Contacts of the helix formed by residues 334 - 349 (chain B) in PDB entry 3CL1
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 SER 334 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238B LYS 4.4 6.8 + - - -
239B LEU* 3.6 26.2 - - - +
330B LEU 2.7 17.0 + - - +
331B CYS 3.0 11.9 - - - +
333B SER* 1.3 75.1 - - - +
335B PRO* 1.3 61.0 - - - +
336B GLU* 3.8 7.4 + - - +
337B ILE* 3.2 28.8 + - - +
338B ALA 3.0 19.4 + - - -
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Residues in contact with PRO 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B CYS 3.6 8.0 - - - +
332B SER* 4.3 8.5 - - - +
333B SER 4.0 6.3 - - - +
334B SER* 1.3 82.3 - - - +
336B GLU* 1.3 60.9 + - - +
338B ALA* 3.5 5.5 - - + +
339B GLU* 3.1 27.4 + - - +
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Residues in contact with GLU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B LYS* 5.5 8.3 - - + +
334B SER* 3.2 7.8 - - - +
335B PRO* 1.3 79.3 - - + +
337B ILE* 1.3 64.9 + - + +
339B GLU* 3.3 9.6 - - - +
340B ILE* 3.1 29.5 + - + +
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Residues in contact with ILE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B LEU* 3.6 44.6 - - + +
236B PHE* 4.6 2.0 - - + -
238B LYS* 4.2 10.5 - - + -
239B LEU* 3.6 38.8 - - + -
330B LEU* 4.0 15.9 - - + +
334B SER* 3.2 13.8 + - - +
336B GLU* 1.3 75.5 - - + +
338B ALA* 1.3 66.9 + - - +
340B ILE* 3.1 9.3 + - + +
341B PHE* 3.0 53.9 + - + -
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B CYS* 3.5 48.9 - - + +
334B SER 3.0 6.4 + - - +
335B PRO* 3.5 11.4 - - + +
337B ILE* 1.3 77.5 - - - +
339B GLU* 1.3 54.8 - - - +
341B PHE* 3.5 3.3 + - - +
342B ARG* 3.0 31.0 + - - +
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Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B PRO 3.1 15.2 + - - +
336B GLU* 3.3 13.0 - - - +
337B ILE 3.2 0.2 - - - -
338B ALA* 1.3 73.5 - - - +
340B ILE* 1.3 61.2 + - + +
342B ARG* 2.7 46.4 + - - +
343B LYS* 2.9 51.4 + - + +
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Residues in contact with ILE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B LEU* 3.7 33.7 - - + -
238B LYS* 6.2 2.2 - - + -
295B PHE* 4.0 13.9 - - + -
336B GLU* 3.1 17.0 + - + +
337B ILE* 3.1 14.1 + - + +
339B GLU* 1.3 74.8 - - + +
341B PHE* 1.3 59.2 + - + +
343B LYS* 4.3 3.9 - - - +
344B THR* 2.6 47.1 + - - +
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Residues in contact with PHE 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B LEU* 3.7 29.6 - - + -
272B MET* 3.8 18.4 - - + -
274B PHE* 3.8 18.6 - + - -
295B PHE* 3.6 31.0 - + - -
298B GLU* 4.0 4.9 - - + +
302B ILE* 3.6 15.0 - - + +
327B PHE* 3.5 28.5 - + + -
330B LEU* 3.8 12.8 - - + -
331B CYS* 4.1 8.1 - - - -
337B ILE* 3.0 36.1 + - + -
338B ALA 3.7 5.2 - - - +
340B ILE* 1.3 76.1 - - + +
342B ARG* 1.3 57.5 + - - +
344B THR* 3.9 3.2 - - - -
345B ALA* 2.9 33.1 + - - +
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Residues in contact with ARG 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B ILE* 4.2 17.9 - - + +
338B ALA 3.0 18.0 + - - +
339B GLU* 2.7 33.4 + - - +
340B ILE 3.2 0.2 - - - -
341B PHE* 1.3 77.3 - - - +
343B LYS* 1.3 79.5 + - - +
345B ALA* 3.5 3.1 + - - +
346B LEU* 3.1 59.2 + - - +
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Residues in contact with LYS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B GLU* 2.9 38.4 + - + +
340B ILE* 4.3 3.8 - - - +
342B ARG* 1.3 98.4 - - - +
344B THR* 1.3 60.8 + - - +
346B LEU* 3.1 9.1 + - + +
347B GLU* 2.9 41.8 + - + +
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Residues in contact with THR 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B PHE* 3.6 29.5 - - + -
298B GLU* 4.6 0.4 - - - +
340B ILE* 2.6 28.8 + - - +
341B PHE 3.9 0.7 - - - -
343B LYS* 1.3 76.9 - - - +
345B ALA* 1.3 55.9 + - - +
347B GLU* 3.3 15.8 + - + +
348B ARG* 3.0 65.3 + - + +
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Residues in contact with ALA 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B GLU* 3.9 8.4 + - + -
299B MET* 3.7 29.1 - - + +
302B ILE* 3.7 22.0 - - + -
341B PHE 2.9 19.6 + - - +
342B ARG 3.8 3.4 - - - +
344B THR* 1.3 76.5 - - - +
346B LEU* 1.3 59.0 + - + +
348B ARG* 3.9 0.6 - - - -
349B ARG* 3.1 31.0 + - - +
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B ARG* 3.1 45.6 + - - +
343B LYS* 3.1 11.4 + - + +
345B ALA* 1.3 76.3 - - + +
347B GLU* 1.3 66.6 + - + +
348B ARG 3.3 0.2 + - - -
349B ARG* 3.6 16.5 + - + +
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Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LYS* 2.9 30.4 + - + +
344B THR* 3.3 17.5 + - + +
346B LEU* 1.3 73.5 - - + +
348B ARG* 1.3 63.5 + - + +
349B ARG 4.6 2.6 - - - -
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Residues in contact with ARG 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 3.8 21.4 - - - +
294B ALA* 5.2 1.4 - - - +
295B PHE* 2.7 35.0 + - - +
296B PHE* 3.9 0.6 - - - +
298B GLU* 3.1 32.9 + - - -
299B MET* 3.8 16.2 - - - -
344B THR* 3.0 38.1 + - + +
346B LEU 3.2 0.2 - - - -
347B GLU* 1.3 79.4 - - + +
349B ARG* 1.3 63.9 + - - +
402B PCG 3.0 71.0 + - + +
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Residues in contact with ARG 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B MET* 3.6 22.8 - - + +
345B ALA 3.1 17.1 + - - +
346B LEU* 3.6 14.1 + - + +
347B GLU 3.5 3.3 - - - -
348B ARG* 1.3 81.5 - - - +
402B PCG 5.0 1.5 + - - -
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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