Contacts of the helix formed by residues 331 - 344 (chain A) in PDB entry 5LS6
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 ALA 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A LYS* 4.3 4.0 - - - +
325A TYR* 3.1 49.0 - - - +
326A GLN* 3.8 15.5 - - - -
327A HIS* 4.2 7.0 - - - -
328A LEU 3.0 15.6 + - - +
330A GLY* 1.3 83.2 - - - +
332A LYS* 1.3 60.4 + - + +
333A GLU* 5.4 0.6 - - - +
335A ALA* 3.3 10.6 - - - +
467A TYR* 3.7 5.4 - - - -
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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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315A LEU 5.2 1.4 + - - -
316A ASP* 3.4 39.0 + - - +
317A ASN* 4.2 14.6 + - - +
318A LYS* 4.3 21.5 - - + +
325A TYR* 3.5 28.7 + - + +
331A ALA* 1.3 78.1 - - + +
333A GLU* 1.3 64.1 + - + +
335A ALA* 3.9 1.5 - - - +
336A ALA* 3.1 35.2 + - + +
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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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327A HIS 5.8 0.2 - - - +
329A GLU* 3.6 32.8 - - - +
330A GLY* 3.8 13.6 + - - +
331A ALA 3.3 0.8 - - - -
332A LYS* 1.3 82.5 - - + +
334A PHE* 1.3 52.9 + - - +
336A ALA* 3.7 2.4 - - - +
337A ALA* 2.7 35.1 + - - +
422A PRO* 4.7 9.2 - - + +
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Residues in contact with PHE 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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330A GLY* 3.4 26.2 + - - +
333A GLU* 1.3 77.0 - - - +
335A ALA* 1.3 56.8 + - - +
337A ALA* 3.6 11.2 - - + -
338A LEU* 2.8 67.0 + - + +
341A GLU* 3.9 18.2 - - - -
422A PRO* 4.0 33.0 - - + +
423A ASN* 4.9 7.9 - - + -
467A TYR* 4.3 11.4 - - - +
471A VAL* 4.5 15.0 - - + -
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Residues in contact with ALA 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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325A TYR* 3.9 6.5 - - + +
330A GLY 3.8 0.8 + - - -
331A ALA 3.3 22.0 + - - +
332A LYS* 3.9 4.0 - - - +
334A PHE* 1.3 81.3 - - - +
336A ALA* 1.3 63.9 + - - +
338A LEU* 3.2 12.0 + - - +
339A THR* 3.4 5.5 + - - -
449A ASP* 2.8 20.2 - - + +
451A PHE* 3.7 30.3 - - + -
467A TYR* 4.2 7.8 - - + -
470A ARG* 5.7 2.5 - - - +
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LYS* 3.1 20.5 + - + +
333A GLU* 4.0 2.0 - - - +
335A ALA* 1.3 78.7 - - - +
337A ALA* 1.3 56.5 + - - +
339A THR* 3.8 3.4 + - - -
340A ALA* 3.0 28.8 + - - +
449A ASP* 4.4 5.1 - - - +
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Residues in contact with ALA 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 2.7 23.0 + - - +
334A PHE* 3.6 19.7 - - + +
336A ALA* 1.3 70.6 - - - +
338A LEU* 1.3 55.9 + - - +
340A ALA* 2.9 8.5 + - - +
341A GLU* 2.5 47.2 + - + +
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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
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334A PHE* 2.8 58.5 + - + +
335A ALA* 3.2 4.2 + - - +
337A ALA* 1.3 71.1 - - - +
339A THR* 1.3 51.7 + - - +
341A GLU* 3.3 20.2 + - + +
342A ARG* 2.7 35.8 + - - +
470A ARG* 3.4 24.7 + - + +
471A VAL* 4.2 13.7 - - + -
474A SER* 3.2 37.5 - - - +
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Residues in contact with THR 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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335A ALA 3.4 2.9 + - - -
336A ALA* 4.4 4.3 - - - -
337A ALA 3.1 0.4 - - - -
338A LEU* 1.3 75.0 - - - +
340A ALA* 1.3 59.3 + - - +
342A ARG* 3.6 7.4 - - + -
343A ILE* 2.9 29.2 + - + +
448A TYR* 5.2 14.4 - - + -
449A ASP* 2.7 40.8 + - - +
470A ARG* 2.9 12.9 + - - +
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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 ALA 3.0 21.1 + - - +
337A ALA* 2.9 8.2 + - - +
339A THR* 1.3 75.3 - - - +
341A GLU* 1.3 55.4 - - + +
343A ILE* 3.4 23.3 - - + +
344A LYS* 3.5 21.9 - - - +
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Residues in contact with GLU 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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334A PHE* 3.9 16.0 - - - -
337A ALA* 2.5 23.0 + - + +
338A LEU* 3.5 35.3 + - + +
340A ALA* 1.3 72.6 - - + +
342A ARG* 1.3 61.8 + - - +
343A ILE 3.5 0.4 - - - -
344A LYS* 4.1 25.5 + - - +
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Residues in contact with ARG 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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338A LEU* 2.7 18.0 + - - +
339A THR* 3.5 13.0 + - + +
340A ALA 3.5 0.2 - - - -
341A GLU* 1.3 76.8 - - - +
343A ILE* 1.3 61.1 + - - +
344A LYS 3.5 5.3 + - - +
345A THR* 5.2 0.3 + - - -
470A ARG* 4.8 14.4 - - - +
474A SER* 6.2 2.5 - - - -
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Residues in contact with ILE 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 THR* 2.9 18.5 + - + +
340A ALA* 3.4 23.1 - - + +
342A ARG* 1.3 76.2 - - - +
344A LYS* 1.3 72.8 + - + +
345A THR* 3.4 9.7 + - - -
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Residues in contact with LYS 344 (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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340A ALA* 3.5 22.9 - - - +
341A GLU* 4.1 19.9 + - - +
342A ARG 3.5 6.6 - - - +
343A ILE* 1.3 85.8 - - + +
345A THR* 1.3 62.6 + - - +
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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