Contacts of the helix formed by residues 218 - 230 (chain A) in PDB entry 1SA4
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 ASN 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A LEU* 6.2 3.6 - - + -
215A LEU 4.8 2.0 + - - -
216A TRP 3.0 1.8 + - - -
217A ASP* 1.3 86.8 - - - +
219A GLU* 1.3 65.0 + - - +
220A LEU 3.4 2.7 - - - -
221A GLN* 2.9 36.3 + - + +
222A TYR* 3.2 19.1 + - - +
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Residues in contact with GLU 219 (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 LEU* 4.7 3.6 - - - +
206A ARG* 2.7 46.4 + - - -
210A ILE* 3.4 24.0 - - + +
215A LEU 4.7 2.8 + - - +
216A TRP* 3.2 15.9 + - - +
218A ASN* 1.3 75.9 - - - +
220A LEU* 1.3 60.8 + - - +
222A TYR* 3.1 9.8 + - - +
223A VAL* 2.8 27.9 + - - +
239A GLN* 2.8 25.1 - - + +
243A VAL* 3.3 29.2 - - + -
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Residues in contact with LEU 220 (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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216A TRP 4.6 1.4 + - - +
217A ASP 5.3 1.3 + - - +
218A ASN 3.4 0.8 - - - -
219A GLU* 1.3 78.3 - - - +
221A GLN* 1.3 59.4 + - + +
223A VAL* 3.3 8.5 + - + +
224A ASP* 2.9 39.9 + - - +
240A ARG* 3.8 40.4 - - + +
243A VAL* 4.2 18.5 - - + +
244A ILE* 4.6 13.7 - - + -
258A ARG* 4.2 26.5 - - - +
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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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217A ASP 3.7 6.8 + - - +
218A ASN* 2.9 45.2 + - + +
219A GLU 3.2 0.4 - - - -
220A LEU* 1.3 75.9 - - + +
222A TYR* 1.3 65.8 + - - +
224A ASP* 3.3 10.6 + - - +
225A GLN* 3.0 22.3 + - - +
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Residues in contact with TYR 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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190A ALA* 3.6 26.3 + - + +
193A LEU* 3.5 23.1 - - + +
203A TRP* 3.9 11.9 - + - -
206A ARG* 3.2 43.3 - - - +
218A ASN 3.2 8.2 + - - +
219A GLU* 3.1 23.0 + - - +
221A GLN* 1.3 77.5 - - - +
223A VAL* 1.3 66.9 + - + +
225A GLN* 3.2 10.3 + - + +
226A LEU* 3.1 58.0 + - + +
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Residues in contact with VAL 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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203A TRP* 5.7 0.7 - - + -
219A GLU* 2.8 21.9 + - + +
220A LEU* 3.5 11.7 - - - +
222A TYR* 1.3 78.8 - - + +
224A ASP* 1.3 62.3 + - - +
226A LEU* 3.2 2.2 + - - -
227A LEU* 3.0 24.7 + - + +
236A VAL* 3.4 25.0 - - + +
239A GLN* 3.7 36.3 - - + +
240A ARG* 3.8 43.7 - - + +
243A VAL* 4.5 0.9 - - + -
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Residues in contact with ASP 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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220A LEU* 2.9 30.8 + - - +
221A GLN* 3.6 8.6 - - - +
222A TYR 3.3 0.2 - - - -
223A VAL* 1.3 75.5 - - - +
225A GLN* 1.3 62.6 + - - +
227A LEU* 3.5 5.8 + - - +
228A LYS* 3.1 22.0 + - - +
240A ARG* 2.8 31.4 + - - -
262A TYR* 4.0 13.0 + - - +
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Residues in contact with GLN 225 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A GLN 3.0 13.4 + - - +
222A TYR* 3.2 14.6 + - + +
224A ASP* 1.3 77.0 - - - +
226A LEU* 1.3 65.8 + - + +
228A LYS* 3.2 22.1 + - - +
229A GLU* 3.1 47.9 + - - +
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Residues in contact with LEU 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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193A LEU* 4.9 5.8 - - + -
197A ALA* 5.3 8.3 - - + +
203A TRP* 3.7 36.6 - - + -
222A TYR* 3.1 46.8 + - + +
223A VAL* 3.8 2.2 - - - +
225A GLN* 1.3 75.7 - - + +
227A LEU* 1.3 60.5 + - - +
229A GLU* 3.2 28.6 + - - +
230A ASP* 2.9 30.0 + - - +
233A ASN* 5.1 5.1 + - - +
236A VAL* 3.7 19.5 - - + +
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Residues in contact with LEU 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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223A VAL* 3.0 25.9 + - + +
224A ASP* 3.8 4.0 - - - +
226A LEU* 1.3 74.3 - - - +
228A LYS* 1.3 62.2 + - - +
230A ASP 3.9 4.5 - - - +
231A VAL* 2.9 42.6 + - + +
236A VAL* 3.5 19.3 - - + +
237A TRP* 3.5 42.6 - - + +
240A ARG* 3.9 22.7 - - - +
262A TYR* 3.1 35.7 - - + +
266A MET* 6.0 1.1 - - - -
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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 ASP 3.1 13.9 + - - +
225A GLN* 3.4 27.8 - - - +
227A LEU* 1.3 79.7 - - - +
229A GLU* 1.3 61.9 + - + +
230A ASP* 4.7 0.2 - - - -
231A VAL 5.0 0.3 + - - -
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Residues in contact with GLU 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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194A ASN* 5.3 4.2 - - - +
197A ALA* 6.2 0.3 - - - +
225A GLN* 3.1 42.0 + - - +
226A LEU* 3.5 26.5 - - - +
227A LEU 3.2 0.2 - - - -
228A LYS* 1.3 80.9 - - + +
230A ASP* 1.3 62.3 + - + +
42B THR* 4.2 12.5 - - - +
43B VAL* 5.4 1.2 + - - +
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Residues in contact with ASP 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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197A ALA* 6.3 1.3 - - + -
198A LYS* 4.7 3.6 - - - -
226A LEU 2.9 12.9 + - - +
227A LEU* 3.3 5.2 - - - +
229A GLU* 1.3 80.2 - - + +
231A VAL* 1.3 58.1 + - - +
232A ARG* 2.9 20.8 + - - +
233A ASN* 3.0 29.1 + - + +
42B THR* 2.8 28.3 + - - -
43B VAL* 3.8 11.9 + - + +
44B THR* 2.6 34.1 + - - -
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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