Contacts of the helix formed by residues 221 - 228 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175C ASP* 3.8 36.6 - - + -
178C THR* 3.9 30.3 - - + +
183C TRP* 4.8 0.2 - - + -
201C ALA* 4.0 19.3 - - + -
203C ASN* 4.0 20.4 - - + -
212C TYR* 3.9 16.8 - - + +
220C THR* 1.3 71.6 - - - +
222C ALA* 1.3 67.0 + - - +
223C ASP 3.1 0.4 - - - -
224C LYS* 2.9 31.2 + - + +
262C LEU* 3.4 20.4 - - + +
264C GLU* 2.8 16.5 + - + +
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Residues in contact with ALA 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C PHE* 3.2 14.5 - - + -
220C THR* 3.3 7.4 - - - +
221C ILE* 1.3 77.7 - - - +
223C ASP* 1.3 60.8 + - - +
225C ALA* 3.0 24.4 + - - +
232C GLY* 3.8 2.8 - - - +
233C TYR 3.6 41.1 - - - +
234C LEU* 4.0 9.2 - - + +
262C LEU* 4.5 7.9 - - - -
264C GLU* 3.0 12.9 + - + +
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Residues in contact with ASP 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A HIS* 3.9 21.2 - - + +
11C PHE* 4.0 23.7 - - - +
218C SER* 4.7 1.3 - - - -
219C PRO* 3.0 30.7 - - + +
220C THR* 2.8 36.6 + - - +
221C ILE 3.1 0.2 - - - -
222C ALA* 1.3 76.5 - - - +
224C LYS* 1.3 61.3 + - - +
225C ALA 3.0 1.7 + - - -
226C HIS* 3.1 31.2 + - + +
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Residues in contact with LYS 224 (chain C).
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* 3.0 26.6 + - - +
188A ASN* 3.9 2.6 + - - -
227A ALA* 2.8 42.6 + - + +
178C THR* 3.8 20.6 - - - -
183C TRP* 3.7 26.9 - - + -
216C THR* 2.7 32.7 + - - -
218C SER* 3.4 16.3 + - - +
220C THR 4.2 0.2 - - - +
221C ILE* 2.9 26.2 + - + +
223C ASP* 1.3 77.8 - - - +
225C ALA* 1.3 62.0 + - - +
226C HIS 3.1 0.2 - - - -
227C ALA* 3.0 22.4 + - - +
228C PHE* 3.6 7.0 - - - -
262C LEU* 4.2 1.8 - - + -
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Residues in contact with ALA 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C PHE* 3.8 2.2 - - + -
222C ALA 3.0 16.8 + - - +
224C LYS* 1.3 78.1 - - - +
226C HIS* 1.3 61.6 + - - +
227C ALA 3.1 0.4 - - - -
228C PHE* 3.0 23.3 + - - +
229C GLY 3.1 9.2 + - - -
230C ILE* 3.3 31.6 + - + +
231C PRO 3.8 3.8 - - - +
232C GLY* 3.6 18.6 - - - +
262C LEU* 3.8 12.5 - - + +
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Residues in contact with HIS 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A SER* 3.6 9.7 - - - -
219A PRO* 5.1 1.2 - - - +
223A ASP* 3.9 12.8 - - + +
226A HIS* 3.6 45.3 + + + -
11C PHE* 3.4 49.5 - + - +
223C ASP* 3.1 25.1 + - + +
224C LYS 3.1 0.8 - - - -
225C ALA* 1.3 77.8 - - - +
227C ALA* 1.3 60.4 + - - +
228C PHE 3.1 1.3 + - - -
229C GLY* 3.3 11.8 + - - +
230C ILE 5.0 0.2 - - - -
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Residues in contact with ALA 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A THR* 4.0 0.3 + - - -
218A SER* 3.4 5.6 - - - -
223A ASP 4.3 0.8 + - - -
224A LYS* 2.9 54.2 + - + +
227A ALA* 3.8 22.4 - - + +
184C TYR* 4.3 15.5 - - + -
223C ASP 4.6 0.2 + - - -
224C LYS 3.0 14.3 + - - +
226C HIS* 1.3 78.4 - - - +
228C PHE* 1.3 64.9 + - + +
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Residues in contact with PHE 228 (chain C).
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* 6.0 0.2 - + - -
216A THR* 5.0 1.6 - - - -
217A HIS* 3.0 28.5 - - - +
218A SER 3.7 7.9 - - - +
183C TRP* 3.9 27.1 - + - -
184C TYR* 3.4 50.5 - + - -
187C ILE* 3.5 28.5 - - + -
188C ASN* 3.6 25.1 - - + -
191C ALA* 3.9 15.5 - - + -
224C LYS* 3.6 20.9 - - + -
225C ALA* 3.0 13.1 + - - +
227C ALA* 1.3 82.8 - - + +
229C GLY* 1.3 62.6 + - - +
230C ILE* 3.4 12.3 + - + +
262C LEU* 4.9 2.2 - - + -
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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