Contacts of the helix formed by residues 220 - 233 (chain A) in PDB entry 1A0P
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 ARG 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A GLU* 3.3 45.3 + - - +
19A LYS* 4.8 5.5 - - - +
149A VAL* 3.8 32.1 - - + +
150A SER* 4.3 22.2 + - - +
153A VAL* 4.0 6.7 - - + +
219A THR* 1.3 75.8 - - - +
221A GLN* 1.3 60.5 + - - +
223A PHE 3.5 0.9 + - - -
224A TRP* 2.9 31.2 + - + +
243A PRO* 6.4 2.5 - - - -
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Residues in contact with GLN 221 (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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219A THR* 3.7 7.9 + - - +
220A ARG* 1.3 82.2 - - + +
222A THR* 1.3 70.3 + - + +
224A TRP* 3.1 15.2 + - - +
225A HIS* 3.3 33.6 + - + +
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Residues in contact with THR 222 (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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218A MET* 3.5 22.2 - - - +
219A THR* 2.8 50.3 + - + +
221A GLN* 1.3 78.2 - - + +
223A PHE* 1.3 59.5 + - - +
225A HIS* 3.6 24.9 - - + +
226A ARG* 3.9 10.7 - - - +
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Residues in contact with PHE 223 (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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135A ASP* 3.7 21.8 - - + -
138A MET* 3.3 57.2 - - + -
139A LEU* 3.6 20.6 - - + -
142A LEU* 4.0 10.8 - - + -
149A VAL* 3.8 20.2 - - + -
152A LEU* 4.5 0.7 - - + -
153A VAL* 4.4 2.5 - - + -
218A MET* 4.0 13.0 - - + -
219A THR 2.9 14.2 + - - +
220A ARG 4.2 2.7 - - - +
222A THR* 1.3 74.1 + - - +
224A TRP* 1.3 67.1 + - - +
225A HIS 3.1 2.0 - - - -
226A ARG* 3.2 15.9 + - + +
227A ILE* 3.1 46.1 + - + +
230A TYR* 6.0 0.2 - + - -
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Residues in contact with TRP 224 (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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149A VAL* 4.6 11.2 - - + -
220A ARG* 2.9 21.0 + - + +
221A GLN* 3.1 7.5 + - - +
223A PHE* 1.3 76.2 - - - +
225A HIS* 1.3 66.0 + + - +
227A ILE* 2.8 38.4 + - + +
228A LYS* 2.9 41.4 + - + +
241A LEU* 3.3 45.9 + - + -
242A SER* 3.5 10.1 - - - -
243A PRO* 3.4 39.9 - - + +
246A LEU* 3.8 24.0 - - + -
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Residues in contact with HIS 225 (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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221A GLN* 3.3 35.1 + - + +
222A THR* 3.6 20.0 - - + +
224A TRP* 1.3 76.3 - + - +
226A ARG* 1.3 63.8 + - + +
228A LYS* 3.0 22.9 + - - +
229A HIS* 3.0 22.2 + - - +
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Residues in contact with ARG 226 (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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131A LEU* 4.1 13.8 - - - +
132A GLU* 3.9 13.9 + - - +
134A ARG* 3.5 16.3 - - - +
135A ASP* 2.5 33.3 + - - +
218A MET* 4.4 1.8 - - + -
222A THR 3.9 15.0 - - - +
223A PHE* 3.2 17.9 + - + +
225A HIS* 1.3 74.7 - - - +
227A ILE* 1.3 60.3 + - - +
229A HIS* 3.3 24.7 + - - +
230A TYR* 2.8 64.7 + - + -
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Residues in contact with ILE 227 (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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121A LEU* 4.0 7.5 - - + +
139A LEU* 4.0 16.8 - - + -
142A LEU* 4.3 2.9 - - + -
149A VAL* 4.2 8.5 - - + -
223A PHE* 3.1 42.5 + - + +
224A TRP* 2.8 47.0 + - + +
226A ARG* 1.3 75.3 - - - +
228A LYS* 1.3 51.5 + - - +
230A TYR* 3.2 8.4 + - + +
231A ALA* 2.7 32.6 + - - +
241A LEU* 4.2 9.9 - - + -
246A LEU* 3.7 28.9 - - + -
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Residues in contact with LYS 228 (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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224A TRP* 2.9 48.8 + - + +
225A HIS* 3.0 23.7 + - - +
227A ILE* 1.3 72.2 - - + +
229A HIS* 1.4 55.3 + - - +
231A ALA* 2.6 11.5 + - - -
232A VAL* 2.6 40.4 + - + +
238A SER* 3.2 43.3 - - - +
239A GLU* 4.1 15.2 - - - +
241A LEU* 5.9 0.7 - - + -
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Residues in contact with HIS 229 (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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132A GLU* 4.0 13.1 + - - -
225A HIS 3.0 12.0 + - - +
226A ARG* 3.6 26.5 + - - +
228A LYS* 1.4 77.2 - - - +
230A TYR* 1.3 91.4 + + - +
232A VAL* 3.4 7.1 + - - +
233A LEU* 3.2 41.7 + - + +
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Residues in contact with TYR 230 (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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121A LEU* 3.9 26.4 - - + +
124A ALA* 3.7 18.1 - - + +
125A PRO* 3.6 34.8 - - + -
132A GLU* 3.1 25.3 - - - +
135A ASP* 2.6 46.0 + - + -
139A LEU* 4.0 10.8 - - + -
226A ARG* 2.8 52.9 + - + +
227A ILE* 3.9 5.4 - - + +
229A HIS* 1.3 87.5 - + - +
231A ALA* 1.4 62.1 + - - +
233A LEU* 3.3 4.4 + - + +
234A ALA* 3.1 22.3 + - - +
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Residues in contact with ALA 231 (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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121A LEU* 3.6 15.9 - - + +
227A ILE 2.7 14.0 + - - +
228A LYS* 2.6 20.4 + - - +
230A TYR* 1.4 68.0 - - - +
232A VAL* 1.3 66.1 + - - +
234A ALA* 2.9 12.3 + - - -
236A ILE* 3.0 45.4 + - + +
238A SER* 4.3 9.0 - - - -
241A LEU* 4.1 11.2 - - + -
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Residues in contact with VAL 232 (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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228A LYS* 2.6 19.7 + - + +
229A HIS* 3.6 7.4 - - - +
231A ALA* 1.3 71.4 - - - +
233A LEU* 1.3 70.3 + - + +
235A GLY* 3.0 16.3 + - - -
236A ILE 4.0 6.9 + - - -
238A SER* 3.3 28.5 - - - +
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Residues in contact with LEU 233 (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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120A ARG* 5.3 2.1 - - - -
124A ALA* 4.2 25.8 - - + +
126A LEU* 6.5 0.9 - - + -
132A GLU* 6.0 0.2 - - - +
229A HIS* 3.2 47.6 + - + +
230A TYR* 3.9 5.2 - - + +
231A ALA 3.3 0.2 - - - -
232A VAL* 1.3 82.9 - - + +
234A ALA* 1.3 58.3 + - - +
235A GLY 3.2 1.3 + - - -
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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