLN* 3.3 4.0 + - - +
221A ARG* 2.9 49.4 + - - +
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Residues in contact with THR 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ASP* 2.8 27.6 + - - +
215A THR* 4.4 1.8 - - - -
217A LYS* 1.3 73.0 - - - +
219A MET* 1.3 60.2 + - - +
221A ARG* 3.5 20.0 + - + +
222A ASN* 3.0 46.5 + - - +
4B C 4.1 29.2 - - - +
5B G 6.0 0.2 - - - -
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Residues in contact with MET 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A THR 3.3 23.3 + - - +
216A VAL* 3.3 8.2 + - - +
217A LYS 3.3 0.6 - - - -
218A THR* 1.3 77.9 - - - +
220A GLN* 1.3 57.5 + - - +
222A ASN* 3.4 2.1 + - - +
223A TRP* 2.9 30.7 + - - +
531A ILE* 4.4 16.8 - - + +
534A ALA* 3.5 25.6 - - + -
535A ILE* 3.9 30.3 - - + +
3B C 4.3 11.3 + - - +
4B C 3.2 33.7 - - - +
70B G 3.8 24.5 - - - +
71B G 5.9 1.3 - - - -
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Residues in contact with GLN 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU* 4.0 10.7 - - + +
212A TRP* 3.9 14.5 - - - -
216A VAL* 3.0 17.1 + - - +
217A LYS 3.7 7.2 - - - +
219A MET* 1.3 72.4 - - - +
221A ARG* 1.3 65.7 + - - +
223A TRP* 3.8 6.4 - - - +
224A ILE* 3.1 33.1 + - + +
534A ALA 2.9 26.0 + - - +
535A ILE* 4.5 8.3 - - + -
538A LEU* 3.5 27.9 + - - +
539A LEU* 3.4 22.4 - - + +
542A ARG* 2.9 29.6 + - - -
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Residues in contact with ARG 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LEU* 3.7 26.0 + - + +
206A LEU* 3.5 31.6 + - + +
207A ASP* 3.6 24.5 + - - +
214A ASP* 5.8 1.2 + - - -
217A LYS* 2.9 26.5 + - - +
218A THR* 3.7 39.3 + - + +
220A GLN* 1.3 76.1 - - - +
222A ASN* 1.3 61.4 + - - +
224A ILE* 3.9 1.2 - - - +
225A GLY* 2.9 28.1 + - - -
226A ARG 4.8 0.2 + - - -
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Residues in contact with ASN 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A THR* 3.0 27.1 + - - +
219A MET 3.9 1.3 - - - +
221A ARG* 1.3 78.7 - - - +
223A TRP* 1.3 64.5 + - - +
225A GLY* 3.9 7.8 + - - +
416A ARG* 3.5 15.1 + - - -
3B C 2.8 52.9 + - - +
4B C 3.8 7.3 + - - -
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Residues in contact with TRP 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A MET 2.9 17.7 + - - +
220A GLN* 3.8 5.2 - - - +
221A ARG 3.3 0.2 - - - -
222A ASN* 1.3 75.1 - - - +
224A ILE* 1.3 66.1 + - - +
416A ARG* 3.3 48.3 + - - +
417A LEU* 3.7 20.3 + - + +
535A ILE* 3.2 37.0 - - + +
536A MET* 3.7 18.9 - - + +
539A LEU* 3.6 30.8 - - + +
71B G 4.7 7.0 - - - -
72B U 3.9 31.2 - - - -
73B A 3.3 53.0 + + - -
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Residues in contact with ILE 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ALA* 4.0 15.5 - - + +
202A LEU* 4.1 7.2 - - + +
203A LEU* 3.9 39.0 - - + +
206A LEU* 4.9 0.7 - - + -
220A GLN* 3.1 23.9 + - + +
221A ARG 3.9 2.2 - - - +
223A TRP* 1.3 74.7 - - - +
225A GLY* 1.3 59.1 + - - +
226A ARG 4.3 7.6 - - - +
415A TYR* 3.8 14.3 - - + +
416A ARG 2.9 23.9 + - - -
417A LEU* 3.0 34.4 + - + -
539A LEU* 4.0 27.6 - - + -
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Residues in contact with GLY 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ARG 2.9 20.8 + - - -
222A ASN* 4.1 9.9 - - - -
223A TRP 3.5 0.2 - - - -
224A ILE* 1.3 75.3 - - - +
226A ARG* 1.3 66.9 + - - +
227A SER* 3.5 7.4 + - - -
330A TYR* 5.6 0.9 + - - -
414A ASN 3.7 1.2 - - - +
415A TYR* 3.6 1.7 - - - -
416A ARG* 3.3 20.2 + - - +
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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