Contacts of the helix formed by residues 335 - 351 (chain A) in PDB entry 5LUQ
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 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A ALA 5.0 1.1 - - - +
332A GLU* 3.0 48.2 + - + +
333A MSE 3.5 2.6 + - - -
334A HIS* 1.3 75.6 - - - +
336A ASN* 1.3 73.3 + - - +
337A LYS* 3.5 3.0 - - - +
338A LEU* 3.0 32.4 - - + +
339A GLN* 3.1 49.7 + - - +
375A VAL* 4.2 9.1 - - + +
378A ALA* 3.2 36.8 + - + +
379A LYS* 4.5 7.5 - - - +
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Residues in contact with ASN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A GLU* 4.9 5.9 + - - -
333A MSE 5.1 3.2 + - - -
335A LYS* 1.3 90.5 + - - +
337A LYS* 1.3 68.6 + - + +
338A LEU 3.0 1.6 - - - -
339A GLN* 3.0 33.9 + - - +
340A TYR* 3.1 12.0 + - - +
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Residues in contact with LYS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 3.6 25.3 - - + +
288A ASP* 4.0 30.8 + - + +
291A VAL* 5.1 0.2 - - - +
334A HIS* 5.8 2.9 - - + +
335A LYS 3.5 1.5 - - - +
336A ASN* 1.3 76.6 - - + +
338A LEU* 1.3 67.3 + - + +
340A TYR* 3.5 18.1 - - - +
341A PHE* 4.1 1.6 + - - +
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Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 3.5 23.1 - - + -
323A VAL* 5.7 2.7 - - + -
327A VAL* 3.3 43.7 - - + +
334A HIS* 2.9 55.6 - - + +
335A LYS* 3.0 20.9 - - + +
337A LYS* 1.3 74.5 - - + +
339A GLN* 1.3 60.5 + - - +
340A TYR 2.8 11.4 + - - -
341A PHE* 3.0 17.5 + - - +
342A MSE 3.5 10.1 + - - +
375A VAL* 4.7 9.6 - - + -
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Residues in contact with GLN 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LYS* 3.1 43.9 + - - +
336A ASN* 3.0 27.1 + - - +
338A LEU* 1.3 76.9 - - - +
340A TYR* 1.3 63.0 + - - +
342A MSE 4.8 11.0 - - - +
343A GLU* 3.0 34.3 + - + +
375A VAL* 3.4 28.8 + - + +
378A ALA* 4.4 3.0 - - - +
379A LYS* 4.7 12.9 - - - +
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Residues in contact with TYR 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU 5.9 0.4 - - - -
291A VAL* 4.7 17.3 - - + -
336A ASN 3.1 10.5 + - - +
337A LYS* 3.5 16.6 - - - +
338A LEU 2.8 1.0 + - - -
339A GLN* 1.3 77.9 - - - +
341A PHE* 1.3 63.8 + - - +
343A GLU* 3.1 4.2 + - - +
344A GLN* 3.0 47.0 + - + +
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Residues in contact with PHE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 4.1 15.5 - - + -
291A VAL* 3.7 26.7 - - + -
294A PHE* 3.1 33.0 - + - -
295A GLU* 2.8 42.4 - - + -
316A LEU* 5.0 0.9 - - + -
320A LEU* 4.1 19.1 - - + -
323A VAL* 3.9 24.7 - - + -
337A LYS 4.7 0.2 - - - +
338A LEU 3.0 9.1 + - - +
340A TYR* 1.3 78.5 - - - +
342A MSE 1.3 62.1 + - + +
344A GLN* 2.9 32.0 + - - +
345A PHE* 3.1 29.1 + + - -
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Residues in contact with MSE 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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323A VAL* 6.4 1.6 - - + -
338A LEU 3.5 7.7 + - - +
339A GLN* 4.4 11.9 - - - +
340A TYR 3.4 0.4 - - - -
341A PHE* 1.3 84.3 - - + +
343A GLU* 1.3 78.4 + - + +
345A PHE* 3.0 16.7 - - + +
346A TYR* 2.9 27.6 + - + +
367A GLY 5.0 5.4 - - - +
368A LEU* 4.9 4.7 - - + -
371A GLY* 4.7 11.0 - - - +
372A PRO* 4.2 28.5 - - + -
375A VAL* 4.8 15.3 - - + -
376A ILE 6.1 0.2 - - - -
381A VAL* 5.5 4.3 - - + -
384A MSE 4.0 36.1 - - + +
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Residues in contact with GLU 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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339A GLN* 3.0 28.3 + - + +
340A TYR* 3.1 4.5 + - - +
342A MSE 1.3 88.4 - - + +
344A GLN* 1.3 65.9 + - - +
346A TYR* 3.2 46.8 - - - +
347A GLY* 3.0 18.5 + - - -
