Contacts of the helix formed by residues 194 - 213 (chain A) in PDB entry 2BQZ
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 SER 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A ARG* 3.3 8.8 + - - +
193A LYS* 1.3 80.5 - - - +
195A LYS* 1.3 59.9 + - - +
196A ALA* 3.4 7.4 + - - +
197A GLU* 3.2 28.5 + - - +
198A LEU* 3.0 23.7 + - - +
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Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A SER* 1.3 70.2 - - - +
196A ALA* 1.3 67.4 + - - +
198A LEU* 3.2 9.8 + - - +
199A GLN* 3.0 48.4 + - + +
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Residues in contact with ALA 196 (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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194A SER* 3.4 7.0 + - - +
195A LYS* 1.3 79.1 - - - +
197A GLU* 1.3 59.3 + - + +
199A GLN* 3.3 13.9 + - - +
200A SER* 2.8 29.0 + - - -
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Residues in contact with GLU 197 (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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192A ARG 5.7 1.1 - - - +
193A LYS* 4.8 4.7 - - + -
194A SER* 3.2 24.9 + - - +
196A ALA* 1.3 75.0 - - + +
198A LEU* 1.3 66.3 + - - +
199A GLN 3.1 1.1 - - - -
200A SER* 2.8 35.0 + - - -
201A GLU* 2.9 35.2 + - - +
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Residues in contact with LEU 198 (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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193A LYS* 3.3 48.7 - - + +
194A SER 3.0 15.9 + - - +
195A LYS* 3.7 7.4 - - - +
197A GLU* 1.3 77.3 - - - +
199A GLN* 1.3 62.8 + - + +
201A GLU* 4.0 5.9 - - + +
202A GLU* 3.1 24.8 + - - +
205A ARG* 5.0 1.6 + - - -
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Residues in contact with GLN 199 (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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195A LYS* 3.0 34.3 + - + +
196A ALA* 3.4 15.9 - - - +
198A LEU* 1.3 76.2 - - + +
200A SER* 1.3 59.8 + - - +
202A GLU* 3.3 5.8 + - - +
203A ARG* 2.9 30.7 + - - +
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Residues in contact with SER 200 (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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196A ALA 2.8 14.3 + - - -
197A GLU* 2.8 41.3 + - - -
199A GLN* 1.3 71.7 - - - +
201A GLU* 1.3 56.4 + - - +
203A ARG* 3.3 7.1 + - - +
204A LYS* 3.0 30.8 + - - +
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Residues in contact with GLU 201 (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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193A LYS* 2.6 45.7 + - - +
197A GLU* 2.9 35.1 + - - +
198A LEU* 4.0 6.2 - - + +
200A SER* 1.3 81.9 + - - +
202A GLU* 1.3 56.6 + - - +
204A LYS* 3.4 7.0 + - - +
205A ARG* 3.0 45.6 + - - +
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Residues in contact with GLU 202 (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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198A LEU 3.1 19.4 + - - +
199A GLN* 3.7 4.7 - - - +
201A GLU* 1.3 72.8 - - - +
203A ARG* 1.3 68.3 + - - +
205A ARG* 2.6 41.6 + - - +
206A ILE* 3.0 49.2 + - + +
239A GLY 4.6 11.3 - - - +
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Residues in contact with ARG 203 (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 GLN 2.9 16.9 + - - +
200A SER* 3.6 6.3 - - - +
202A GLU* 1.3 78.5 - - - +
204A LYS* 1.3 57.7 + - - +
206A ILE* 3.3 1.6 + - - +
207A ASP* 2.9 52.4 + - - +
310A HIS* 4.5 18.6 - - + -
311A ASP* 3.6 35.3 + - - -
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Residues in contact with LYS 204 (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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200A SER 3.0 16.7 + - - +
