Contacts of the helix formed by residues 189 - 200 (chain A) in PDB entry 1KKU
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 ALA 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A ALA* 5.4 3.4 - - + +
187A THR* 2.8 12.0 + - - +
188A ARG* 1.3 80.5 - - + +
190A GLY* 1.3 55.8 + - - +
191A ASN* 2.8 9.9 - - - -
192A ASP* 2.7 47.1 + - + +
193A ALA* 3.0 7.6 + - - +
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Residues in contact with GLY 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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187A THR* 3.8 11.7 - - - -
188A ARG 3.9 1.2 - - - -
189A ALA* 1.3 75.5 - - - +
191A ASN* 1.3 65.2 + - - +
193A ALA* 2.9 14.0 + - - +
194A GLN* 2.6 42.6 + - - +
212A VAL* 4.0 7.6 - - - -
214A ASN* 3.9 15.4 + - - -
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Residues in contact with ASN 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 ALA* 4.3 3.4 - - - -
190A GLY* 1.3 93.5 + - - +
192A ASP* 1.3 60.9 + - - +
194A GLN* 3.5 12.2 + - - +
195A LYS* 3.3 19.2 + - - +
214A ASN* 4.3 10.0 + - - +
216A TRP* 6.1 0.9 - - - -
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Residues in contact with ASP 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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157A ALA* 5.5 2.9 - - + -
189A ALA* 2.7 30.3 + - + +
191A ASN* 1.3 69.5 - - - +
193A ALA* 1.3 68.9 + - - +
195A LYS* 3.0 20.8 + - - +
196A PHE* 3.0 34.2 + - + -
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Residues in contact with ALA 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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157A ALA* 4.9 4.4 - - + +
160A LEU* 4.1 16.2 - - + +
185A CYS* 4.4 4.9 - - - -
187A THR* 4.1 11.4 - - + -
189A ALA 3.0 5.1 + - - -
190A GLY* 2.9 21.0 + - - +
192A ASP* 1.3 77.8 - - - +
194A GLN* 1.3 64.4 + - - +
196A PHE* 3.0 21.4 + - - +
197A ILE* 3.1 16.2 + - - +
212A VAL* 3.8 17.7 - - + -
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Residues in contact with GLN 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 GLY 2.6 25.0 + - - +
191A ASN* 3.9 10.8 - - - +
193A ALA* 1.3 73.1 - - - +
195A LYS* 1.3 62.9 + - - +
197A ILE* 3.3 12.6 + - - +
198A TYR* 3.0 22.7 + - - +
212A VAL* 4.0 32.0 + - - +
214A ASN* 5.9 2.6 - - - +
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Residues in contact with LYS 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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191A ASN 3.3 10.5 + - - +
192A ASP* 3.0 15.3 + - - +
194A GLN* 1.3 76.2 - - - +
196A PHE* 1.3 70.0 + - + +
198A TYR* 2.9 14.5 + - + +
199A GLU* 2.9 59.0 + - + +
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Residues in contact with PHE 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 ALA* 4.4 12.6 - - + -
160A LEU* 3.8 31.0 - - + +
161A GLU* 3.8 51.6 - - + -
164A ALA* 5.8 7.2 - - + -
192A ASP* 3.0 45.4 + - + -
193A ALA* 3.0 6.0 + - - +
195A LYS* 1.3 79.1 - - + +
197A ILE* 1.3 65.0 + - - +
199A GLU* 3.3 23.2 + - - +
200A SER* 3.3 16.3 + - - -
203A LEU* 4.0 5.4 - - + +
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Residues in contact with ILE 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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160A LEU* 4.2 9.0 - - + -
193A ALA 3.1 12.5 + - - +
194A GLN* 3.6 12.3 - - - +
195A LYS 3.1 0.4 - - - -
196A PHE* 1.3 79.2 - - - +
198A TYR* 1.3 62.3 + - - +
200A SER 3.2 18.0 - - - +
203A LEU* 4.0 24.9 - - + +
204A TRP* 3.5 19.4 + - + +
207A ARG* 3.9 27.1 - - + -
210A ILE* 3.3 36.3 - - + -
212A VAL* 4.0 19.1 - - + -
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Residues in contact with TYR 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 GLN 3.0 14.6 + - - +
195A LYS* 2.9 15.2 + - + +
197A ILE* 1.3 78.3 - - - +
199A GLU* 1.3 77.8 + - + +
200A SER 3.4 2.8 + - - +
204A TRP* 3.9 35.5 - + + +
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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 LYS* 2.9 52.5 + - + +
196A PHE* 3.9 18.5 - - + +
197A ILE 3.2 0.4 - - - -
198A TYR* 1.3 92.9 - - + +
200A SER* 1.3 57.0 + - - +
201A ASP* 4.2 4.7 + - - +
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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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164A ALA* 5.6 9.4 - - - -
196A PHE 3.3 12.7 + - - -
197A ILE 3.2 2.9 - - - +
198A TYR 3.3 2.3 - - - -
199A GLU* 1.3 77.8 - - - +
201A ASP* 1.3 54.8 + - - +
202A VAL* 3.2 8.8 + - - +
203A LEU* 2.7 34.9 + - - +
204A TRP* 2.7 34.2 + - - +
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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