Contacts of the helix formed by residues 198 - 207 (chain A) in PDB entry 1KXM
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 ASN 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A THR* 1.3 73.6 + - - +
199A GLU* 1.3 65.4 + - - +
200A PHE 3.0 4.9 + - - -
201A TYR* 3.1 19.3 + - + -
202A LEU* 3.6 21.3 + - - +
249A TYR 3.0 27.8 + - - +
250A ALA 3.4 17.8 + - - -
252A ASP 4.5 0.2 - - - +
253A GLN* 3.4 40.5 + - + +
256A PHE* 3.7 26.1 - - + -
257A PHE* 4.8 1.8 - - + -
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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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176A ALA* 4.7 8.3 - - + -
193A ASN* 5.9 4.3 - - - +
197A THR* 3.0 19.3 + - - +
198A ASN* 1.3 79.1 + - - +
200A PHE* 1.3 56.4 + - - +
202A LEU* 3.2 24.0 + - - +
203A ASN* 2.9 57.6 + - - +
227A TYR* 4.9 7.5 + - + +
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Residues in contact with PHE 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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2A BZI 4.4 0.9 - + - -
172A MET* 3.8 24.7 - - + -
173A GLY* 3.9 9.9 - - - +
175A HIS* 3.5 26.7 - - + -
176A ALA* 3.9 20.6 - - - +
198A ASN 3.0 1.6 + - - -
199A GLU* 1.3 78.8 - - - +
201A TYR* 1.3 82.5 + + + +
203A ASN* 4.6 5.6 - - - +
204A LEU* 3.1 43.9 + - + +
229A MET* 3.5 32.0 - - + +
233A ASP* 3.5 31.9 - - + -
236A LEU* 3.9 16.2 - - + -
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Residues in contact with TYR 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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169A VAL* 2.6 42.5 + - + -
170A ALA* 3.2 2.9 + - - -
173A GLY* 3.1 22.2 - - - -
198A ASN* 3.1 20.8 + - + +
200A PHE* 1.3 91.4 - + + +
202A LEU* 1.3 65.0 + - - +
204A LEU* 3.3 3.9 + - - +
205A LEU* 3.0 27.9 + - - +
246A VAL* 3.8 29.8 - - + +
249A TYR* 3.7 18.8 - + + -
250A ALA* 3.7 20.4 - - + +
256A PHE* 3.1 40.6 - + - -
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Residues in contact with LEU 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 ASN* 3.6 26.0 - - - +
199A GLU* 3.2 32.3 + - - +
201A TYR* 1.3 76.1 - - - +
203A ASN* 1.3 53.4 + - - +
205A LEU* 3.2 2.5 + - - -
206A ASN* 2.7 54.9 + - - +
250A ALA* 3.0 45.3 - - + +
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Residues in contact with ASN 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLU* 2.9 51.2 + - - +
200A PHE* 3.8 2.8 - - - +
202A LEU* 1.3 76.1 - - - +
204A LEU* 1.3 64.4 + - - +
207A GLU* 2.9 37.1 + - + +
209A TRP* 3.3 12.0 + - + -
227A TYR* 3.8 36.7 - - - +
229A MET* 3.8 17.4 - - + +
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Residues in contact with LEU 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 PHE* 3.1 43.0 + - + +
201A TYR* 3.3 7.6 + - - +
203A ASN* 1.3 79.0 - - - +
205A LEU* 1.3 60.2 + - - +
207A GLU 4.5 0.7 - - - +
209A TRP* 3.0 21.6 + - - +
229A MET* 3.7 31.6 - - + +
233A ASP 3.8 20.0 - - - +
234A TYR* 4.2 12.1 - - + -
236A LEU* 4.3 2.5 - - + -
237A ILE* 3.6 34.9 - - + +
246A VAL* 4.2 26.0 - - + -
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Residues in contact with LEU 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 TYR 3.0 13.6 + - - +
202A LEU* 3.9 2.2 - - - +
204A LEU* 1.3 77.4 - - - +
206A ASN* 1.3 72.1 + - - +
207A GLU 4.7 2.5 - - - +
237A ILE* 4.2 6.1 - - + -
243A LEU* 4.0 27.8 - - + -
246A VAL* 3.9 10.5 - - + -
247A LYS* 3.9 31.0 - - + -
250A ALA* 3.6 31.0 - - + -
251A ASN* 5.0 4.0 - - - +
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Residues in contact with ASN 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 LEU* 2.7 40.3 + - - +
205A LEU* 1.3 87.0 + - - +
207A GLU* 1.3 72.9 + - - +
208A ASP 4.0 0.3 + - - -
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Residues in contact with GLU 207 (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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203A ASN* 2.9 29.8 + - - +
204A LEU 4.5 1.6 - - - +
205A LEU 4.7 1.9 - - - +
206A ASN* 1.3 91.3 + - - +
208A ASP* 1.3 60.6 + - - +
209A TRP* 3.4 38.5 + - + -
223A SER* 3.4 7.6 + - - -
225A SER* 2.3 32.1 + - - -
227A TYR* 3.6 27.1 - - + -
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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