Contacts of the helix formed by residues 221 - 232 (chain A) in PDB entry 1MWT
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 ASP 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A LYS* 3.5 15.9 + - + +
220A MET* 1.3 74.3 - - - +
222A GLU* 1.3 56.1 + - - +
223A TYR* 3.1 38.2 - - + +
224A LEU* 3.0 28.8 + - - +
225A SER* 2.7 37.0 + - - -
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Residues in contact with GLU 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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220A MET 4.6 2.6 - - - +
221A ASP* 1.3 73.8 - - - +
223A TYR* 1.3 76.0 + - + +
225A SER* 3.6 16.7 + - - -
226A ASP* 3.1 36.2 + - - +
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Residues in contact with TYR 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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189A GLU* 6.2 0.2 - - - -
221A ASP* 3.1 26.7 + - + +
222A GLU* 1.3 86.6 - - + +
224A LEU* 1.3 71.6 + - + +
226A ASP* 4.0 2.6 - - - +
227A PHE* 3.2 18.7 + - - +
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Residues in contact with LEU 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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171A ILE* 4.1 10.7 - - + +
189A GLU* 5.1 12.1 - - + +
190A LEU* 4.9 10.1 - - + -
217A VAL* 4.0 28.9 - - + -
219A LYS 5.6 1.3 - - - +
220A MET* 3.3 19.0 - - + +
221A ASP* 3.0 12.2 + - - +
223A TYR* 1.3 95.9 - - + +
225A SER* 1.3 66.6 + - - +
226A ASP 3.0 2.5 - - - -
227A PHE* 2.7 28.7 + - + +
228A ALA* 2.9 14.7 + - - +
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Residues in contact with SER 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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220A MET* 3.8 23.8 + - - +
221A ASP 2.7 27.2 + - - -
222A GLU* 3.6 20.4 + - - -
223A TYR 3.4 0.2 - - - -
224A LEU* 1.3 74.0 - - - +
226A ASP* 1.3 61.2 + - - +
228A ALA* 3.7 6.9 + - - +
229A LYS* 3.3 30.2 + - - +
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Residues in contact with ASP 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 GLU* 3.1 34.3 + - - +
223A TYR 4.0 2.2 - - - +
224A LEU 3.0 0.4 - - - -
225A SER* 1.3 78.9 + - - +
227A PHE* 1.3 60.0 + - - +
228A ALA 3.1 1.6 - - - -
229A LYS* 2.9 16.5 + - + +
230A LYS* 2.9 29.5 + - - +
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Residues in contact with PHE 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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171A ILE* 5.0 6.1 - - + -
186A ILE* 4.0 20.6 - - + -
189A GLU* 3.3 43.7 - - + +
190A LEU* 3.8 27.8 - - + -
223A TYR 3.2 9.4 + - - +
224A LEU* 2.7 29.8 + - + +
226A ASP* 1.3 78.2 - - - +
228A ALA* 1.3 61.0 + - + +
230A LYS* 3.4 8.5 + - + +
231A PHE* 3.2 52.0 - + - -
233A LEU* 3.7 22.7 - - + -
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Residues in contact with ALA 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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171A ILE* 5.1 5.4 - - + -
224A LEU 2.9 9.3 + - - +
225A SER* 3.8 11.0 - - - +
226A ASP 3.1 0.2 - - - -
227A PHE* 1.3 78.3 - - + +
229A LYS* 1.3 56.4 + - + +
231A PHE 3.4 0.7 + - - -
232A HIS* 2.6 32.8 + - - -
233A LEU* 2.7 43.8 + - + +
235A THR* 4.4 19.3 - - + -
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Residues in contact with LYS 229 (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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225A SER* 3.3 23.4 + - - +
226A ASP* 2.9 19.0 + - + +
228A ALA* 1.3 79.6 - - + +
230A LYS* 1.3 63.0 - - - +
232A HIS* 3.4 20.5 + - - +
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Residues in contact with LYS 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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182A ASP* 5.4 2.1 - - - +
226A ASP 2.9 11.5 + - - +
227A PHE* 3.6 13.4 - - + +
228A ALA 3.2 0.2 - - - -
229A LYS* 1.3 80.3 - - - +
231A PHE* 1.3 93.4 + - + +
232A HIS* 3.4 15.8 + - - -
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Residues in contact with PHE 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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177A ASN 3.9 1.6 - - - +
178A VAL* 3.2 17.9 - - + +
182A ASP* 3.2 43.5 - - + +
185A ALA* 3.4 35.2 - - + -
186A ILE* 3.5 19.3 - - + -
227A PHE* 3.2 45.3 - + - -
228A ALA 3.4 2.0 + - - -
230A LYS* 1.3 105.8 - - + +
232A HIS* 1.3 76.3 + - - +
233A LEU* 3.2 15.5 - - + -
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Residues in contact with HIS 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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174A VAL 5.8 0.3 + - - -
177A ASN* 3.7 42.9 + - + +
178A VAL* 3.7 3.3 - - - +
228A ALA 2.6 14.0 + - - -
229A LYS* 3.4 9.8 + - - +
230A LYS 3.3 15.6 + - - -
231A PHE* 1.3 81.0 + - - +
233A LEU* 1.3 64.2 + - - +
234A THR* 4.5 0.2 + - - -
1003A CD 2.2 31.8 - - - -
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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