Contacts of the helix formed by residues 189 - 200 (chain A) in PDB entry 3K9O
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 ASP 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A LEU* 4.3 1.3 + - - -
186A LYS 3.0 15.9 + - - +
187A SER* 3.0 5.5 - - - +
188A TRP* 1.3 77.0 - - - +
190A VAL* 1.3 68.5 + - - +
191A GLU* 3.3 16.7 + - - +
192A THR* 2.8 40.2 + - - +
193A ALA* 2.9 24.8 + - - +
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Residues in contact with VAL 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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165A LYS* 3.8 42.8 - - + +
168A ASN* 6.3 3.6 - - + -
169A LEU* 4.8 9.9 - - + -
183A LEU* 4.2 10.5 - - + -
188A TRP 3.4 0.6 + - - -
189A ASP* 1.3 73.6 + - - +
191A GLU* 1.3 64.3 + - + +
193A ALA* 3.9 0.5 - - - +
194A THR* 2.8 33.2 + - - +
8B LEU* 3.9 37.7 - - + +
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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 ASP* 3.3 14.0 + - - +
190A VAL* 1.3 80.3 - - + +
192A THR* 1.3 60.4 + - + +
194A THR* 3.4 3.5 + - - -
195A GLU* 3.0 28.1 + - - +
8B LEU* 4.0 22.1 - - + +
70B VAL* 5.9 0.7 - - - +
73B LEU* 4.5 23.9 - - + +
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Residues in contact with THR 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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186A LYS* 3.6 27.0 + - - +
189A ASP* 2.8 37.1 + - - +
191A GLU* 1.3 73.0 - - + +
193A ALA* 1.3 60.4 + - - +
195A GLU* 3.4 6.6 + - + +
196A LEU* 3.0 27.0 + - - +
73B LEU* 4.4 16.2 - - + -
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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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169A LEU* 4.4 4.3 - - + -
182A ALA* 3.7 24.2 - - + +
183A LEU* 3.7 27.4 - - + +
186A LYS* 3.9 11.8 - - + +
189A ASP 2.9 17.3 + - - +
190A VAL 3.9 2.0 - - - +
192A THR* 1.3 77.1 + - - +
194A THR* 1.3 59.7 + - - +
196A LEU* 3.2 3.6 + - - +
197A LEU* 3.0 31.7 + - - +
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Residues in contact with THR 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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169A LEU* 3.3 19.5 - - - +
172A MET* 4.4 9.9 - - + -
174A PHE* 4.5 8.5 - - + -
190A VAL 2.8 24.4 + - - -
191A GLU 3.6 4.0 - - - -
193A ALA* 1.3 78.2 - - - +
195A GLU* 1.3 61.2 + - - +
197A LEU* 3.2 10.2 + - - +
198A LEU* 2.9 28.7 + - + +
8B LEU* 3.6 18.1 - - + +
70B VAL* 3.9 34.8 - - + -
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Residues in contact with GLU 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 GLU 3.0 14.8 + - - +
192A THR* 3.5 10.1 - - + +
193A ALA 3.2 0.2 - - - -
194A THR* 1.3 77.4 - - - +
196A LEU* 1.3 61.4 + - - +
198A LEU* 3.3 7.2 + - - +
199A SER* 3.0 28.4 + - - +
42B ARG* 2.7 46.6 + - - -
70B VAL* 5.0 1.4 - - - +
73B LEU* 3.4 35.3 + - + +
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A VAL* 5.4 0.7 - - + -
182A ALA* 3.8 27.4 - - + +
185A SER* 4.5 8.7 - - - -
186A LYS* 3.8 32.1 - - + +
192A THR 3.0 12.9 + - - +
193A ALA 3.2 7.6 + - - +
195A GLU* 1.3 76.8 - - - +
197A LEU* 1.3 62.5 + - - +
199A SER* 3.0 22.6 + - - -
200A ASN 3.3 26.1 + - - +
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Residues in contact with LEU 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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169A LEU* 4.2 17.0 - - + -
174A PHE* 3.8 51.0 - - + -
178A ALA* 3.5 43.1 - - + +
179A VAL* 4.0 13.7 - - + +
182A ALA* 3.8 10.1 - - + -
193A ALA 3.0 19.1 + - - +
194A THR* 3.2 8.9 + - - +
196A LEU* 1.3 76.4 - - + +
198A LEU* 1.3 57.3 + - - +
200A ASN* 3.3 20.4 + - - +
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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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174A PHE* 3.8 17.9 - - + -
194A THR* 2.9 24.1 + - + +
195A GLU* 3.3 6.9 + - - +
197A LEU* 1.3 73.7 - - - +
199A SER* 1.3 59.6 + - - +
200A ASN 3.3 0.7 - - - -
42B ARG* 3.8 37.2 - - - +
44B ILE* 3.6 36.8 - - + -
49B GLN* 4.2 26.5 + - + +
70B VAL* 4.0 18.4 - - + -
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Residues in contact with SER 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 GLU* 3.0 17.0 + - - +
196A LEU* 3.0 19.3 + - - -
198A LEU* 1.3 77.5 - - - +
200A ASN* 1.3 67.4 - - - +
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Residues in contact with ASN 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 LEU* 3.3 23.0 + - - +
197A LEU* 3.3 13.1 + - - +
198A LEU 3.3 3.4 + - - -
199A SER* 1.3 85.8 - - - +
48B LYS* 5.9 3.6 - - - +
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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