Contacts of the helix formed by residues 187 - 198 (chain A) in PDB entry 1XAI
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 GLY 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A ALA 3.3 1.3 + - - +
184A LEU 3.7 2.5 + - - -
185A LEU 3.2 5.4 + - - -
186A ASN* 1.3 80.3 - - - +
188A GLU* 1.3 64.9 + - - -
189A SER* 3.1 5.0 + - - -
190A ALA 3.5 1.0 + - - -
191A THR* 3.1 26.0 + - - -
329A PHE* 3.5 20.2 - - - -
330A GLY* 5.1 1.6 - - - -
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Residues in contact with GLU 188 (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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187A GLY* 1.3 71.4 - - - -
189A SER* 1.3 60.7 + - - +
191A THR* 4.0 0.6 - - - -
192A GLN* 3.0 50.6 + - - +
329A PHE* 3.3 48.8 - - + +
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Residues in contact with SER 189 (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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186A ASN 5.7 1.1 - - - -
187A GLY* 3.1 2.2 - - - -
188A GLU* 1.3 76.2 - - - +
190A ALA* 1.3 56.3 + - - +
192A GLN* 3.4 3.5 + - - +
193A ASP* 2.8 39.3 + - - +
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Residues in contact with ALA 190 (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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183A ALA* 4.0 8.9 - - + +
186A ASN* 3.6 40.8 + - + +
187A GLY* 3.5 2.9 + - - +
189A SER* 1.3 79.0 + - - +
191A THR* 1.3 57.7 + - - +
193A ASP* 3.7 9.5 - - - +
194A ILE* 2.9 31.6 + - - +
213A TYR* 5.1 1.4 - - - -
216A LYS* 4.0 16.8 - - - +
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Residues in contact with THR 191 (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 TYR* 3.7 20.2 - - + +
183A ALA* 3.3 3.2 + - - -
184A LEU* 3.2 25.1 - - + -
187A GLY 3.1 16.1 + - - -
188A GLU 4.0 2.5 - - - -
189A SER 3.2 0.8 - - - -
190A ALA* 1.3 74.2 - - - +
192A GLN* 1.3 55.4 + - + +
193A ASP 3.0 3.8 - - - -
194A ILE* 3.0 9.6 - - - +
195A GLU* 2.7 58.1 + - - +
284A TYR* 4.6 1.8 - - - +
329A PHE* 3.2 24.9 - - + -
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Residues in contact with GLN 192 (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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188A GLU* 3.0 51.0 + - + +
189A SER* 4.1 2.2 - - - +
191A THR* 1.3 82.4 - - + +
193A ASP* 1.3 56.4 + - - +
195A GLU* 3.6 19.5 - - - +
196A GLN* 2.9 30.7 + - - +
283A HIS* 6.1 0.7 - - + -
329A PHE* 5.5 2.1 - - + -
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Residues in contact with ASP 193 (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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189A SER* 2.8 21.7 + - - +
190A ALA* 3.7 9.8 - - - +
191A THR 3.0 0.2 - - - -
192A GLN* 1.3 78.0 - - - +
194A ILE* 1.3 60.2 + - - +
196A GLN* 3.4 17.4 + - - +
197A HIS* 3.1 20.3 + - - +
212A LYS* 3.7 12.0 + - - -
213A TYR* 3.1 25.7 + - - -
216A LYS* 5.8 1.9 - - - -
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Residues in contact with ILE 194 (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 TYR* 3.4 26.2 - - + +
179A VAL* 3.7 40.2 - - + +
180A TYR* 4.0 10.3 - - + -
183A ALA* 3.9 13.2 - - + -
190A ALA 2.9 17.7 + - - +
191A THR* 3.0 22.9 - - - +
193A ASP* 1.3 74.6 - - - +
195A GLU* 1.3 57.9 + - - +
196A GLN 3.1 0.2 - - - -
198A PHE* 2.8 43.0 + - + +
213A TYR* 3.7 33.0 - - + -
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Residues in contact with GLU 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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180A TYR* 3.0 24.4 + - + -
191A THR* 2.7 30.9 + - - +
192A GLN* 3.6 23.3 - - - +
194A ILE* 1.3 76.4 - - - +
196A GLN* 1.3 59.9 + - - +
198A PHE 3.4 14.6 - - - +
199A LYS* 3.7 8.0 - - - +
283A HIS* 2.7 39.5 + - + -
284A TYR* 3.6 4.9 - - - -
287A TYR* 3.7 37.8 - - + -
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Residues in contact with GLN 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 GLN 2.9 22.5 + - - +
193A ASP* 3.5 17.8 + - - +
195A GLU* 1.3 77.0 - - - +
197A HIS* 1.3 59.2 + - - +
199A LYS* 3.0 28.9 - - + +
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Residues in contact with HIS 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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193A ASP 3.1 8.4 + - - +
194A ILE 3.2 3.3 + - - +
196A GLN* 1.3 77.0 - - - +
198A PHE* 1.3 89.1 + + - +
199A LYS* 3.0 15.4 + - - +
203A ILE* 3.4 19.6 - - + +
208A ASN* 2.5 37.8 + - + -
209A GLY* 3.5 12.9 - - - -
213A TYR* 3.6 30.8 + + + +
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Residues in contact with PHE 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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176A TYR* 3.6 31.2 - + + +
194A ILE* 2.8 24.4 + - + +
195A GLU 3.4 3.8 - - - +
197A HIS* 1.3 91.0 - + - +
199A LYS* 1.3 58.9 + - - +
200A ASP 3.6 2.2 - - - -
203A ILE* 3.9 17.0 - - + -
204A LEU* 3.7 26.0 - - + +
207A LEU* 4.7 1.1 - - - -
208A ASN 3.4 24.2 - - - -
210A MET* 3.8 40.2 - - + -
213A TYR* 3.6 18.8 - + - -
287A TYR* 2.8 27.8 + - - +
291A LEU* 3.6 9.1 - - + +
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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