Contacts of the helix formed by residues 236 - 249 (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 GLU 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A GLU 4.9 1.4 + - - +
234A PHE 3.0 2.4 + - - -
235A SER* 1.3 87.0 + - - +
237A THR* 1.3 64.4 + - - +
238A GLU 3.3 0.9 - - - -
239A SER* 2.8 33.8 + - - +
240A MET* 3.1 21.7 + - + +
287A LYS* 4.0 23.8 - - + +
290A SER* 3.2 30.2 + - - -
332A LEU* 4.8 4.8 - - + +
333A PHE* 3.6 28.3 - - - -
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Residues in contact with THR 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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214A ILE* 4.6 8.3 - - - -
218A THR* 4.0 16.2 - - + +
234A PHE* 2.8 18.9 + - - +
235A SER 3.2 1.8 + - - -
236A GLU* 1.3 74.8 - - - +
238A GLU* 1.3 66.1 + - - +
240A MET* 2.9 20.9 + - - +
241A LEU* 3.0 15.4 + - + +
256A TYR* 3.5 37.7 - - + -
258A LEU* 3.7 16.3 - - + +
293A ILE* 3.7 8.9 - - + +
297A ILE* 4.3 4.7 - - + -
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Residues in contact with GLU 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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214A ILE 5.2 3.9 + - - +
215A GLY* 4.5 9.0 - - - -
216A PRO* 3.9 26.6 - - + +
217A ARG* 2.8 48.3 + - - +
218A THR* 4.8 2.4 + - - +
235A SER 4.4 3.9 + - - +
236A GLU 3.3 1.0 - - - -
237A THR* 1.3 79.6 - - - +
239A SER* 1.3 63.5 + - - +
241A LEU* 3.2 12.0 + - - +
242A LYS* 2.4 71.7 + - + +
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Residues in contact with SER 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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235A SER 5.4 0.2 + - - -
236A GLU* 2.8 30.9 + - - +
238A GLU* 1.3 80.6 - - - +
240A MET* 1.3 60.6 + - - +
242A LYS* 3.5 11.5 + - - +
243A ILE* 3.2 27.8 + - - +
332A LEU* 4.1 20.0 - - - +
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Residues in contact with MET 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 GLU* 3.1 26.2 + - + +
237A THR 2.9 8.1 + - - +
239A SER* 1.3 75.4 - - - +
241A LEU* 1.3 65.9 + - - +
243A ILE* 3.0 6.0 + - - +
244A ALA* 3.0 24.7 + - - +
290A SER* 3.6 37.2 - - - +
293A ILE* 4.2 12.6 - - - -
294A ALA* 3.7 30.5 - - + -
297A ILE* 3.4 14.4 - - + -
328A ILE* 3.9 21.8 - - + +
329A CYS* 4.8 6.5 - - - -
332A LEU* 3.8 24.5 - - + -
333A PHE* 5.1 1.6 - - + -
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Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ARG* 3.7 22.0 - - - +
218A THR* 3.9 11.4 - - - +
237A THR* 3.0 19.4 + - + +
238A GLU* 3.3 26.2 - - - +
240A MET* 1.3 76.4 - - - +
242A LYS* 1.3 64.1 + - - +
244A ALA* 3.3 5.8 + - - +
245A GLU* 3.0 26.3 + - - +
251A TYR* 4.2 26.5 - - + -
256A TYR* 3.7 38.6 - - + -
297A ILE* 4.3 20.4 - - + -
301A TRP* 4.5 1.9 - - + -
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Residues in contact with LYS 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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216A PRO* 4.7 7.7 - - - +
217A ARG* 4.0 6.7 - - - +
238A GLU* 2.4 71.8 + - + +
239A SER* 3.9 10.5 - - - +
240A MET 3.2 0.2 - - - -
241A LEU* 1.3 77.9 - - - +
243A ILE* 1.3 62.9 + - + +
245A GLU* 3.2 11.8 + - - +
246A ASP* 3.2 19.9 + - - +
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Residues in contact with ILE 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 SER* 3.2 13.9 + - - +
240A MET 3.0 6.7 + - - +
242A LYS* 1.3 76.4 - - + +
244A ALA* 1.3 52.9 + - - +
246A ASP* 2.9 8.4 + - - -
247A LEU* 2.7 56.5 + - + +
328A ILE* 4.0 17.7 - - + +
331A ARG* 3.9 44.0 - - + +
332A LEU* 3.4 36.1 - - + -
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Residues in contact with ALA 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 MET 3.0 15.0 + - - +
241A LEU 3.6 3.8 - - - +
243A ILE* 1.3 77.5 - - - +
245A GLU* 1.3 53.0 + - - +
247A LEU* 3.7 7.5 - - - +
248A GLY* 2.6 34.5 + - - -
297A ILE* 3.7 14.6 - - + -
298A SER* 5.1 2.2 - - - +
301A TRP* 3.5 31.2 - - + -
328A ILE* 4.0 14.3 - - + +
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Residues in contact with GLU 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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217A ARG* 2.5 40.7 + - - -
241A LEU 3.0 14.0 + - - +
242A LYS* 3.6 12.7 - - - +
243A ILE 3.1 0.2 - - - -
244A ALA* 1.3 76.3 - - - +
246A ASP* 1.3 58.5 + - - +
249A GLY* 2.6 40.4 + - - +
250A PRO* 4.1 4.7 - - + +
251A TYR* 3.1 37.6 + - + +
301A TRP* 3.8 6.5 - - + -
408A LYS* 4.7 1.0 + - - -
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Residues in contact with ASP 246 (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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242A LYS 3.2 8.9 + - - +
243A ILE* 2.9 11.7 + - + +
245A GLU* 1.3 82.1 - - - +
247A LEU* 1.3 70.9 + - + +
331A ARG* 3.9 12.5 + - - -
408A LYS* 3.0 27.4 + - - +
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Residues in contact with LEU 247 (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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243A ILE* 2.7 32.7 + - + +
244A ALA* 3.7 6.5 - - - +
246A ASP* 1.3 92.8 - - - +
248A GLY* 1.3 59.2 + - - +
249A GLY 3.6 0.2 - - - -
324A LEU* 4.2 20.6 - - + +
327A HIS* 3.9 26.2 - - + -
328A ILE* 4.2 13.0 - - + -
331A ARG* 3.3 34.1 - - - +
404A LEU* 4.3 22.1 - - + +
407A LEU* 4.9 3.8 - - - +
408A LYS* 3.5 24.5 + - - +
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Residues in contact with GLY 248 (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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244A ALA 2.6 17.8 + - - -
247A LEU* 1.3 75.5 - - - +
249A GLY* 1.3 61.1 + - - +
250A PRO* 4.6 0.5 - - - +
301A TRP* 3.3 27.9 - - - -
324A LEU* 5.5 3.8 - - - +
407A LEU* 5.3 3.4 - - - -
408A LYS* 4.2 14.9 - - - +
411A VAL* 3.7 19.2 - - - +
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Residues in contact with GLY 249 (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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245A GLU* 2.6 39.4 + - - +
247A LEU 3.6 1.2 - - - -
248A GLY* 1.3 75.6 - - - +
250A PRO* 1.3 77.2 - - - +
301A TRP* 3.1 5.9 + - - -
408A LYS* 4.2 15.1 - - - +
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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