383A PHE* 5.6 3.6 - - - -
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Residues in contact with GLN 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A VAL* 4.6 11.9 - - - +
292A SER* 5.3 5.9 - - - -
295A GLU* 3.5 19.1 - - - +
299A LYS* 5.4 4.1 + - - +
340A TYR* 3.0 51.6 + - + +
341A PHE* 3.1 16.4 - - - +
343A GLU* 1.3 77.4 - - - +
345A PHE* 1.3 58.5 + - - -
347A GLY* 3.1 5.3 + - - -
348A ILE* 3.1 23.9 + - - +
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Residues in contact with PHE 345 (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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295A GLU* 3.0 28.9 - - - -
299A LYS* 4.5 0.9 - - + -
316A LEU* 4.4 7.6 - - + -
320A LEU* 3.6 21.8 - - + -
341A PHE* 3.1 29.8 + + - -
342A MSE 3.0 22.5 + - + +
344A GLN* 1.3 72.8 - - - +
346A TYR* 1.3 55.5 + - - +
348A ILE* 2.5 43.3 + - + +
349A ILE* 2.9 14.7 + - + +
363A ILE* 3.8 23.1 - - + -
364A ARG* 4.1 9.8 - - - +
367A GLY* 3.1 39.5 - - - -
368A LEU* 5.4 1.1 - - - +
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Residues in contact with TYR 346 (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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342A MSE 2.9 19.7 + - + +
343A GLU* 3.2 43.1 - - - +
345A PHE* 1.3 71.8 - - - +
347A GLY* 1.3 59.0 + - - +
349A ILE* 2.9 31.0 + - + +
350A ARG* 3.1 37.7 + - + +
368A LEU* 5.0 5.8 - - + -
383A PHE* 3.2 27.4 + + + +
384A MSE 3.9 31.2 - - + -
387A GLU* 5.4 7.5 - - + +
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Residues in contact with GLY 347 (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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343A GLU 3.0 11.9 + - - -
344A GLN* 3.1 6.0 + - - -
345A PHE 3.0 1.2 - - - -
346A TYR* 1.3 80.0 - - - +
348A ILE* 1.3 55.8 + - - +
349A ILE 3.1 0.2 - - - -
350A ARG* 4.3 4.3 - - - -
351A ASN* 2.9 45.2 + - - +
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Residues in contact with ILE 348 (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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299A LYS* 3.5 36.8 - - + +
344A GLN 3.1 10.4 + - - +
345A PHE* 2.5 37.4 + - + +
347A GLY* 1.3 72.4 - - - +
349A ILE* 1.3 57.4 + - - -
352A VAL* 3.4 16.4 - - - +
357A LYS* 3.5 38.1 - - + +
360A SER* 4.4 8.3 - - - +
363A ILE* 5.5 4.7 - - + -
364A ARG* 3.1 27.7 - - + +
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Residues in contact with ILE 349 (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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345A PHE* 3.5 10.3 - - + +
346A TYR* 2.9 23.3 + - + +
348A ILE* 1.3 77.8 - - - +
350A ARG* 1.3 61.3 + - + +
352A VAL* 3.0 17.2 - - - +
364A ARG* 3.4 34.8 - - + +
368A LEU* 3.3 44.6 - - + -
387A GLU* 3.6 33.2 - - + +
388A LEU* 4.9 8.5 - - + +
391A ARG* 3.6 17.2 + - + +
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Residues in contact with ARG 350 (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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346A TYR* 3.1 40.6 + - + +
347A GLY* 4.2 4.3 - - - +
349A ILE* 1.3 78.1 - - + +
351A ASN* 1.3 63.2 + - - +
352A VAL 3.0 4.0 - - - -
353A ASP* 2.6 45.0 + - - +
387A GLU* 2.5 43.5 + - + +
390A GLN* 5.0 2.2 + - - -
391A ARG* 4.9 2.4 - - - +
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Residues in contact with ASN 351 (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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347A GLY* 2.9 34.3 + - - +
350A ARG* 1.3 76.6 - - - +
352A VAL* 1.3 57.8 + - - +
353A ASP* 3.1 1.6 - - - +
354A SER* 3.1 16.4 + - - +
355A ASN* 2.9 43.1 + - - +
357A LYS* 4.5 7.9 - - - +
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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