Contacts of the helix formed by residues 327 - 343 (chain A) in PDB entry 3SHE
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 HIS 327 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A ASP* 3.1 31.6 + - + +
326A ASP* 1.3 91.7 - - + +
328A TRP* 1.3 64.0 + - - +
329A ASP* 3.3 2.7 - - - +
330A GLU* 3.2 39.9 + - + +
331A VAL* 3.2 23.3 + - + +
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Residues in contact with TRP 328 (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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125A GLU* 4.7 8.5 + - - -
127A PHE* 3.7 39.7 - + + +
128A SER* 5.4 6.0 + - - +
131A GLN* 5.5 9.2 - - - +
169A PRO* 3.8 25.6 - - + -
234A ILE* 4.1 17.7 - - + -
238A GLY 4.8 4.3 - - - -
240A PRO* 5.9 1.6 - - + -
321A LEU* 3.9 23.1 - - + -
324A ASP 3.7 3.6 + - - +
325A LYS* 3.3 22.6 + - - +
326A ASP 3.7 0.2 - - - -
327A HIS* 1.3 75.5 - - - +
329A ASP* 1.3 67.9 + - - +
331A VAL* 3.3 34.5 - - + +
332A LYS* 3.1 58.8 + - + +
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Residues in contact with ASP 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LYS 4.9 0.6 + - - -
326A ASP 5.4 2.0 - - - +
327A HIS* 3.3 1.3 - - - +
328A TRP* 1.3 81.7 - - - +
330A GLU* 1.3 56.8 + - + +
332A LYS* 3.4 27.9 + - - +
333A GLU* 3.0 28.9 + - - +
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Residues in contact with GLU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ASP 4.7 2.4 - - - +
327A HIS* 3.2 38.8 + - + +
328A TRP 3.2 0.6 - - - -
329A ASP* 1.3 76.8 - - + +
331A VAL* 1.3 60.1 + - + +
333A GLU* 3.3 13.2 + - - +
334A GLU* 2.8 45.3 + - - +
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PRO* 5.9 1.6 - - + -
234A ILE* 5.4 3.6 - - + -
240A PRO* 3.9 33.9 - - + -
242A PHE* 4.4 3.1 - - - -
327A HIS* 3.2 18.7 + - + +
328A TRP* 3.3 45.1 - - + +
330A GLU* 1.3 74.6 - - + +
332A LYS* 1.3 66.5 + - + +
334A GLU* 3.7 13.3 - - - +
335A MET* 3.0 29.1 + - - +
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Residues in contact with LYS 332 (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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125A GLU* 4.7 12.3 + - - +
168A LYS* 5.3 0.5 - - - +
169A PRO* 4.5 10.3 - - + -
170A GLU* 3.6 42.9 - - - +
328A TRP* 3.1 50.7 + - + +
329A ASP* 3.4 25.8 + - - +
331A VAL* 1.3 79.9 - - - +
333A GLU* 1.3 59.6 + - - +
335A MET* 3.4 4.6 + - - +
336A THR* 3.0 33.4 + - - -
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Residues in contact with GLU 333 (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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329A ASP 3.0 19.7 + - - +
330A GLU* 3.3 12.1 + - - +
332A LYS* 1.3 73.7 - - - +
334A GLU* 1.3 69.6 + - - +
336A THR* 3.5 7.7 + - - +
337A SER* 3.0 24.3 + - - -
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Residues in contact with GLU 334 (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 PRO* 4.8 1.4 - - - +
242A PHE* 3.5 34.6 - - + +
330A GLU* 2.8 34.1 + - - +
331A VAL* 3.7 15.0 - - - +
332A LYS 3.3 0.2 - - - -
333A GLU* 1.3 79.4 - - + +
335A MET* 1.3 56.7 + - - +
337A SER* 3.4 8.0 + - - -
338A ALA* 3.0 26.2 + - - +
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Residues in contact with MET 335 (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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167A VAL 3.4 24.7 - - - +
168A LYS* 4.0 5.4 - - + -
169A PRO* 3.6 27.1 - - + -
226A TRP* 4.5 8.3 - - + -
227A SER* 4.0 18.2 - - - +
230A VAL* 3.7 36.1 - - + -
231A ILE* 4.5 4.9 - - + -
234A ILE* 5.1 3.6 - - - -
242A PHE* 4.4 16.4 - - + -
331A VAL 3.0 17.6 + - - +
332A LYS* 3.4 5.6 + - - +
334A GLU* 1.3 73.4 - - - +
