Contacts of the helix formed by residues 190 - 195 (chain B) in PDB entry 2ONL
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 ALA 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B TYR 4.0 0.6 + - - -
189B ARG* 1.3 82.2 - - - +
191B PRO* 1.3 77.0 - - + +
192B GLU* 3.5 19.3 - - - +
193B ILE* 3.6 18.7 - - + +
194B MET* 3.2 19.2 + - - +
204B VAL* 4.2 14.9 + - + -
207B TRP* 3.4 26.4 - - + +
296B ARG* 4.4 0.4 - - - +
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Residues in contact with PRO 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ALA* 1.3 88.4 - - + +
192B GLU* 1.3 75.1 + - - +
194B MET* 3.6 18.0 + - + +
195B LEU* 3.4 20.3 + - - +
197B TRP* 4.6 14.7 - - + -
207B TRP* 3.6 35.9 - - + -
232B LEU* 5.1 3.0 - - + +
235B ILE* 3.9 12.8 - - + -
236B LEU* 5.0 4.0 - - + -
291B LEU* 3.6 30.3 - - + -
296B ARG* 4.0 0.7 - - - +
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Residues in contact with GLU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ALA* 3.7 8.4 - - + +
191B PRO* 1.3 81.6 - - - +
193B ILE* 1.3 60.6 + - + +
195B LEU 3.3 0.3 + - - -
196B ASN 2.6 31.2 + - - -
197B TRP* 2.7 40.2 + - + +
198B MET* 4.7 19.1 - - + +
200B TYR* 5.1 8.1 - - + -
204B VAL* 3.6 15.0 - - + +
246B LEU* 6.0 0.9 - - - +
291B LEU* 3.9 5.8 - - - +
293B SER* 3.3 13.1 - - - -
296B ARG* 2.6 47.7 + - - -
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Residues in contact with ILE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ARG* 5.0 9.6 - - + +
189B ARG* 3.0 55.6 - - + +
190B ALA* 3.4 23.8 - - + +
192B GLU* 1.3 82.6 - - + +
194B MET* 1.3 71.3 + - - +
196B ASN* 2.9 26.6 + - - +
198B MET 5.4 1.3 - - - -
200B TYR* 4.1 39.9 - - + -
204B VAL* 4.9 6.1 - - + -
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Residues in contact with MET 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ARG* 4.8 15.3 - - + -
189B ARG* 4.4 15.3 - - + +
190B ALA 3.2 11.2 + - - +
191B PRO* 3.7 22.7 - - + +
192B GLU 3.3 0.4 - - - -
193B ILE* 1.3 85.7 - - - +
195B LEU* 1.3 83.7 + - + +
196B ASN* 3.7 6.8 + - - -
228B HIS* 3.5 46.4 + - + +
231B GLN* 3.7 32.3 - - + +
232B LEU* 4.4 8.1 - - + -
235B ILE* 4.2 7.6 - - + -
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Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B PRO 3.4 5.0 + - - +
192B GLU 3.3 2.0 + - - -
194B MET* 1.3 111.0 - - + +
196B ASN* 1.3 73.5 + - - +
197B TRP* 3.3 29.1 + - + +
228B HIS* 3.9 29.4 - - + +
229B ILE* 4.9 9.4 - - + -
232B LEU* 3.9 25.6 - - + -
255B ALA* 5.6 1.7 - - - +
258B TYR* 6.4 1.6 - - + -
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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