Contacts of the helix formed by residues 227 - 245 (chain A) in PDB entry 1HYH
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 LEU 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A TRP* 3.3 50.4 - - + +
216A ILE* 3.9 40.6 - - + +
217A VAL* 4.2 19.1 - - + -
219A LEU 5.3 3.4 - - - +
225A ILE* 3.4 16.1 + - + +
226A ASP* 1.3 72.4 - - - +
228A ALA* 1.3 51.7 + - - +
230A ILE* 3.2 13.6 + - + +
231A GLU 2.6 30.0 + - - -
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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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226A ASP 3.2 1.0 - - - -
227A LEU* 1.3 74.7 - - - +
229A ALA* 1.3 55.5 + - - +
231A GLU* 3.5 12.8 - - - +
232A GLU* 2.7 34.9 + - - +
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Residues in contact with ALA 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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226A ASP* 2.9 19.3 + - - +
228A ALA* 1.3 73.0 - - - +
230A ILE* 1.4 62.0 + - + +
232A GLU* 3.2 12.4 + - - +
233A GLU* 2.9 29.8 + - - +
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Residues in contact with ILE 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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175A MET* 4.8 2.0 - - + +
178A ALA* 3.8 17.5 - - + +
179A VAL* 3.5 34.1 - - + +
182A ALA* 4.3 25.6 - - + -
183A PHE* 5.0 1.1 - - + -
206A TRP* 3.7 9.9 - - + -
216A ILE* 4.6 4.9 - - + -
225A ILE* 4.4 13.5 - - + -
226A ASP 3.1 12.6 + - - +
227A LEU* 3.4 24.9 - - + +
229A ALA* 1.4 78.4 - - + +
231A GLU* 1.3 62.7 + - - +
232A GLU 3.2 0.2 + - - -
233A GLU* 3.2 7.9 + - - +
234A ALA* 2.9 21.6 + - + +
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Residues in contact with GLU 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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203A PHE* 4.2 8.3 - - - +
204A VAL* 3.3 37.2 + - + +
206A TRP* 3.2 28.2 + - + -
227A LEU 2.6 20.3 + - - +
228A ALA* 3.6 12.4 - - - +
230A ILE* 1.3 74.1 - - - +
232A GLU* 1.3 55.5 + - - +
234A ALA* 3.3 6.0 + - - +
235A ARG* 2.8 36.1 + - + +
310A LYS* 5.0 6.5 + - - -
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Residues in contact with GLU 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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228A ALA 2.7 20.8 + - - +
229A ALA* 3.2 12.0 + - - +
231A GLU* 1.3 70.3 - - - +
233A GLU* 1.3 59.0 + - - +
235A ARG* 4.6 4.3 - - - -
236A LYS* 2.6 79.0 + - + +
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Residues in contact with GLU 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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177A ARG* 3.5 27.3 + - - +
178A ALA* 3.9 17.9 - - + -
181A GLU* 4.8 8.1 - - - +
229A ALA 2.9 15.4 + - - +
230A ILE* 3.5 7.4 - - - +
232A GLU* 1.3 76.0 - - - +
234A ALA* 1.3 57.6 + - - +
236A LYS* 5.1 1.1 - - - -
237A GLY* 3.0 32.0 + - - +
64C ILE* 5.3 5.9 - - - +
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Residues in contact with ALA 234 (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 ASP 5.1 1.8 - - - +
174A ARG* 3.9 35.6 - - + +
175A MET* 3.9 33.2 - - + +
177A ARG* 4.9 0.2 - - - +
178A ALA* 4.3 1.3 - - + +
194A ASN* 5.5 2.9 - - - +
202A GLN* 5.9 0.4 - - - -
204A VAL* 5.1 5.4 - - + -
230A ILE* 2.9 14.8 + - + +
231A GLU* 3.5 11.9 - - - +
233A GLU* 1.3 78.9 - - - +
235A ARG* 1.3 62.1 + - - +
237A GLY 3.6 4.7 + - - -
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Residues in contact with ARG 235 (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 ARG* 5.9 0.2 + - - -
202A GLN* 4.8 17.2 - - - +
231A GLU* 2.8 24.7 + - + +
232A GLU* 4.1 2.5 - - - +
234A ALA* 1.3 74.5 - - - +
236A LYS* 1.3 66.8 + - + +
238A GLY* 4.2 5.4 + - - -
239A PHE* 3.7 19.0 - - + -
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Residues in contact with LYS 236 (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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232A GLU* 2.6 62.4 + - + +
233A GLU* 5.0 1.3 - - - +
235A ARG* 1.3 78.2 - - + +
237A GLY* 1.3 57.7 + - - +
