Contacts of the helix formed by residues 195 - 206 (chain A) in PDB entry 3H47
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 ASN 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A GLN* 2.9 53.3 + - - +
156A GLY 3.1 19.7 + - - +
157A PRO* 3.7 16.7 + - + -
159A GLU 4.2 1.6 + - - -
194A ALA* 1.3 73.2 - - - +
196A PRO* 1.3 67.2 - - + +
197A ASP* 3.4 10.8 + - - +
198A CYS* 3.0 20.1 + - - +
199A LYS* 2.7 33.4 + - - +
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Residues in contact with PRO 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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157A PRO* 6.1 0.9 - - + -
194A ALA 4.7 0.2 - - - +
195A ASN* 1.3 91.7 - - + +
197A ASP* 1.3 69.0 + - - +
199A LYS* 3.3 10.1 + - + +
200A THR* 3.0 29.5 + - - -
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Residues in contact with ASP 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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157A PRO 4.9 5.5 - - - +
195A ASN* 3.4 10.9 - - - +
196A PRO* 1.3 83.1 - - - +
198A CYS* 1.3 63.4 + - - +
200A THR* 3.5 6.8 + - - -
201A ILE* 3.4 26.6 + - + +
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Residues in contact with CYS 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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155A GLN* 3.6 13.7 - - - +
161A PHE* 3.3 16.6 - - + -
194A ALA* 4.3 1.1 - - + -
195A ASN* 3.0 17.1 + - - +
197A ASP* 1.3 73.9 - - - +
199A LYS* 1.3 62.3 + - - +
201A ILE* 3.0 8.2 + - - +
202A LEU* 2.8 49.0 + - - +
218A CYS* 2.0 52.5 - - + -
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Residues in contact with LYS 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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191A VAL* 3.3 21.8 - - + +
192A GLN* 3.1 45.6 + - - +
194A ALA* 3.8 13.7 + - - +
195A ASN 2.7 22.8 + - - +
196A PRO* 3.6 9.5 - - + +
198A CYS* 1.3 73.5 - - - +
200A THR* 1.3 55.9 + - - +
202A LEU* 3.3 6.5 + - - +
203A LYS* 2.8 55.5 + - + +
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Residues in contact with THR 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 PRO 3.0 15.0 + - - -
197A ASP* 3.7 9.5 - - - -
198A CYS 3.2 0.2 - - - -
199A LYS* 1.3 76.0 - - - +
201A ILE* 1.3 65.0 + - + +
203A LYS* 3.8 9.9 - - - +
204A ALA* 3.2 23.2 + - + +
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Residues in contact with ILE 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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197A ASP* 3.4 17.0 + - + +
198A CYS* 3.0 14.2 + - - +
200A THR* 1.3 77.4 - - + +
202A LEU* 1.3 61.6 + - - +
204A ALA* 3.2 9.4 + - - +
205A LEU* 3.2 20.8 + - + +
217A ALA* 3.7 44.0 - - + +
218A CYS* 4.3 8.3 - - - -
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Residues in contact with LEU 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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161A PHE* 3.8 8.7 - - + -
191A VAL* 4.1 22.3 - - + +
194A ALA* 4.2 11.9 - - + -
198A CYS* 2.8 40.1 + - - +
199A LYS 3.8 3.1 - - - +
201A ILE* 1.3 72.5 - - - +
203A LYS* 1.3 63.4 + - - +
205A LEU* 3.0 27.5 + - + +
206A GLY 3.9 3.1 + - - +
214A MET* 3.3 59.0 - - + +
217A ALA* 4.5 1.8 - - + -
218A CYS* 3.6 15.3 - - - -
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Residues in contact with LYS 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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191A VAL* 4.3 10.8 - - + -
199A LYS* 2.8 53.4 + - + +
200A THR* 3.8 7.9 - - - +
202A LEU* 1.3 72.4 - - - +
204A ALA* 1.3 62.3 + - - +
205A LEU 3.3 0.5 + - - -
206A GLY* 3.4 12.3 + - - -
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Residues in contact with ALA 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 THR* 3.2 14.4 + - + +
201A ILE* 3.6 10.8 - - - +
202A LEU 3.2 0.4 - - - -
203A LYS* 1.3 71.4 - - - +
205A LEU* 1.3 66.1 + - - +
206A GLY* 3.1 4.6 + - - -
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Residues in contact with LEU 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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201A ILE* 3.2 16.5 + - + +
202A LEU* 3.0 37.6 + - + +
204A ALA* 1.3 78.1 - - - +
206A GLY* 1.3 64.4 + - - +
207A PRO 4.8 1.0 - - - +
209A ALA* 4.0 16.2 - - + +
213A GLU* 4.2 7.0 - - + +
214A MET* 3.9 24.9 - - + +
217A ALA* 4.0 16.8 - - + -
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Residues in contact with GLY 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 LEU 3.9 2.6 + - - +
203A LYS 3.4 10.6 + - - -
204A ALA 3.1 5.1 - - - -
205A LEU* 1.3 87.0 - - - +
207A PRO* 1.3 78.3 - - - +
208A GLY 3.9 0.2 + - - -
209A ALA* 4.1 8.5 + - - +
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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