Contacts of the helix formed by residues 202 - 211 (chain A) in PDB entry 1XZQ
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 ALA 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A GLU 3.7 2.4 + - - -
199A LEU* 3.1 21.5 + - - +
201A LYS* 1.3 76.7 - - - +
203A ASP* 1.3 63.9 + - - +
205A GLY* 3.4 0.9 + - - -
206A ILE* 3.1 30.7 + - - +
381A SER* 3.9 6.5 + - - -
383A ILE* 4.0 21.6 - - + +
389A LYS* 3.6 33.4 - - + -
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Residues in contact with ASP 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 LEU 5.2 2.3 - - - +
200A LYS 4.5 5.6 + - - +
201A LYS 3.5 0.6 - - - -
202A ALA* 1.3 73.7 - - - +
204A ALA* 1.3 67.0 + - - +
206A ILE* 3.1 18.2 + - - +
207A LEU* 3.1 19.4 + - + +
377A ARG* 5.2 7.9 - - - +
386A LEU* 5.9 0.7 - - - +
389A LYS* 3.3 28.4 + - - +
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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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200A LYS 5.0 0.6 + - - -
201A LYS 3.3 5.1 + - - +
203A ASP* 1.3 79.3 - - - +
205A GLY* 1.3 62.1 + - - +
207A LEU* 3.3 7.2 + - - +
208A LEU* 3.2 23.6 + - - +
374A ILE* 3.7 21.0 - - + +
377A ARG* 3.7 30.4 - - + +
378A GLY* 3.2 28.5 - - - +
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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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140A LEU* 3.4 15.5 - - - +
201A LYS 3.0 15.1 + - - -
202A ALA 3.9 1.3 - - - -
204A ALA* 1.3 77.3 - - - +
206A ILE* 1.3 62.1 + - - +
208A LEU* 3.4 1.4 + - - -
209A ASN* 3.2 19.1 + - - +
378A GLY* 3.4 23.2 - - - -
381A SER* 4.0 9.2 - - - -
383A ILE 4.5 4.7 - - - -
384A THR* 4.4 1.3 - - - +
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Residues in contact with ILE 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 ALA 3.1 21.4 + - - +
203A ASP* 3.1 11.9 + - - +
205A GLY* 1.3 74.9 - - - +
207A LEU* 1.3 71.0 + - + +
209A ASN* 3.3 2.8 + - - +
210A ARG* 3.1 44.2 + - - +
383A ILE* 4.6 1.8 - - + -
384A THR* 3.5 7.4 - - - +
385A ASN* 3.4 48.0 - - - +
386A LEU* 3.9 11.9 - - + +
389A LYS* 3.8 24.5 - - + -
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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 ASP* 3.1 14.7 + - + +
204A ALA* 3.3 10.5 + - - +
206A ILE* 1.3 80.8 - - + +
208A LEU* 1.3 57.4 + - - +
210A ARG* 4.8 11.2 - - - +
211A GLY* 2.7 34.2 + - - -
212A LEU* 3.4 25.0 - - + +
293A ASP* 3.5 33.2 - - + +
320A ARG* 4.5 9.0 - - - +
374A ILE* 3.7 30.3 - - + -
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Residues in contact with LEU 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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134A SER* 4.7 4.3 + - - -
136A THR* 4.2 33.3 + - + +
137A SER* 3.7 14.1 - - - +
140A LEU* 4.1 9.9 - - + -
204A ALA 3.2 13.3 + - - +
205A GLY 3.6 6.3 - - - +
206A ILE 3.1 0.2 - - - -
207A LEU* 1.3 77.6 - - - +
209A ASN* 1.3 65.3 + - - +
211A GLY* 3.6 7.2 + - - -
212A LEU* 4.9 1.6 - - + -
259A ILE* 4.5 27.4 - - + -
260A LEU* 4.9 2.9 + - - +
374A ILE* 3.9 25.4 - - + +
375A PHE* 4.7 7.0 - - + +
378A GLY 3.4 31.4 - - - +
379A SER* 4.0 8.5 - - - +
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Residues in contact with ASN 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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128A ASP* 3.5 30.8 + - - +
137A SER* 3.3 33.3 + - - +
140A LEU* 4.4 10.2 - - + +
141A SER* 3.7 16.8 + - - -
205A GLY 3.2 11.7 + - - +
206A ILE 3.3 7.6 + - - +
208A LEU* 1.3 80.8 - - - +
210A ARG* 1.3 68.5 + - + +
260A LEU* 4.8 5.5 - - - +
384A THR* 3.8 23.0 + - - +
385A ASN* 5.5 2.8 - - - +
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Residues in contact with ARG 210 (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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206A ILE* 3.1 31.8 + - + +
207A LEU* 4.8 11.1 - - - +
209A ASN* 1.3 86.0 - - + +
211A GLY* 1.3 59.9 + - - +
260A LEU* 4.1 7.2 - - - +
262A ARG* 2.8 58.5 + - - +
293A ASP* 5.2 0.8 + - - -
384A THR 5.8 0.7 - - - +
385A ASN* 6.2 3.8 - - - -
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Residues in contact with GLY 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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207A LEU* 2.7 17.2 + - - +
208A LEU* 3.6 4.1 + - - -
209A ASN 3.4 2.8 + - - -
210A ARG* 1.3 78.3 + - - +
212A LEU* 1.3 59.9 + - - -
259A ILE* 5.9 0.2 - - - -
260A LEU* 3.1 30.3 - - - -
262A ARG* 2.7 33.7 + - - -
293A ASP* 4.5 0.5 - - - +
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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