Contacts of the helix formed by residues 189 - 201 (chain A) in PDB entry 4KPD
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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186A VAL 3.5 22.2 - - - +
187A ARG* 3.0 9.3 + - - +
188A PHE* 1.3 76.6 - - - +
190A GLU* 1.3 57.1 + - - +
191A LYS* 3.5 8.3 + - - +
192A ARG* 3.1 23.9 + - - +
193A TYR* 3.0 29.1 + - - +
267A CYS* 4.4 0.3 - - - -
272A VAL* 3.7 6.0 - - - +
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Residues in contact with GLU 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* 1.3 70.4 - - - +
191A LYS* 1.4 59.7 + - - +
193A TYR* 3.4 14.9 + - - +
194A LYS* 3.0 67.4 + - + +
237A GLU* 4.8 2.4 - - - +
241A ILE* 5.6 0.7 - - - +
269A TRP* 4.6 5.6 + - - -
272A VAL* 3.4 14.9 - - - +
273A GLN* 3.0 29.1 + - - -
276A GLN* 4.0 19.6 + - - +
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Residues in contact with LYS 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* 3.4 6.9 - - - +
190A GLU* 1.4 76.3 - - - +
192A ARG* 1.3 60.6 + - - +
194A LYS* 3.7 9.0 + - - +
195A SER* 2.9 29.9 + - - +
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Residues in contact with ARG 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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173A LEU* 4.3 28.5 + - - +
176A LEU* 5.2 4.0 - - - +
177A THR* 3.0 36.1 + - + +
187A ARG* 3.4 50.1 - - + +
189A THR* 3.1 18.0 + - - +
191A LYS* 1.3 71.9 - - - +
193A TYR* 1.3 66.0 + - - +
195A SER* 3.2 8.0 + - - -
196A ILE* 3.1 33.8 + - + +
267A CYS* 4.4 2.0 - - - -
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Residues in contact with TYR 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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189A THR 3.0 18.8 + - - +
190A GLU* 3.6 20.2 - - - +
191A LYS 3.4 0.2 - - - -
192A ARG* 1.3 76.5 - - - +
194A LYS* 1.4 66.3 + - + +
196A ILE* 3.3 5.1 + - + +
197A VAL* 3.2 54.3 + - + +
237A GLU* 4.9 2.2 - - + -
240A GLN 3.7 0.5 - - - -
241A ILE* 3.3 45.2 + - + +
244A ASP* 2.7 29.9 + - - -
267A CYS* 3.3 27.1 - - - -
268A SER 4.1 2.5 - - - -
269A TRP* 3.4 26.0 - + + +
272A VAL* 4.1 10.8 - - + -
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Residues in contact with LYS 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 GLU* 3.0 48.2 + - + +
191A LYS* 3.9 8.3 - - - +
192A ARG 3.4 0.2 - - - -
193A TYR* 1.4 78.3 - - + +
195A SER* 1.3 58.3 + - - +
197A VAL* 4.1 3.1 - - - +
198A LYS* 3.0 32.6 + - - +
234A GLU* 5.8 1.8 - - - -
237A GLU* 3.5 41.1 + - - +
317A TYR* 6.2 0.6 - - - -
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Residues in contact with SER 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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173A LEU* 3.9 16.8 - - - +
191A LYS* 2.9 16.8 + - - +
192A ARG* 3.2 12.3 + - - -
194A LYS* 1.3 76.0 - - - +
196A ILE* 1.4 65.7 + - - +
198A LYS* 4.5 5.4 - - - -
199A TYR* 3.2 37.1 + - - +
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Residues in contact with ILE 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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170A GLY* 4.0 2.0 - - - +
173A LEU* 3.9 23.1 - - + +
174A ASP* 3.8 33.0 - - + +
177A THR* 3.8 12.8 - - - +
192A ARG* 3.1 42.0 + - + +
193A TYR* 3.3 6.9 + - - +
195A SER* 1.4 75.6 - - - +
197A VAL* 1.3 57.7 + - + +
199A TYR* 3.2 1.4 + - - +
200A LYS* 2.7 53.3 + - + +
267A CYS* 3.9 31.4 - - + +
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Residues in contact with VAL 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 TYR* 3.2 48.9 + - + +
194A LYS* 4.1 2.0 - - - +
196A ILE* 1.3 75.0 - - + +
198A LYS* 1.4 64.0 + - - +
200A LYS* 4.0 12.6 - - - -
201A THR* 3.1 19.8 + - - -
202A ALA* 3.2 8.4 + - - +
236A GLY 4.3 0.9 - - - +
237A GLU* 3.6 34.1 - - + +
240A GLN* 3.4 36.8 - - + -
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Residues in contact with LYS 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 LYS 3.0 21.8 + - - +
195A SER* 3.9 6.7 - - - +
196A ILE 3.3 0.2 - - - -
197A VAL* 1.4 75.0 - - - +
199A TYR* 1.3 84.8 + - + +
202A ALA* 3.4 22.6 - - + +
203A PHE* 3.2 48.0 + - + -
233A LEU* 4.1 23.1 - - + +
237A GLU* 5.8 2.4 - - + +
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Residues in contact with TYR 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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165A TYR* 6.6 0.4 - + - -
166A GLN* 3.2 45.6 - - + +
167A THR* 3.3 9.5 + - - -
169A ILE* 4.0 18.8 - - + -
170A GLY* 3.4 15.3 - - - +
173A LEU* 5.2 4.9 - - + -
195A SER* 3.2 27.3 + - - +
196A ILE 3.2 1.8 + - - -
198A LYS* 1.3 113.2 + - + +
200A LYS* 1.4 64.5 + - - +
201A THR* 3.5 1.0 + - - -
203A PHE* 4.0 24.6 - + - +
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Residues in contact with LYS 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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167A THR* 3.3 16.7 - - - +
170A GLY* 3.5 22.1 - - - -
171A GLN* 3.8 16.6 - - - +
174A ASP* 2.9 28.1 + - + +
196A ILE* 2.7 37.8 + - + +
197A VAL* 4.0 5.2 - - - -
199A TYR* 1.4 72.7 - - - +
201A THR* 1.3 61.1 + - - +
204A PHE* 3.4 2.9 - - - -
240A GLN* 3.5 32.9 - - - +
244A ASP* 4.9 2.4 + - - -
405A RIS 2.5 57.5 + - + +
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Residues in contact with THR 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 VAL 3.1 9.7 + - - -
199A TYR 3.4 0.6 - - - -
200A LYS* 1.3 77.6 - - - +
202A ALA* 1.3 67.8 + - - +
203A PHE 3.3 2.8 + - - -
204A PHE* 3.6 7.9 + - - -
205A SER* 3.0 30.2 + - - +
206A PHE* 4.9 0.7 - - + -
236A GLY 4.0 18.2 - - - +
239A PHE* 4.2 12.6 - - + -
240A GLN* 2.6 33.0 + - + +
404A IPE 3.6 13.6 - - + +
405A RIS 3.0 19.8 + - - -
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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