Contacts of the helix formed by residues 189 - 199 (chain A) in PDB entry 2ZB8
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 THR 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A CYS 3.6 0.8 - - - -
188A GLY* 1.3 85.1 - - - +
190A HIS* 1.4 63.5 + - - +
191A GLU* 3.5 7.8 + - - +
192A LYS* 3.0 43.5 + - + +
193A CYS* 3.1 22.3 + - - -
207A ASN* 3.5 8.3 - - - +
209A LYS* 5.7 2.9 - - - +
335A GLY 5.0 4.3 - - - +
600A SO4 3.5 26.5 - - - +
700A NAP 4.5 4.9 - - - +
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Residues in contact with HIS 190 (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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189A THR* 1.4 68.8 - - - +
191A GLU* 1.3 67.3 + - - +
193A CYS* 3.1 11.2 + - + +
194A ILE* 2.9 26.2 + - - +
207A ASN* 3.2 28.3 + - + +
210A LYS* 3.8 27.4 + - + +
211A ASP* 3.2 24.7 + - - -
600A SO4 2.9 20.7 + - - +
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Residues in contact with GLU 191 (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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189A THR* 3.7 6.7 + - - +
190A HIS* 1.3 77.5 - - - +
192A LYS* 1.3 62.6 + - - +
194A ILE* 3.1 14.0 - - + +
195A LEU* 3.1 22.3 + - + +
338A ILE* 3.5 28.4 - - + +
600A SO4 2.9 18.6 + - - +
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Residues in contact with LYS 192 (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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164A ALA* 3.5 27.3 + - + +
187A CYS* 3.5 22.0 - - + -
189A THR* 3.0 28.3 + - - +
190A HIS 3.2 0.2 - - - -
191A GLU* 1.3 75.5 - - - +
193A CYS* 1.3 64.4 + - - +
195A LEU* 3.2 7.4 + - - +
196A LEU* 2.9 28.1 + - - +
335A GLY 2.8 24.0 + - - -
336A GLY 5.2 0.2 - - - -
337A ASN 3.2 24.3 + - - -
338A ILE* 4.0 20.4 - - + -
700A NAP 2.5 41.9 + - - +
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Residues in contact with CYS 193 (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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187A CYS* 3.5 13.0 - - - -
189A THR 3.1 17.4 + - - -
190A HIS* 3.1 16.2 + - + +
192A LYS* 1.3 76.2 - - - +
194A ILE* 1.3 63.7 + - - +
196A LEU* 3.1 2.9 + - - +
197A THR* 3.1 24.1 + - - -
205A ALA* 3.5 30.4 - - + +
206A ILE 3.5 5.6 - - - -
207A ASN* 3.5 33.9 - - - -
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Residues in contact with ILE 194 (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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190A HIS 2.9 14.5 + - - +
191A GLU* 3.1 24.9 - - + +
193A CYS* 1.3 78.3 - - - +
195A LEU* 1.3 52.9 + - - +
197A THR* 3.7 10.1 - - - +
198A SER* 2.6 53.8 + - - +
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Residues in contact with LEU 195 (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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164A ALA* 5.7 2.5 - - + -
191A GLU* 3.1 18.4 + - + +
192A LYS* 3.6 6.5 - - - +
193A CYS 3.2 0.2 - - - -
194A ILE* 1.3 78.8 - - + +
196A LEU* 1.3 67.5 + - + +
198A SER* 4.0 4.0 - - - -
199A GLU* 2.8 67.7 + - - +
200A LEU* 3.5 25.8 + - + -
315A LYS* 3.5 29.4 - - + +
338A ILE* 4.2 21.3 - - + -
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Residues in contact with LEU 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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163A ALA* 3.5 48.5 - - + +
164A ALA* 4.0 10.8 - - + +
169A SER* 4.8 0.2 - - - -
185A GLY* 4.6 1.1 - - - -
187A CYS* 4.1 17.3 - - - -
192A LYS 2.9 21.5 + - - +
193A CYS 3.1 4.5 + - - +
195A LEU* 1.3 82.5 - - + +
197A THR* 1.3 59.4 + - - +
200A LEU* 3.3 29.3 + - + -
201A GLY 3.3 0.2 + - - -
202A PHE* 3.0 52.4 + - + +
205A ALA* 4.1 12.6 - - + -
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Residues in contact with THR 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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193A CYS 3.1 16.3 + - - +
194A ILE* 3.4 15.8 + - - +
196A LEU* 1.3 77.5 - - - +
198A SER* 1.3 64.8 + - - +
199A GLU 3.7 0.2 + - - -
201A GLY* 4.2 7.6 + - - -
202A PHE 3.5 23.6 - - - +
203A ASP 4.4 2.5 - - - +
204A ALA* 3.8 10.1 - - - +
205A ALA* 3.8 26.0 - - + +
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Residues in contact with SER 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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194A ILE* 2.6 44.7 + - - +
195A LEU* 3.9 2.6 + - - -
197A THR* 1.3 77.1 + - - +
199A GLU* 1.3 69.6 + - - +
201A GLY 5.0 0.2 - - - -
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Residues in contact with GLU 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 LEU* 2.8 36.0 + - + +
198A SER* 1.3 88.4 + - - +
200A LEU* 1.3 70.2 + - + +
201A GLY 3.4 3.0 + - - -
313A LYS* 3.6 24.8 - - + +
315A LYS* 3.0 28.2 + - - +
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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