Contacts of the helix formed by residues 191 - 204 (chain A) in PDB entry 3P8P
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 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A SER* 1.3 84.8 - - - +
192A GLU* 1.3 60.8 + - - +
193A SER* 3.3 21.0 + - - -
194A ALA 3.1 2.9 + - - -
195A GLN* 2.8 26.5 + - - +
217A ASP* 2.7 37.0 + - - -
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Residues in contact with GLU 192 (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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190A SER 3.4 1.7 + - - -
191A SER* 1.3 73.2 - - - +
193A SER* 1.3 57.8 + - - +
195A GLN* 3.8 5.8 - - - +
196A LYS* 2.8 31.4 + - - +
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Residues in contact with SER 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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172A LEU* 5.6 7.2 - - - +
177A PHE* 4.9 6.1 - - - -
191A SER* 3.3 14.7 + - - -
192A GLU* 1.3 78.5 - - - +
194A ALA* 1.3 66.2 + - - +
196A LYS* 3.6 5.6 - - - +
197A ALA* 3.0 23.9 + - - +
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Residues in contact with ALA 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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177A PHE* 4.0 25.3 - - + -
188A ILE* 3.8 9.0 - - + +
189A GLY* 3.1 22.2 - - - +
191A SER* 3.1 4.4 + - - +
193A SER* 1.3 81.6 + - - +
195A GLN* 1.3 63.8 + - - +
197A ALA* 3.0 6.4 + - - +
198A LEU 2.9 18.5 + - - -
217A ASP* 3.0 27.6 - - - +
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Residues in contact with GLN 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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188A ILE* 3.2 17.7 - - - +
189A GLY 2.7 22.2 - - - +
190A SER* 3.4 13.7 - - - +
191A SER 2.8 22.1 + - - +
192A GLU* 3.9 6.1 - - - +
194A ALA* 1.3 72.5 - - - +
196A LYS* 1.3 56.5 - - - +
198A LEU* 3.4 7.5 + - - +
199A LYS* 3.0 43.3 + - - +
211A LYS* 3.3 29.5 - - - +
213A THR* 3.9 13.7 + - - +
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Residues in contact with LYS 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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192A GLU 2.8 19.7 + - - +
193A SER* 3.6 7.0 - - - +
194A ALA 3.1 0.2 - - - -
195A GLN* 1.3 72.3 - - - +
197A ALA* 1.3 68.2 + - - +
198A LEU 3.1 0.2 + - - -
199A LYS* 3.2 10.2 + - - +
200A ILE* 2.9 33.8 + - + +
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Residues in contact with ALA 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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166A VAL* 3.6 21.1 - - + +
167A PRO 4.7 6.1 - - - +
177A PHE* 3.3 32.3 - - + -
193A SER 3.0 12.0 + - - +
194A ALA 3.3 8.7 - - - +
196A LYS* 1.3 77.3 - - - +
198A LEU* 1.3 64.4 + - - +
200A ILE* 3.2 9.3 + - - +
201A MET* 3.1 24.6 + - + +
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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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186A ILE* 5.0 17.3 - - + -
188A ILE* 3.8 32.8 - - + -
194A ALA 2.9 11.2 + - - +
195A GLN* 3.6 12.3 - - - +
197A ALA* 1.3 76.5 - - - +
199A LYS* 1.3 59.2 + - + +
201A MET* 2.6 52.2 + - + +
202A GLN* 3.2 27.5 + - + +
211A LYS* 3.9 35.7 - - + +
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Residues in contact with LYS 199 (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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195A GLN* 3.0 30.1 + - - +
196A LYS* 3.7 7.6 - - - +
198A LEU* 1.3 79.6 - - + +
200A ILE* 1.3 64.4 + - + +
201A MET 3.1 0.5 + - - -
202A GLN* 3.4 5.3 + - - +
203A GLN* 3.3 21.5 + - - +
211A LYS* 6.0 3.4 - - - +
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Residues in contact with ILE 200 (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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165A THR 4.9 0.9 - - - +
166A VAL* 4.1 17.9 - - + -
167A PRO* 4.2 24.0 - - + +
196A LYS* 2.9 25.9 + - + +
197A ALA* 3.3 16.4 - - - +
199A LYS* 1.3 76.8 - - + +
201A MET* 1.3 64.0 + - - +
203A GLN* 3.6 21.8 - - - +
204A MET* 3.0 30.9 - - + +
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Residues in contact with MET 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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132A LEU* 4.3 15.3 - - - -
139A PHE* 3.7 51.0 - - + -
166A VAL* 4.2 11.7 - - + -
174A LEU* 3.5 27.1 - - + -
177A PHE* 4.6 2.0 - - + -
178A CYS* 4.5 8.7 - - - -
186A ILE* 5.6 5.6 - - + -
188A ILE* 5.3 2.2 - - + -
197A ALA* 3.1 33.8 + - + +
198A LEU* 2.6 33.4 + - + +
200A ILE* 1.3 71.8 - - - +
202A GLN* 1.3 61.6 + - + +
204A MET* 3.0 27.4 + - - +
205A SER 3.7 2.6 + - - -
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Residues in contact with GLN 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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139A PHE* 5.1 0.6 - - - -
186A ILE* 5.6 0.4 - - + -
198A LEU* 3.2 29.0 + - + +
199A LYS* 3.4 5.1 + - - +
201A MET* 1.3 76.6 - - + +
203A GLN* 1.3 66.2 + - - +
205A SER* 3.1 23.8 + - - +
207A HIS 4.8 4.2 - - - +
208A ARG* 3.6 21.1 - - - +
209A TYR* 3.0 51.4 + - + +
211A LYS* 5.3 5.7 - - - +
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Residues in contact with GLN 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 LYS 3.3 11.8 + - - +
200A ILE* 3.6 20.9 - - - +
201A MET 3.1 0.6 - - - -
202A GLN* 1.3 78.8 - - - +
204A MET* 1.3 76.4 + - - +
205A SER 3.3 7.3 + - - +
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Residues in contact with MET 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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137A GLU* 4.4 4.6 - - - +
139A PHE* 4.5 4.0 - - + -
164A SER* 3.8 39.4 + - - +
165A THR 4.0 20.4 - - - +
166A VAL* 5.1 0.4 - - + -
200A ILE* 3.0 37.0 - - + +
201A MET* 3.0 14.8 + - + +
203A GLN* 1.3 94.2 - - - +
205A SER* 1.3 57.8 + - - +
206A ASP* 5.8 0.2 - - - -
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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