Contacts of the helix formed by residues 323 - 339 (chain A) in PDB entry 5F0L
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 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A ALA 4.2 10.3 - - - +
321A ASP* 3.1 15.0 + - - +
322A ILE* 1.3 67.8 - - - +
324A LEU* 1.3 64.8 + - - +
325A PHE 3.4 2.2 - - - -
326A ASP* 3.3 32.7 + - + +
327A ILE* 3.1 32.3 + - + +
362A TYR* 4.1 5.8 - - - -
368A TYR* 5.9 2.7 - - - +
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Residues in contact with LEU 324 (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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276A LEU* 3.8 15.9 - - + -
279A LEU* 3.5 29.6 - - + -
306A LEU* 4.4 7.4 - - + -
318A ILE* 3.4 46.0 - - + -
322A ILE* 3.0 11.9 + - + +
323A LYS* 1.3 69.7 - - - +
325A PHE* 1.3 59.7 + - - +
327A ILE* 3.1 7.9 + - - +
328A PHE* 2.8 46.3 + - + -
357A LEU* 4.3 13.5 - - + -
361A CYS* 3.6 19.5 - - + -
362A TYR* 3.3 13.6 + - + +
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Residues in contact with PHE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LYS 3.4 0.4 - - - -
324A LEU* 1.3 77.6 - - - +
326A ASP* 1.3 64.8 + - - +
329A SER* 2.9 60.3 + - - -
354A LEU* 4.2 15.3 - - + -
357A LEU* 4.6 9.6 - - + -
358A ALA* 4.2 17.7 - - + -
362A TYR* 4.1 10.0 - - + -
368A TYR* 3.4 70.7 - + + +
371A LYS* 4.4 17.9 - - + -
372A VAL* 3.5 27.1 - - + -
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Residues in contact with ASP 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LYS* 3.3 38.2 + - + +
324A LEU 3.3 0.6 - - - -
325A PHE* 1.3 89.5 - - - +
327A ILE* 1.3 61.6 + - + +
329A SER* 4.5 3.1 - - - -
330A GLN* 3.2 33.2 + - - +
368A TYR* 4.1 16.3 + - - -
509A EDO 5.1 6.1 + - - -
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Residues in contact with ILE 327 (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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279A LEU* 4.0 33.0 - - + -
280A ASN* 3.6 29.2 - - - +
283A LEU* 4.4 9.9 - - + -
322A ILE* 4.3 5.2 - - + -
323A LYS* 3.1 33.7 + - + +
324A LEU* 3.1 6.8 + - - +
326A ASP* 1.3 78.2 - - + +
328A PHE* 1.3 60.0 + - + +
330A GLN* 3.9 1.4 - - - +
331A GLN* 3.0 33.4 + - - +
503A SO4 3.5 20.9 - - - +
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Residues in contact with PHE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 4.0 10.5 - - + -
283A LEU* 4.0 19.3 - - + -
299A ILE* 4.5 9.0 - - + -
302A LEU* 3.7 24.9 - - + -
303A ILE* 3.5 30.3 - - + -
306A LEU* 3.6 32.5 - - + -
324A LEU* 2.8 39.2 + - + +
325A PHE 4.2 0.9 - - - +
327A ILE* 1.3 75.3 - - + +
329A SER* 1.3 59.4 + - - +
331A GLN* 4.5 1.8 - - - +
332A VAL* 2.9 37.6 + - + +
354A LEU* 3.8 16.4 - - + -
357A LEU* 3.6 22.7 - - + -
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Residues in contact with SER 329 (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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325A PHE* 2.9 55.9 + - - -
326A ASP* 4.5 3.8 - - - -
328A PHE* 1.3 71.5 - - - +
330A GLN* 1.3 62.1 + - - +
332A VAL* 4.3 1.2 - - - +
333A ALA* 3.4 23.0 + - - +
354A LEU* 3.7 20.4 - - - +
372A VAL* 5.3 0.2 - - - +
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Residues in contact with GLN 330 (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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326A ASP* 3.2 22.7 + - - +
327A ILE* 3.9 2.2 - - - +
328A PHE 3.2 0.4 - - - -
329A SER* 1.3 80.2 - - - +
331A GLN* 1.3 57.1 + - + +
333A ALA* 3.8 5.2 - - - +
334A THR* 2.7 35.1 + - - +
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Residues in contact with GLN 331 (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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280A ASN* 3.0 47.1 + - - +