238A GLY 3.2 2.9 - - - -
239A PHE* 2.9 46.3 + - + +
240A THR* 3.1 15.2 + - - +
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Residues in contact with GLY 237 (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 ARG* 4.7 4.7 - - - -
177A ARG* 4.1 13.9 - - - -
233A GLU* 3.0 25.6 + - - -
234A ALA 4.0 2.9 - - - -
235A ARG 3.4 1.0 - - - -
236A LYS* 1.3 76.2 - - - +
238A GLY* 1.3 58.5 + - - +
240A THR* 3.4 12.0 - - - -
241A VAL* 3.3 26.0 + - - +
64C ILE* 4.4 3.9 - - - +
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Residues in contact with GLY 238 (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 ARG* 3.6 36.5 - - - +
234A ALA 4.3 2.4 + - - -
235A ARG 4.2 6.5 + - - -
236A LYS 3.2 1.2 - - - -
237A GLY* 1.3 73.1 - - - +
239A PHE* 1.4 68.0 + - - +
241A VAL* 3.5 5.0 + - - +
242A LEU* 3.3 22.2 + - - +
248A THR* 3.9 5.9 - - - +
331A SO4 4.6 6.3 + - - -
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Residues in contact with PHE 239 (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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199A GLY* 6.6 0.2 - - - -
235A ARG* 3.7 19.5 - - + -
236A LYS* 2.9 40.6 + - + +
238A GLY* 1.4 76.2 - - - +
240A THR* 1.3 60.7 + - - +
242A LEU* 4.5 14.1 - - + -
243A ASN* 2.7 48.4 + - - +
331A SO4 5.9 2.9 - - - -
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Residues in contact with THR 240 (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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236A LYS* 3.1 14.9 + - - +
237A GLY* 3.4 14.8 + - - -
239A PHE* 1.3 75.9 - - - +
241A VAL* 1.3 56.8 + - - +
243A ASN* 3.5 6.3 - - - +
244A GLY* 2.8 26.9 + - - -
60C LYS* 5.6 5.4 - - + -
61C ALA* 4.6 3.6 - - - +
64C ILE* 4.0 24.5 - - + -
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Residues in contact with VAL 241 (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 ARG* 5.4 1.1 - - - +
237A GLY 3.3 14.7 + - - +
238A GLY* 3.9 7.6 - - - +
239A PHE 3.2 0.4 - - - -
240A THR* 1.3 75.7 - - - +
242A LEU* 1.3 61.8 + - - +
244A GLY* 3.2 1.4 + - - -
245A LYS* 3.1 40.1 + - - +
247A TYR 3.6 14.6 - - - +
248A THR* 3.6 18.2 - - + -
61C ALA* 3.8 23.4 - - + +
64C ILE* 3.5 28.0 - - + -
65C ASP* 4.0 12.1 - - - +
68C ASP* 4.8 4.7 - - - +
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Residues in contact with LEU 242 (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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100A ILE* 4.2 15.3 - - + -
103A GLN* 4.1 26.9 - - + +
104A GLN* 4.3 14.1 - - + -
238A GLY 3.3 15.3 + - - +
239A PHE* 3.9 15.3 - - + +
241A VAL* 1.3 77.5 - - - +
243A ASN* 1.3 61.8 - - - +
246A GLY* 2.6 56.1 + - - +
247A TYR* 3.8 16.1 + - - +
248A THR* 4.1 6.7 - - + +
331A SO4 4.8 11.0 - - - +
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Residues in contact with ASN 243 (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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239A PHE* 2.7 43.3 + - - +
240A THR* 3.5 6.1 - - - +
242A LEU* 1.3 80.3 - - - +
244A GLY* 1.3 59.8 + - - +
246A GLY 4.5 0.9 + - - -
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Residues in contact with GLY 244 (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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240A THR 2.8 19.5 + - - -
241A VAL 3.2 1.5 + - - -
243A ASN* 1.3 75.3 - - - +
245A LYS* 1.4 59.6 + - - +
55C ASN* 5.3 1.7 + - - -
57C ALA* 3.9 19.6 - - - +
58C LYS* 3.7 18.2 + - - +
61C ALA* 3.9 13.0 - - - -
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Residues in contact with LYS 245 (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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241A VAL* 3.1 16.5 + - - +
244A GLY* 1.4 75.0 - - - +
246A GLY* 1.3 58.8 + - - +
247A TYR* 3.4 64.4 + - + +
249A SER* 3.8 3.2 + - - -
250A TYR* 3.5 14.1 - - - -
58C LYS* 3.6 24.0 - - + -
61C ALA* 4.0 10.8 - - + -
62C ASP* 2.8 30.8 + - - +
65C ASP* 2.7 33.9 + - - +
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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