201A GLU* 3.7 8.3 - - - +
202A GLU 3.2 0.2 - - - -
203A ARG* 1.3 75.3 - - - +
205A ARG* 1.3 59.2 + - - +
207A ASP* 3.3 8.9 + - + +
208A GLU* 2.9 61.7 + - + +
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Residues in contact with ARG 205 (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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198A LEU 5.0 1.0 + - - -
201A GLU* 3.0 34.8 + - - +
202A GLU* 2.6 45.2 + - - +
204A LYS* 1.3 77.3 - - - +
206A ILE* 1.3 66.4 + - + +
208A GLU* 3.4 8.9 + - - +
209A LEU* 3.2 36.9 + - + +
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Residues in contact with ILE 206 (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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202A GLU* 3.0 44.1 + - + +
203A ARG* 3.8 2.7 - - - +
205A ARG* 1.3 77.1 - - + +
207A ASP* 1.3 65.8 + - - +
209A LEU* 3.2 9.2 + - + +
210A ILE* 2.9 36.4 + - + +
241A PHE* 4.5 13.7 - - + -
310A HIS* 3.6 35.4 - - + +
319A ILE* 3.9 20.0 - - + -
321A ILE* 5.4 5.4 - - + -
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Residues in contact with ASP 207 (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 ARG* 2.9 40.7 + - - +
204A LYS* 3.7 7.7 - - - +
206A ILE* 1.3 76.9 - - - +
208A GLU* 1.3 59.0 + - + +
210A ILE* 3.3 1.0 + - - +
211A GLU* 2.9 50.0 + - - +
310A HIS* 2.7 34.4 + - - -
311A ASP 4.5 1.2 - - - +
312A ILE* 3.7 22.7 - - + +
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Residues in contact with GLU 208 (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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204A LYS* 2.9 48.1 + - + +
205A ARG* 3.8 7.4 - - - +
207A ASP* 1.3 75.7 - - + +
209A LEU* 1.3 59.7 + - + +
211A GLU* 3.9 9.9 - - - +
212A SER* 2.9 32.2 + - - -
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Residues in contact with LEU 209 (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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205A ARG* 3.2 30.3 + - + +
206A ILE* 3.2 7.9 + - + +
208A GLU* 1.3 74.8 - - + +
210A ILE* 1.3 66.2 + - - +
212A SER* 3.2 19.7 + - - +
213A GLY* 3.2 9.7 + - - -
214A LYS* 4.1 16.0 + - + +
241A PHE* 3.6 54.1 - - + -
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Residues in contact with ILE 210 (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 ILE* 2.9 25.2 + - + +
207A ASP 3.7 3.6 - - - +
209A LEU* 1.3 77.9 - - - +
211A GLU* 1.3 64.7 + - + +
213A GLY* 3.3 10.2 + - - -
241A PHE* 4.0 11.0 - - + -
244A GLU* 3.6 25.9 - - - +
292A ARG* 5.2 3.6 + - - -
310A HIS* 3.7 30.3 - - + -
312A ILE* 3.8 21.8 - - + -
317A HIS* 3.8 22.9 - - + +
319A ILE* 3.8 26.7 - - + -
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Residues in contact with GLU 211 (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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207A ASP* 2.9 31.2 + - - +
208A GLU* 3.9 10.2 - - - +
210A ILE* 1.3 78.4 - - + +
212A SER* 1.3 60.4 + - - +
213A GLY 3.5 0.3 + - - -
312A ILE* 3.8 32.5 - - + +
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Residues in contact with SER 212 (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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208A GLU 2.9 15.9 + - - -
209A LEU* 3.2 13.7 + - - +
211A GLU* 1.3 77.4 - - - +
213A GLY* 1.3 64.4 + - - +
214A LYS* 3.1 33.0 + - - +
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Residues in contact with GLY 213 (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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209A LEU 3.2 8.0 + - - -
210A ILE 3.3 9.1 + - - -
211A GLU 3.2 3.6 - - - -
212A SER* 1.3 79.2 + - - +
214A LYS* 1.3 64.8 + - - +
215A GLU* 3.3 16.3 + - - +
292A ARG* 3.9 26.3 + - - -
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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