336A THR* 1.3 66.2 + - - +
338A ALA* 3.2 5.4 + - - +
339A LEU* 3.0 32.9 + - + +
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Residues in contact with THR 336 (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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166A ASP* 5.6 0.2 - - - -
168A LYS* 2.8 40.0 + - - +
170A GLU* 4.1 5.9 + - - -
332A LYS 3.0 20.1 + - - -
333A GLU* 3.7 8.7 - - - +
335A MET* 1.3 76.2 - - - +
337A SER* 1.3 58.5 + - - +
339A LEU* 3.4 4.7 + - - +
340A ALA* 3.0 29.7 + - + +
343A ARG* 4.8 5.4 + - - +
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Residues in contact with SER 337 (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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333A GLU* 3.0 19.2 + - - -
334A GLU* 3.5 8.5 - - - -
335A MET 3.2 0.2 - - - -
336A THR* 1.3 79.6 - - - +
338A ALA* 1.3 60.7 + - - +
340A ALA* 3.4 7.6 + - - +
341A THR* 3.2 32.0 + - - +
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Residues in contact with ALA 338 (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 TRP* 3.8 26.5 - - + -
242A PHE* 5.1 5.6 - - + -
334A GLU 3.0 14.3 + - - +
335A MET* 3.2 8.9 + - - +
337A SER* 1.3 73.4 - - - +
339A LEU* 1.3 64.8 + - - +
341A THR* 3.0 22.3 + - - -
342A MET* 3.3 19.0 + - + +
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Residues in contact with LEU 339 (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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165A ARG 4.5 9.2 - - - +
166A ASP* 3.7 22.7 - - - +
167A VAL 3.7 20.4 - - - +
168A LYS* 3.9 17.7 - - + -
223A CYS* 4.7 6.7 - - + +
226A TRP* 4.1 19.1 - - + -
227A SER* 3.3 21.8 - - - +
335A MET* 3.0 22.9 + - + +
336A THR* 3.8 4.3 - - - +
338A ALA* 1.3 73.6 - - - +
340A ALA* 1.3 65.4 + - - +
342A MET* 3.3 12.6 + - + +
343A ARG* 3.3 38.2 + - - +
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Residues in contact with ALA 340 (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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336A THR* 3.0 19.7 + - + +
337A SER* 3.5 9.9 - - - +
338A ALA 3.3 0.4 - - - -
339A LEU* 1.3 76.5 - - - +
341A THR* 1.3 58.7 + - + +
343A ARG* 3.1 40.1 + - - +
344A VAL* 3.5 11.6 + - - +
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Residues in contact with THR 341 (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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337A SER* 3.2 20.1 + - - +
338A ALA* 3.0 18.5 + - - -
340A ALA* 1.3 78.8 - - + +
342A MET* 1.3 59.4 + - - +
344A VAL* 2.9 38.1 - - + +
347A ASP* 4.4 20.3 + - - +
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Residues in contact with MET 342 (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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219A TYR* 2.6 44.3 + - + +
223A CYS* 4.1 23.5 - - + -
226A TRP* 3.3 62.8 - - + +
292A ARG* 5.3 7.2 - - - +
338A ALA* 3.3 16.3 + - + +
339A LEU* 3.6 17.3 - - + +
340A ALA 3.3 0.6 - - - -
341A THR* 1.3 79.6 + - - +
343A ARG* 1.3 61.6 + - + +
344A VAL 3.3 3.7 + - - +
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Residues in contact with ARG 343 (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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165A ARG* 2.8 82.7 + - + +
166A ASP* 3.3 18.6 + - - -
168A LYS* 6.0 0.4 - - - +
190A PHE* 3.2 54.1 - - - -
223A CYS* 6.3 1.6 - - + -
336A THR* 4.8 5.7 + - - +
339A LEU* 3.3 24.5 + - - +
340A ALA* 3.1 31.2 + - - +
342A MET* 1.3 77.6 - - + +
344A VAL* 1.3 64.0 + - - +
345A ASP 3.8 0.3 + - - -
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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