Contacts of the helix formed by residues 217 - 227 (chain A) in PDB entry 1E0W
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 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A ASN* 3.1 29.9 + - - +
177A TRP* 3.2 25.9 + - + +
178A THR* 4.0 15.2 - - - +
215A ASN* 2.9 26.5 + - - +
216A SER* 1.3 75.3 + - - +
218A PHE* 1.3 65.2 + - - +
219A ARG 3.2 0.9 - - - +
220A THR* 3.0 25.5 + - - +
221A THR* 3.0 12.6 + - - -
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Residues in contact with PHE 218 (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* 3.5 48.9 - - + +
204A PHE* 4.3 9.0 - + + -
206A SER* 3.8 18.6 - - - -
208A PHE* 4.5 7.0 - + + -
214A TYR* 4.0 12.1 - + + -
215A ASN 3.0 17.2 + - - +
216A SER 3.1 0.4 - - - -
217A ASN* 1.3 79.2 + - - +
219A ARG* 1.3 61.3 + - - +
221A THR* 3.2 2.4 + - - -
222A LEU* 3.0 53.0 + - + +
234A ILE* 3.9 25.6 - - + -
250A VAL* 4.3 12.1 - - + -
253A ASP* 3.7 21.5 - - + +
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Residues in contact with ARG 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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216A SER 3.5 10.3 + - - +
217A ASN 3.2 1.2 - - - -
218A PHE* 1.3 77.0 - - - +
220A THR* 1.3 58.0 + - - +
222A LEU* 3.4 4.8 + - - +
223A GLN* 3.0 52.5 + - - +
249A ASN 5.0 0.4 + - - -
252A ASN* 3.8 23.6 + - - +
253A ASP* 2.9 44.5 + - - +
256A ALA* 3.7 25.6 - - - +
257A VAL* 4.4 11.9 - - + -
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Residues in contact with THR 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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177A TRP* 4.2 18.2 - - + +
216A SER 5.2 0.3 + - - -
217A ASN* 3.0 22.8 + - + +
219A ARG* 1.3 75.7 - - - +
221A THR* 1.3 66.6 + - - +
223A GLN* 3.4 15.4 + - - +
224A ASN* 2.9 50.4 + - - +
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Residues in contact with THR 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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174A VAL 3.8 12.1 - - - +
175A GLU 2.9 20.3 + - - +
177A TRP* 3.2 31.7 + - + +
182A THR* 4.1 5.4 - - + -
204A PHE* 3.6 30.5 - - + -
217A ASN 3.0 5.7 + - - -
218A PHE* 3.4 9.4 - - + -
220A THR* 1.3 77.3 - - - +
222A LEU* 1.3 62.6 + - - +
224A ASN* 3.9 0.3 - - - -
225A PHE* 3.1 41.5 + - + -
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Residues in contact with LEU 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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204A PHE* 3.7 32.5 - - + -
218A PHE* 3.0 50.2 + - + +
219A ARG* 3.8 4.7 - - - +
221A THR* 1.3 76.9 - - - +
223A GLN* 1.3 62.3 + - - +
225A PHE* 3.5 1.5 + - - -
226A ALA* 3.0 24.3 + - - +
232A VAL* 4.0 23.7 - - + +
233A ALA 5.7 0.4 - - - +
234A ILE* 4.8 8.1 - - + -
253A ASP* 4.1 29.4 - - + +
254A CYS* 4.3 8.3 - - - +
257A VAL* 4.0 13.5 - - + +
260A CYS* 5.0 4.9 - - - -
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Residues in contact with GLN 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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219A ARG* 3.0 38.8 + - - +
220A THR* 3.8 18.3 + - - +
222A LEU* 1.3 76.1 - - - +
224A ASN* 1.3 63.1 + - - +
226A ALA* 3.4 7.7 + - - +
227A ALA* 3.1 28.6 + - - +
256A ALA* 5.1 4.6 - - - +
257A VAL* 3.9 19.6 - - + +
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Residues in contact with ASN 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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177A TRP* 3.2 50.9 - - + +
186A TYR* 3.8 17.5 + - + +
220A THR* 2.9 33.2 + - - +
221A THR 3.3 0.6 + - - +
223A GLN* 1.3 81.8 + - - +
225A PHE* 1.3 61.7 + - - +
227A ALA* 3.5 16.9 + - - +
228A LEU* 3.7 5.4 + - - +
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Residues in contact with PHE 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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177A TRP* 4.3 4.7 - + - -
182A THR* 3.9 12.6 - - + -
185A MET* 3.5 33.7 - - + -
186A TYR* 3.5 49.6 - + + -
189A VAL* 4.3 7.4 - - + -
202A VAL* 4.2 17.0 - - + -
204A PHE* 3.8 11.7 - + + -
221A THR* 3.1 42.8 + - + +
222A LEU 4.0 2.9 - - - +
224A ASN* 1.3 74.0 - - - +
226A ALA* 1.3 65.1 + - - +
228A LEU* 3.0 27.3 + - + +
230A VAL* 3.3 20.0 - - + +
232A VAL* 4.1 14.6 - - + -
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Residues in contact with ALA 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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222A LEU 3.0 18.5 + - - +
223A GLN* 3.4 6.0 + - - +
225A PHE* 1.3 75.0 - - - +
227A ALA* 1.3 57.0 + - - +
229A GLY* 3.0 21.3 + - - -
230A VAL 3.4 18.5 - - - +
232A VAL* 4.2 5.5 - - + +
257A VAL* 4.3 11.9 - - + -
258A SER* 6.1 0.2 - - - +
259A ARG* 4.1 28.6 + - + +
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Residues in contact with ALA 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 GLN 3.1 17.0 + - - +
224A ASN* 3.7 9.9 - - - +
225A PHE 3.2 0.4 - - - -
226A ALA* 1.3 74.5 - - - +
228A LEU* 1.3 61.1 + - + +
229A GLY 3.4 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