Contacts of the helix formed by residues 202 - 214 (chain A) in PDB entry 2K86
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 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A PHE* 4.0 0.5 - - - -
196A ASP* 5.4 0.2 + - - -
197A LYS* 3.5 41.3 + - - +
200A SER* 3.0 10.7 - - - -
201A ASN* 1.3 73.8 + - - +
203A SER* 1.3 59.0 + - - +
205A GLY* 4.1 6.3 - - - -
206A TRP* 2.7 46.4 + - - +
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Residues in contact with SER 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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184A TYR* 3.4 36.8 + - - -
194A PHE* 4.3 6.6 - - - -
197A LYS 3.0 19.9 + - - -
198A GLY 4.6 1.0 + - - -
200A SER 3.0 13.2 + - - -
201A ASN* 3.9 2.9 - - - -
202A SER* 1.3 77.1 - - - +
204A ALA* 1.3 59.8 + - - +
205A GLY 2.7 14.7 + - - -
207A LYS* 3.0 25.5 + - - +
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Residues in contact with ALA 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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201A ASN* 3.3 11.3 + - + +
203A SER* 1.3 77.7 + - - +
205A GLY* 1.3 55.2 + - - +
207A LYS* 3.8 15.3 - - + -
208A ASN* 5.7 1.3 - - - +
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Residues in contact with GLY 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 ASN 3.6 6.5 - - - -
202A SER* 3.5 7.6 - - - -
203A SER 2.7 7.3 + - - -
204A ALA* 1.3 75.0 - - - +
206A TRP* 1.3 56.4 + - - -
207A LYS* 3.0 2.4 - - - +
208A ASN* 2.5 43.4 + - - +
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Residues in contact with TRP 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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162A TYR* 3.9 23.6 - + + -
193A TYR* 3.5 32.6 + + - -
194A PHE* 3.5 20.6 - - + -
197A LYS* 4.1 9.2 - - + +
202A SER* 2.7 43.7 + - - +
205A GLY* 1.3 71.7 - - - -
207A LYS* 1.3 56.8 + - - +
208A ASN* 3.1 2.9 - - - -
209A SER* 3.1 28.2 + - - -
210A ILE* 2.8 29.5 + - - +
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Residues in contact with LYS 207 (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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180A LEU* 3.6 41.6 - - + +
181A SER* 5.8 1.7 + - - -
184A TYR* 6.1 6.1 - - + -
194A PHE* 4.3 4.1 - - + -
203A SER 3.0 21.0 + - - +
204A ALA* 3.8 17.3 - - + -
205A GLY 4.0 0.9 - - - +
206A TRP* 1.3 76.6 - - - +
208A ASN* 1.3 69.3 + - + +
210A ILE* 3.3 22.5 + - - +
211A ARG* 3.4 36.2 + - - +
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Residues in contact with ASN 208 (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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204A ALA 5.7 1.1 - - - -
205A GLY* 2.5 29.9 + - - +
206A TRP* 4.5 2.8 - - - +
207A LYS* 1.3 88.8 - - + +
209A SER* 1.3 70.1 + - - +
211A ARG* 3.5 18.6 + - - +
212A HIS* 3.4 37.7 + - - +
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Residues in contact with SER 209 (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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162A TYR* 4.4 12.0 - - - -
206A TRP* 3.1 39.1 + - - -
208A ASN* 1.3 83.6 - - - +
210A ILE* 1.3 54.0 + - - +
212A HIS* 2.8 35.7 + - - +
213A ASN* 2.7 27.8 + - - -
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Residues in contact with ILE 210 (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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162A TYR* 4.2 17.0 - - + +
166A ILE* 3.7 32.8 - - + -
180A LEU* 3.6 28.3 - - + -
187A MET* 3.3 34.3 - - + -
194A PHE* 3.9 17.9 - - + -
206A TRP 2.8 12.3 + - - +
207A LYS* 3.3 11.2 + - - +
209A SER* 1.3 77.3 - - - +
211A ARG* 1.3 58.7 + - - +
213A ASN* 3.0 23.1 + - - +
214A LEU* 3.1 24.9 + - + +
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Residues in contact with ARG 211 (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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180A LEU* 3.9 26.5 - - + -
207A LYS* 3.4 34.0 + - - +
208A ASN* 3.9 15.5 + - - +
209A SER 3.1 1.0 + - - -
210A ILE* 1.3 77.5 - - - +
212A HIS* 1.3 65.4 + - + +
214A LEU* 3.1 23.0 + - + +
215A SER* 3.3 12.8 + - - -
222A ARG* 3.9 6.1 + - - +
234A TRP* 5.5 12.1 - - - -
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Residues in contact with HIS 212 (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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208A ASN* 3.4 33.2 + - - -
209A SER* 2.8 23.2 + - - +
211A ARG* 1.3 79.6 - - + +
213A ASN* 1.3 56.7 + - - +
215A SER* 3.1 26.6 + - - -
216A LEU* 3.8 8.4 + - - +
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Residues in contact with ASN 213 (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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161A SER* 5.9 0.3 - - - -
162A TYR* 3.5 33.4 + - - +
163A ALA* 4.0 9.0 + - + +
166A ILE* 4.0 13.5 - - + -
209A SER* 2.7 37.8 + - - -
210A ILE* 3.0 9.4 + - - +
212A HIS* 1.3 76.2 - - - +
214A LEU* 1.3 54.4 + - - +
215A SER 3.0 4.9 - - - -
216A LEU* 3.1 46.0 + - + +
220A PHE* 3.3 13.6 - - - -
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Residues in contact with LEU 214 (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 ILE* 3.3 31.9 - - + -
170A ILE* 6.2 0.2 - - + -
180A LEU* 4.4 10.8 - - + -
210A ILE* 3.1 30.5 + - + +
211A ARG* 3.1 15.0 + - + +
213A ASN* 1.3 74.6 - - - +
215A SER* 1.3 56.7 + - - +
216A LEU 3.4 1.1 - - - +
220A PHE* 3.7 40.4 + - + +
222A ARG* 2.9 30.3 + - + +
234A TRP* 3.7 45.3 - - + -
235A ILE 5.5 0.4 - - - +
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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