283A LEU* 3.6 47.9 - - + +
284A ARG* 4.2 13.6 + - - +
327A ILE 3.0 21.7 + - - +
328A PHE 4.2 1.1 - - - +
330A GLN* 1.3 77.0 - - + +
332A VAL* 1.3 56.1 + - - +
334A THR* 2.9 15.6 + - - +
335A VAL* 2.6 40.0 + - - +
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Residues in contact with VAL 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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283A LEU* 6.1 0.9 - - + -
299A ILE* 3.9 31.4 - - + -
303A ILE* 5.1 1.6 - - + -
328A PHE* 2.9 32.5 + - + +
329A SER 4.3 2.5 - - - +
331A GLN* 1.3 70.9 - - + +
333A ALA* 1.3 57.0 + - - +
335A VAL* 3.7 6.9 - - - +
336A ILE* 2.9 54.3 + - + +
350A LEU* 3.8 24.2 - - + +
351A GLN* 4.5 9.9 - - - +
354A LEU* 4.5 17.0 - - + -
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Residues in contact with ALA 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 SER 3.4 17.7 + - - +
330A GLN* 3.8 5.8 - - - +
331A GLN 3.2 0.4 - - - -
332A VAL* 1.3 79.7 - - - +
334A THR* 1.3 58.0 + - - +
336A ILE* 3.9 8.6 + - - +
337A GLN* 3.1 25.6 + - - +
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Residues in contact with THR 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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287A ALA* 4.7 9.4 - - + +
330A GLN* 2.7 24.9 + - - +
331A GLN* 2.9 19.1 + - - +
333A ALA* 1.3 75.9 - - - +
335A VAL* 1.3 59.6 + - - +
337A GLN* 3.2 9.3 + - + +
338A SER* 3.0 26.9 + - - -
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 3.6 28.0 - - + +
286A CYS* 4.1 6.5 - - + -
287A ALA* 4.1 12.1 - - + +
295A VAL* 3.3 35.7 - - + -
299A ILE* 3.7 18.2 - - + -
331A GLN* 2.6 27.7 + - - +
332A VAL 3.7 3.8 - - - +
334A THR* 1.3 69.9 - - - +
336A ILE* 1.3 66.6 + - + +
338A SER* 2.4 28.0 + - - +
339A ARG* 3.4 9.0 + - + +
342A MET* 6.3 1.3 - - + -
350A LEU* 5.9 1.3 - - + -
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Residues in contact with ILE 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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332A VAL* 2.9 41.4 + - + +
333A ALA* 4.1 7.4 - - - +
335A VAL* 1.3 73.5 - - + +
337A GLN* 1.3 66.2 + - - +
339A ARG* 3.1 24.8 + - - +
342A MET* 3.8 15.0 - - + +
347A VAL* 3.9 39.7 - - + +
350A LEU* 3.7 22.7 - - + -
351A GLN* 4.8 4.3 - - - +
379A ILE* 6.1 1.1 - - + -
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Residues in contact with GLN 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 ALA 3.1 16.8 + - - +
334A THR* 3.2 15.5 + - + +
336A ILE* 1.3 78.4 - - - +
338A SER* 1.3 59.3 + - - +
339A ARG 3.4 6.9 + - - +
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Residues in contact with SER 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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287A ALA* 3.4 31.2 + - - -
291A GLN* 3.2 17.8 + - - -
334A THR 3.0 12.9 + - - -
335A VAL* 2.4 24.2 + - - +
337A GLN* 1.3 74.4 - - - +
339A ARG* 1.3 77.3 + - - +
340A GLN* 5.0 1.4 - - - +
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Residues in contact with ARG 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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286A CYS 3.8 3.2 + - - -
287A ALA 3.2 21.2 + - - -
288A GLU 4.3 0.2 - - - -
289A LEU 3.2 27.1 + - - -
290A HIS 3.5 14.1 + - - -
291A GLN* 3.6 28.2 + - - +
293A VAL 5.1 0.7 - - - -
295A VAL* 3.7 33.3 - - + +
335A VAL* 3.6 13.1 + - + +
336A ILE* 3.1 13.5 + - - +
337A GLN 3.5 9.2 - - - +
338A SER* 1.3 109.7 + - - +
340A GLN* 1.3 62.1 + - - +
341A ASP 4.5 0.7 - - - +
342A MET* 4.0 38.8 - - + +
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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