Contacts of the helix formed by residues 227 - 233 (chain A) in PDB entry 1ULH
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 CYS 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A LEU* 4.3 13.0 - - - -
225A SER 4.0 0.2 + - - -
226A ASP* 1.3 81.3 - - - +
228A ILE* 1.3 62.2 + - - +
229A GLY 3.9 0.7 - - - -
230A LYS* 3.4 48.5 + - - +
231A ILE* 3.5 10.4 + - - +
208B GLN 3.4 11.7 - - - +
209B LYS* 3.2 32.8 - - - +
211B VAL 3.3 8.7 - - - +
212B THR* 3.9 5.8 - - + +
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Residues in contact with ILE 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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227A CYS* 1.3 69.1 - - - +
229A GLY* 1.3 68.3 + - - +
230A LYS 3.1 2.0 - - - -
231A ILE* 3.2 8.7 + - - +
232A SER* 3.0 25.6 + - - -
208B GLN* 3.4 23.6 - - + +
211B VAL* 2.8 39.3 + - + +
212B THR 4.1 3.4 - - - +
213B PHE* 4.0 15.3 - - - +
216B VAL* 4.2 4.9 - - + -
231B ILE* 3.5 34.5 - - + +
232B SER* 3.9 30.4 - - - +
234B PRO* 5.0 4.5 - - + -
235B ALA* 4.3 12.1 - - + +
272B MET* 5.9 0.2 - - - -
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Residues in contact with GLY 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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155A LEU* 3.5 17.3 - - - +
227A CYS* 3.3 0.6 - - - -
228A ILE* 1.3 78.8 - - - +
230A LYS* 1.3 57.5 + - - +
232A SER* 3.3 2.1 + - - -
233A PHE* 2.9 28.9 + - - +
208B GLN* 3.3 44.7 + - - -
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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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155A LEU* 4.0 16.2 - - + -
156A TRP* 3.4 69.6 + - + +
222A PHE* 3.6 12.0 - - + -
226A ASP* 3.4 34.1 + - + +
227A CYS* 3.4 28.1 + - - +
228A ILE 3.1 0.6 - - - -
229A GLY* 1.3 74.4 - - - +
231A ILE* 1.3 65.6 + - - +
233A PHE* 2.9 15.2 + - - +
234A PRO* 3.3 10.6 - - - +
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Residues in contact with ILE 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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213A PHE* 3.4 42.0 - - + -
216A VAL* 3.8 7.1 - - + +
222A PHE* 4.1 18.2 - - + -
223A THR 4.3 6.3 - - - +
226A ASP* 4.3 6.3 - - + +
227A CYS 3.5 14.7 + - - +
228A ILE 3.2 7.6 + - - +
230A LYS* 1.3 78.3 - - - +
232A SER* 1.3 62.6 + - - +
234A PRO* 3.6 8.8 - - - +
213B PHE* 3.5 28.3 - - + -
228B ILE* 3.7 22.9 - - + +
231B ILE* 3.7 31.6 - - + -
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Residues in contact with SER 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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208A GLN* 2.7 33.6 + - - -
228A ILE 3.0 13.6 + - - -
229A GLY* 3.6 3.1 - - - -
231A ILE* 1.3 79.0 - - - +
233A PHE* 1.3 63.6 + - - +
234A PRO* 3.3 2.5 - - - -
235A ALA* 3.2 18.4 + - - +
236A ILE* 4.3 3.0 + - - +
208B GLN* 5.3 3.1 - - - -
228B ILE* 3.6 19.8 + - - +
232B SER* 3.3 22.7 + - - -
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Residues in contact with PHE 233 (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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149A THR* 3.7 9.9 - - + -
151A ASP* 3.3 28.3 - - - -
152A GLU* 3.3 41.3 - - + -
155A LEU* 4.3 13.7 - - + -
156A TRP* 4.1 19.1 - + + -
190A ASP* 3.6 15.3 - - - -
229A GLY 2.9 13.5 + - - +
230A LYS 2.9 14.1 + - - +
232A SER* 1.3 76.8 - - - +
234A PRO* 1.4 55.4 - - + +
236A ILE* 2.7 46.1 + - + +
237A GLN* 3.3 40.0 + - + -
201B TYR* 5.4 0.4 - - - -
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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