Contacts of the helix formed by residues 224 - 234 (chain A) in PDB entry 1HS6
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 LYS 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A ALA 4.3 4.4 + - - +
210A GLU* 3.2 43.4 - - + +
212A ARG* 5.4 3.1 + - - +
222A SER 3.5 1.4 + - - -
223A GLU* 1.3 72.4 - - - +
225A GLU* 1.3 74.7 + - - +
226A GLN 3.1 1.7 + - - -
227A VAL* 3.3 15.7 + - - +
228A GLU* 4.6 3.1 + - - +
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Residues in contact with GLU 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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124A SER* 3.0 39.3 - - - +
125A GLY* 4.0 10.2 + - - -
223A GLU* 3.2 24.5 - - + +
224A LYS* 1.3 88.0 + - - +
226A GLN* 1.3 75.9 + - - +
228A GLU* 5.4 1.0 - - - +
229A LYS* 5.6 3.1 + - - +
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Residues in contact with GLN 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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124A SER* 2.6 28.7 + - - -
222A SER* 3.3 21.1 - - - +
223A GLU* 3.0 12.0 + - - +
225A GLU* 1.3 107.8 - - - +
227A VAL* 1.3 57.5 + - - +
228A GLU 3.4 2.2 + - - -
229A LYS* 3.5 7.1 + - - +
230A SER* 2.7 39.5 + - - +
260A VAL* 4.9 6.1 - - + +
261A LEU 5.9 0.9 - - - +
280A PRO* 5.3 6.3 - - + -
283A LEU* 4.4 18.3 - - + +
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLU* 3.8 36.6 - - + +
211A SER* 4.2 9.0 - - - +
212A ARG* 3.0 46.1 - - + +
220A VAL* 4.5 5.1 - - - +
221A TRP 5.1 0.2 - - - -
222A SER* 3.1 22.6 + - - +
223A GLU 3.3 1.0 + - - +
224A LYS* 3.3 11.9 + - - +
226A GLN* 1.3 76.9 - - - +
228A GLU* 1.3 67.1 + - + +
230A SER* 3.3 3.8 + - - -
231A ALA* 2.8 29.6 + - - +
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Residues in contact with GLU 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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212A ARG* 2.9 42.1 + - - +
224A LYS 4.6 2.8 + - - +
225A GLU 5.4 1.1 + - - +
226A GLN 3.4 0.6 - - - -
227A VAL* 1.3 83.2 - - + +
229A LYS* 1.3 58.4 + - - +
231A ALA* 3.2 8.0 + - - +
232A TYR* 3.0 26.0 + - - +
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Residues in contact with LYS 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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225A GLU 5.6 2.0 + - - +
226A GLN* 3.5 9.7 + - - +
227A VAL 3.3 0.4 - - - -
228A GLU* 1.3 75.3 - - - +
230A SER* 1.3 62.2 + - - +
232A TYR* 3.1 9.2 + - + +
233A GLU* 2.7 33.1 + - - +
283A LEU* 3.6 41.7 + - + -
284A ALA 4.8 2.2 + - - -
285A GLY* 3.8 24.7 - - - +
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Residues in contact with SER 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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220A VAL* 3.5 24.9 - - - +
222A SER* 4.2 1.3 + - - -
226A GLN* 2.7 24.6 + - - +
227A VAL* 3.6 4.0 - - - -
229A LYS* 1.3 76.7 - - - +
231A ALA* 1.3 65.4 + - - +
233A GLU 3.1 0.7 + - - -
234A PHE* 3.0 31.9 + - - +
260A VAL* 3.5 25.5 - - - +
283A LEU* 3.9 18.4 - - - +
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Residues in contact with ALA 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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212A ARG* 4.1 21.3 - - + -
214A ILE* 3.8 30.1 - - + +
220A VAL* 4.0 4.3 - - + -
227A VAL 2.8 18.4 + - - +
228A GLU* 3.3 11.2 - - - +
230A SER* 1.3 79.2 - - - +
232A TYR* 1.3 62.2 + - - +
234A PHE 4.2 0.2 - - - -
235A SER* 3.6 15.2 + - - -
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Residues in contact with TYR 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 GLU 3.0 12.4 + - - +
229A LYS* 3.5 12.3 - - + +
231A ALA* 1.3 76.6 - - - +
233A GLU* 1.3 70.7 + - - +
235A SER* 3.2 7.8 + - - -
285A GLY* 3.4 33.1 + - - -
286A ASP* 4.2 4.9 + - - -
287A LYS* 2.6 72.0 + - + +
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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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229A LYS* 2.7 22.7 + - - +
230A SER 3.7 2.0 - - - +
232A TYR* 1.3 80.2 - - - +
234A PHE* 1.3 73.6 + - + +
235A SER 3.6 0.2 + - - -
236A GLU* 4.9 3.1 - - - +
282A LEU 3.4 14.6 - - - +
283A LEU* 3.2 20.4 - - + +
284A ALA* 3.1 18.4 + - - +
285A GLY* 2.5 35.9 + - - -
286A ASP 3.4 0.2 + - - -
287A LYS* 2.7 52.3 + - - +
289A LEU 4.8 1.2 + - - +
290A SER* 4.9 4.5 - - - +
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Residues in contact with PHE 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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214A ILE* 3.6 13.3 - - + +
220A VAL* 4.3 5.8 - - + -
230A SER* 3.0 24.0 + - - +
231A ALA 4.2 0.4 - - - -
233A GLU* 1.3 90.3 - - + +
235A SER* 1.3 65.2 + - - +
236A GLU 3.0 4.1 + - - -
237A THR* 2.8 34.9 + - - +
258A LEU* 3.8 19.5 - - + -
260A VAL* 3.7 24.5 - - + -
278A VAL* 4.0 13.5 - - + -
279A THR 5.1 0.4 - - - -
282A LEU* 3.9 24.9 - - + -
283A LEU* 3.8 26.7 - - + -
289A LEU 5.7 1.1 - - - -
290A SER* 5.6 5.6 - - - -
293A ILE* 3.6 28.3 - - + -
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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