Contacts of the helix formed by residues 194 - 206 (chain A) in PDB entry 2KXH
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 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A ALA* 4.7 19.3 - - + -
110A ILE* 5.6 4.9 - - + -
111A MET* 6.3 0.9 - - + -
190A ASN* 3.2 20.2 + - + +
191A ILE* 5.3 1.1 - - - -
193A GLN* 1.3 82.8 - - + +
195A GLN* 1.3 63.7 + - - +
196A PRO* 3.4 1.8 - - - -
197A ILE* 3.1 13.5 + - + +
198A ILE* 3.0 32.6 + - + +
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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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191A ILE* 4.9 5.2 - - - +
192A GLY* 3.4 29.9 + - - +
193A GLN 3.2 0.2 - - - -
194A ALA* 1.3 77.4 - - - +
196A PRO* 1.4 66.1 - - + +
198A ILE* 3.0 26.2 + - - +
199A ASP* 2.7 57.8 + - - +
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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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192A GLY 3.2 15.7 - - - +
193A GLN 3.5 12.8 - - - +
195A GLN* 1.4 91.8 - - + +
197A ILE* 1.3 64.8 + - + +
199A ASP* 4.3 5.6 - - + +
200A GLN* 3.1 27.8 + - - +
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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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105A GLN* 5.3 9.6 - - - +
107A ALA* 4.1 25.1 - - + -
111A MET* 5.6 0.9 - - - -
193A GLN 4.9 1.6 - - - +
194A ALA* 3.3 20.0 - - + +
195A GLN 3.0 0.4 - - - -
196A PRO* 1.3 85.4 - - + +
198A ILE* 1.3 59.8 + - + +
200A GLN* 3.2 8.5 + - + +
201A LEU* 2.8 52.6 + - + +
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Residues in contact with ILE 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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107A ALA* 6.5 0.2 - - + -
111A MET* 4.1 32.3 - - + -
191A ILE* 5.5 10.8 - - + -
194A ALA* 3.0 23.4 + - + +
195A GLN* 3.0 32.5 + - - +
197A ILE* 1.3 76.5 - - + +
199A ASP* 1.3 59.1 + - - +
201A LEU* 3.2 10.0 + - - +
202A ALA* 3.0 30.5 + - + +
286A VAL* 5.1 5.2 - - + +
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Residues in contact with ASP 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 GLN* 2.7 48.1 + - - +
196A PRO* 4.3 5.3 - - + +
198A ILE* 1.3 78.2 - - - +
200A GLN* 1.3 60.1 + - - +
202A ALA* 4.1 6.5 - - - +
203A GLU* 3.1 24.9 + - - +
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Residues in contact with GLN 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 3.1 21.7 + - - +
197A ILE* 3.4 12.1 - - + +
198A ILE 3.2 0.2 - - - -
199A ASP* 1.3 75.1 - - - +
201A LEU* 1.3 58.8 + - + +
203A GLU* 3.2 6.4 + - - +
204A GLU* 2.7 68.2 + - - +
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Residues in contact with LEU 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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105A GLN* 5.5 9.6 - - - +
108A LEU* 4.6 14.4 - - + -
111A MET* 4.0 31.0 - - + -
197A ILE* 2.8 37.4 + - + +
198A ILE* 3.2 4.5 + - - +
200A GLN* 1.3 77.2 - - + +
202A ALA* 1.3 53.2 + - - +
204A GLU* 3.1 14.1 + - - +
205A ALA* 2.8 32.2 + - - +
286A VAL* 3.0 21.1 - - + +
287A THR* 3.9 22.7 - - - +
288A PRO* 4.5 6.5 - - + +
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Residues in contact with ALA 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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198A ILE* 3.0 19.2 + - + +
199A ASP* 4.1 7.9 - - - +
201A LEU* 1.3 75.3 - - - +
203A GLU* 1.3 58.5 + - - +
205A ALA* 3.6 1.7 + - - +
206A ARG* 3.0 27.9 + - - +
284A LYS* 5.6 6.8 + - - +
285A ALA 4.7 2.6 - - - +
286A VAL* 3.3 22.1 + - + +
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Residues in contact with GLU 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 ASP 3.1 18.0 + - - +
200A GLN* 3.7 7.4 - - - +
202A ALA* 1.3 78.5 - - - +
204A GLU* 1.3 62.2 + - - +
206A ARG* 2.9 55.5 + - - +
207A ALA* 3.6 5.4 + - - +
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Residues in contact with GLU 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 GLN* 2.7 49.3 + - - +
201A LEU* 3.1 14.3 + - - +
203A GLU* 1.3 72.2 - - - +
205A ALA* 1.3 63.9 + - - +
207A ALA* 3.2 22.1 + - - +
208A PHE* 3.6 10.4 - - + -
288A PRO* 3.7 22.8 - - + +
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Residues in contact with ALA 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 LEU 2.8 19.7 + - - +
202A ALA 4.1 0.9 - - - +
204A GLU* 1.3 68.2 - - - +
206A ARG* 1.3 59.5 + - - +
207A ALA 3.0 2.2 - - - -
208A PHE* 2.9 31.8 + - + +
209A ASN* 3.4 6.8 + - - -
210A ARG* 4.5 2.4 + - - +
285A ALA* 3.4 31.9 - - + +
286A VAL 3.9 10.3 - - - +
287A THR 4.0 2.0 - - - +
288A PRO* 3.9 18.5 - - + +
289A PRO* 5.5 0.4 - - + -
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Residues in contact with ARG 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 ALA 3.0 15.7 + - - +
203A GLU* 2.9 47.7 + - - +
204A GLU 3.1 0.2 - - - -
205A ALA* 1.3 77.1 - - - +
207A ALA* 1.3 56.1 + - - +
208A PHE 3.0 0.4 - - - -
209A ASN* 2.9 28.2 + - + +
284A LYS* 5.5 18.2 - - + +
285A ALA 5.0 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