Contacts of the helix formed by residues 221 - 228 (chain A) in PDB entry 1UMD
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 ILE 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ASP* 3.7 36.8 - - + -
178A THR* 3.9 28.0 - - + +
201A ALA* 4.0 22.0 - - + -
203A ASN* 4.0 21.1 - - + +
212A TYR* 3.5 16.3 + - + +
220A THR* 1.3 70.8 - - - +
222A ALA* 1.3 67.2 + - - +
223A ASP 3.1 0.4 - - - -
224A LYS* 2.9 31.0 + - + +
262A LEU* 3.4 19.2 - - + +
264A GLU* 2.7 17.4 + - + +
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Residues in contact with ALA 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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11A PHE* 3.2 20.4 - - + -
220A THR* 3.3 7.8 - - - +
221A ILE* 1.3 78.1 - - - +
223A ASP* 1.3 62.8 + - - +
225A ALA* 3.0 17.0 + - - +
232A GLY* 3.8 3.4 - - - +
233A TYR 3.6 41.1 - - - +
234A LEU* 4.0 9.0 - - + +
262A LEU* 4.5 7.9 - - - -
264A GLU* 3.0 11.3 + - - +
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Residues in contact with ASP 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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11A PHE* 4.0 24.5 - - - +
218A SER* 4.7 1.6 - - - -
219A PRO* 2.9 31.9 - - + +
220A THR* 2.9 36.4 + - - +
221A ILE 3.1 0.2 - - - -
222A ALA* 1.3 75.9 - - - +
224A LYS* 1.3 62.5 + - - +
225A ALA 3.1 1.0 + - - -
226A HIS* 3.1 30.2 + - + +
226C HIS* 3.9 20.9 - - + +
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Residues in contact with LYS 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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178A THR* 3.7 21.7 - - - -
179A SER* 5.8 0.2 + - - -
183A TRP* 3.6 27.8 - - + -
216A THR* 2.9 33.1 + - - -
218A SER* 3.4 14.3 + - - +
221A ILE* 2.9 26.2 + - + +
223A ASP* 1.3 77.9 - - - +
225A ALA* 1.3 61.7 + - - +
226A HIS 3.0 0.2 - - - -
227A ALA* 2.9 22.6 + - - +
228A PHE* 3.6 6.2 - - - -
262A LEU* 4.1 1.8 - - + -
184C TYR* 3.0 27.5 + - - +
188C ASN* 3.8 1.6 + - - -
227C ALA* 2.9 41.3 + - + +
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Residues in contact with ALA 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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11A PHE* 3.8 2.2 - - + -
222A ALA 3.0 17.1 + - - +
224A LYS* 1.3 77.7 - - - +
226A HIS* 1.3 62.6 + - - +
228A PHE* 2.9 24.2 + - - +
229A GLY 3.1 9.4 + - - -
230A ILE* 3.2 30.8 + - + +
231A PRO 3.8 4.3 - - - +
232A GLY* 3.5 19.1 - - - +
262A LEU* 3.7 11.2 - - + +
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Residues in contact with HIS 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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11A PHE* 3.4 50.3 - + - +
223A ASP* 3.1 27.2 + - + +
224A LYS 3.0 1.0 - - - -
225A ALA* 1.3 77.2 - - - +
227A ALA* 1.3 60.8 + - - +
228A PHE 3.1 1.5 + - - -
229A GLY* 3.4 10.3 + - - +
230A ILE 5.0 0.7 - - - -
218C SER* 3.7 9.9 - - - -
219C PRO* 5.2 0.9 - - - +
223C ASP* 3.9 14.5 - - + +
226C HIS* 3.6 45.4 + + + -
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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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184A TYR* 4.1 17.0 - - + -
223A ASP 4.6 0.2 + - - -
224A LYS* 2.9 14.9 + - - +
226A HIS* 1.3 78.6 - - - +
228A PHE* 1.3 64.8 + - + +
216C THR* 4.0 0.2 + - - -
218C SER* 3.5 5.1 - - - -
223C ASP 4.4 0.6 + - - -
224C LYS* 2.8 55.5 + - + +
227C ALA* 3.8 20.6 - - + +
228C PHE* 6.5 0.2 - - + -
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Residues in contact with PHE 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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183A TRP* 3.9 28.5 - + - -
184A TYR* 3.3 50.3 - + - -
187A ILE* 3.6 28.5 - - + -
188A ASN* 3.7 25.6 - - + -
191A ALA* 3.7 15.2 - - + +
224A LYS* 3.6 20.6 - - + -
225A ALA* 2.9 13.5 + - - +
227A ALA* 1.3 81.5 - - + +
229A GLY* 1.3 63.7 + - - +
230A ILE* 3.7 12.7 - - + +
262A LEU* 4.8 2.5 - - + -
217C HIS* 3.0 27.8 - - - +
218C SER 3.7 7.9 - - - +
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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