Contacts of the helix formed by residues 198 - 209 (chain A) in PDB entry 4XK8
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A VAL* 3.6 39.3 - - + +
19A LYS 4.2 7.4 + - - +
21A LEU* 5.8 1.6 - - - +
194A ALA* 3.1 18.7 + - - +
195A TRP* 3.2 19.7 + - + +
196A PHE 3.2 2.4 - - - -
197A GLN* 1.3 74.2 - - - +
199A VAL* 1.3 59.2 + - - +
200A GLU* 3.4 5.5 - - - +
201A SER* 3.5 13.6 + - - +
202A MET* 3.0 28.7 + - - +
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Residues in contact with VAL 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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196A PHE 4.5 7.0 - - - +
197A GLN* 2.7 18.8 + - - +
198A ASP* 1.3 71.2 - - - +
200A GLU* 1.3 66.6 + - - +
202A MET* 3.9 9.8 - - + +
203A LEU* 2.9 41.7 + - + +
327A ILE* 4.8 5.2 - - + -
347A TYR* 3.4 40.6 - - + +
350A LEU 4.9 5.4 - - - +
351A THR* 4.0 16.6 - - + -
357A GLN* 5.3 5.4 - - - +
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Residues in contact with GLU 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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18A VAL* 6.2 2.2 - - + -
197A GLN 4.9 0.3 - - - +
198A ASP* 4.5 2.4 - - - +
199A VAL* 1.3 78.3 + - - +
201A SER* 1.3 58.2 + - - +
203A LEU* 3.7 1.6 - - - +
204A ASN* 2.9 36.2 + - - +
317A TYR* 3.7 20.1 - - + +
318A ARG 3.5 25.6 - - - +
319A THR* 4.5 1.3 - - + -
325A HIS 4.4 7.2 - - - +
326A GLY* 4.5 2.9 - - - -
327A ILE* 3.6 35.5 + - + +
328A LYS* 4.9 0.3 + - - +
347A TYR* 3.3 29.7 + - - -
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Residues in contact with SER 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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18A VAL* 3.9 30.6 - - - +
198A ASP* 3.5 11.7 + - - +
200A GLU* 1.3 77.6 - - - +
202A MET* 1.3 58.6 + - - +
204A ASN* 3.2 2.4 + - - +
205A HIS* 2.7 60.9 + - - -
319A THR* 4.0 18.0 - - - +
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Residues in contact with MET 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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195A TRP* 4.7 9.4 - - + +
196A PHE* 3.4 40.4 - - + +
198A ASP 3.0 16.7 + - - +
199A VAL* 3.9 10.3 - - + +
200A GLU 3.4 0.2 - - - -
201A SER* 1.3 74.7 - - - +
203A LEU* 1.3 59.4 + - + +
205A HIS* 3.4 3.9 + - - -
206A HIS* 2.9 65.6 + - + +
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Residues in contact with LEU 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 VAL* 2.9 26.9 + - + +
202A MET* 1.3 75.1 - - + +
204A ASN* 1.3 60.2 + - - +
206A HIS* 3.8 5.6 - - + +
207A LEU* 2.9 47.0 + - + +
317A TYR* 3.5 38.4 - - + +
327A ILE* 4.2 13.5 - - + -
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Residues in contact with ASN 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 GLU 2.9 16.2 + - - +
201A SER* 3.6 5.8 - - - +
203A LEU* 1.3 76.1 - - - +
205A HIS* 1.3 62.0 + - + +
207A LEU* 5.0 0.4 - - - +
208A ALA* 2.9 34.4 + - - +
313A ALA 4.9 0.2 - - - +
314A GLY* 3.1 28.1 + - - +
315A HIS* 4.5 2.6 - - - +
316A MET 3.9 2.7 + - - +
317A TYR* 2.9 54.4 + - - +
319A THR* 3.9 12.5 + - + +
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Residues in contact with HIS 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 SER* 2.7 48.6 + - - +
202A MET* 3.9 4.7 - - - +
204A ASN* 1.3 80.7 - - + +
206A HIS* 1.3 64.8 + - + +
208A ALA* 5.2 0.4 - - - -
209A GLY* 2.8 27.3 + - - +
210A LEU* 3.2 7.6 + - - +
319A THR* 6.0 2.2 - - + -
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Residues in contact with HIS 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 MET* 2.9 50.3 + - + +
203A LEU* 4.1 7.4 - - + +
205A HIS* 1.3 81.5 - - + +
207A LEU* 1.3 64.5 + - + +
210A LEU* 3.3 27.0 - - + +
211A LEU* 3.1 35.7 + - + +
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Residues in contact with LEU 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 LEU* 2.9 35.9 + - + +
204A ASN 4.9 0.2 - - - +
206A HIS* 1.3 79.5 - - + +
208A ALA* 1.3 56.6 + - - +
211A LEU* 4.5 3.8 - - + -
212A GLY 3.2 19.1 + - - -
310A PHE* 3.2 43.8 - - + +
313A ALA* 3.5 28.5 - - + +
314A GLY* 3.6 13.9 - - - +
316A MET* 6.3 0.9 - - - -
317A TYR* 4.5 17.7 - - + +
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Residues in contact with ALA 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 ASN 2.9 15.8 + - - +
205A HIS* 5.2 0.4 - - - -
207A LEU* 1.3 78.4 - - - +
209A GLY* 1.3 59.5 + - - +
212A GLY* 3.3 3.3 - - - -
213A LEU* 3.0 24.9 + - - +
310A PHE 3.7 5.4 - - - -
311A LEU* 3.5 29.5 - - + +
314A GLY* 3.8 17.3 - - - +
315A HIS* 4.7 7.4 - - + -
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Residues in contact with GLY 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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205A HIS* 2.8 21.1 + - - +
208A ALA* 1.3 73.9 - - - +
210A LEU* 1.3 64.6 + - - +
213A LEU* 3.2 32.0 - - - +
214A GLY 3.9 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