Contacts of the helix formed by residues 198 - 208 (chain A) in PDB entry 2XAT
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 ILE 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A PHE* 3.9 33.7 - - + -
169A ASP* 3.6 37.9 - - - +
172A ASN* 4.1 13.0 - - + -
173A LEU* 3.6 40.8 - - + -
176A MET* 5.4 2.9 - - - -
195A THR 5.2 3.4 - - - +
196A GLY* 3.2 7.9 + - - +
197A ASP* 1.3 72.9 - - - +
199A PRO* 1.3 59.3 - - + +
201A LEU* 3.0 15.6 + - + +
202A TYR* 2.7 34.0 + - + +
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Residues in contact with PRO 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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169A ASP* 3.8 16.2 - - - +
172A ASN* 5.1 6.5 - - - +
196A GLY 4.7 1.8 - - - +
197A ASP* 3.2 14.1 - - - +
198A ILE* 1.3 97.6 - - + +
200A ALA* 1.3 62.1 + - - +
202A TYR* 3.5 8.7 + - + +
203A GLN* 3.2 24.4 + - - +
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Residues in contact with ALA 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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192A LEU* 3.6 22.6 - - + +
197A ASP* 2.7 45.3 + - + +
199A PRO* 1.3 71.2 - - - +
201A LEU* 1.3 62.3 + - - +
203A GLN* 3.0 17.6 + - - +
204A HIS* 3.0 11.3 + - - +
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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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173A LEU* 4.8 14.8 - - + -
176A MET* 3.1 29.6 - - + -
178A TRP* 5.1 2.5 - - + -
181A TRP* 4.8 2.9 - - + -
189A ALA* 4.1 20.9 - - + +
192A LEU* 3.4 45.6 - - + +
193A LEU* 4.0 23.6 - - + +
197A ASP 2.9 11.3 + - - +
198A ILE* 3.3 17.5 - - + +
200A ALA* 1.3 77.0 - - - +
202A TYR* 1.3 55.8 + - - +
204A HIS* 3.4 3.7 + - + +
205A TRP* 2.9 28.9 + - - +
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Residues in contact with TYR 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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172A ASN* 3.6 49.9 + - + -
175A GLU* 4.4 9.1 - - + +
176A MET* 3.9 13.5 - - - -
198A ILE 2.7 19.2 + - - +
199A PRO* 3.6 11.0 - - + +
200A ALA 3.1 0.2 + - - -
201A LEU* 1.3 72.6 - - - +
203A GLN* 1.3 69.1 + - - +
205A TRP* 3.2 39.1 - + - +
206A LYS* 2.9 34.5 + - + +
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Residues in contact with GLN 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 PRO 3.2 11.0 + - - +
200A ALA* 3.0 11.3 + - - +
202A TYR* 1.3 86.2 - - + +
204A HIS* 1.3 66.5 + - - +
205A TRP 2.9 1.6 + - - -
206A LYS* 3.0 13.3 + - - +
207A GLN* 2.7 28.5 + - - +
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Residues in contact with HIS 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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181A TRP* 5.3 3.1 - + - -
185A ASP 4.9 0.4 + - - -
188A ALA* 4.1 15.7 - - + +
189A ALA* 3.3 43.1 + - + +
192A LEU* 3.9 19.0 - - + +
200A ALA 3.0 9.3 + - - +
201A LEU* 3.6 9.6 - - + +
203A GLN* 1.3 77.2 - - - +
205A TRP* 1.3 68.6 + - - +
207A GLN* 3.5 7.6 - - - +
208A ARG* 3.2 32.6 + - + +
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Residues in contact with TRP 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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175A GLU* 3.9 18.6 - - + -
176A MET* 3.3 26.7 - - + -
181A TRP* 3.3 42.0 - + + +
201A LEU 2.9 14.1 + - - +
202A TYR* 3.2 50.5 - + - +
203A GLN 2.9 0.4 + - - -
204A HIS* 1.3 78.6 - - - +
206A LYS* 1.3 80.4 - - + +
207A GLN 2.8 1.7 + - - -
208A ARG* 2.9 17.5 + - + +
209A GLN* 2.9 24.6 + - + +
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Residues in contact with LYS 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 TYR* 2.9 25.6 + - + +
203A GLN* 3.6 15.7 - - - +
205A TRP* 1.3 82.4 - - + +
207A GLN* 1.3 65.5 + - - +
209A GLN* 3.3 19.1 + - - +
210A ALA* 3.7 6.2 + - - +
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Residues in contact with GLN 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 GLN* 2.7 22.0 + - - +
204A HIS* 3.5 9.6 - - - +
205A TRP 2.8 1.8 + - - -
206A LYS* 1.3 71.5 - - - +
208A ARG* 1.3 56.8 + - + +
210A ALA* 2.8 37.4 + - - +
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Residues in contact with ARG 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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184A ALA* 4.5 5.5 + - - +
185A ASP* 2.5 49.9 + - - +
188A ALA* 3.4 30.2 - - - +
204A HIS* 3.2 23.6 + - + +
205A TRP* 2.9 11.9 + - + +
207A GLN* 1.3 75.3 - - + +
209A GLN* 1.3 56.3 + - - +
210A ALA 2.7 25.6 + - - +
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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