Contacts of the helix formed by residues 411 - 421 (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 PRO 411 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A VAL 3.0 25.8 - - - +
408A TYR 3.2 15.0 - - - +
410A MSE 1.3 92.7 - - + +
412A SER* 1.3 58.1 + - - -
414A LEU* 3.4 10.3 - - + +
415A GLN* 2.9 26.2 + - - +
442A GLN* 3.4 14.6 - - - +
449A TYR* 3.3 17.9 - - + +
453A MSE 5.5 0.9 - - - -
456A VAL* 4.8 9.4 - - + +
457A CYS* 3.3 26.0 - - + -
460A ALA* 4.9 3.3 - - + +
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Residues in contact with SER 412 (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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362A ALA* 5.3 6.3 - - - -
366A TYR* 5.0 5.8 - - - -
408A TYR* 3.4 15.9 + - - -
409A GLN* 3.0 22.8 + - - -
411A PRO* 1.3 77.7 - - - +
413A PHE* 1.3 56.1 + - - -
415A GLN* 3.5 6.1 + - - +
416A SER* 2.5 35.1 + - - -
453A MSE 4.8 9.0 - - - +
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Residues in contact with PHE 413 (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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361A ILE* 3.3 34.3 - - + -
362A ALA* 3.9 16.8 - - + -
364A ARG* 6.2 0.4 - - - -
365A GLY* 6.1 3.1 - - - -
388A LEU* 4.9 1.2 - - - +
392A CYS* 3.9 18.6 - - - -
395A MSE 3.1 34.5 - - + -
405A ASP* 6.2 1.3 - - + -
409A GLN* 2.9 60.5 + - + +
410A MSE 3.7 19.5 - - + +
412A SER* 1.3 77.8 - - - +
414A LEU* 1.3 57.7 + - - +
416A SER* 2.7 16.4 + - - -
417A VAL* 2.8 23.9 + - - +
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Residues in contact with LEU 414 (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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392A CYS* 5.4 0.4 - - - -
410A MSE 2.9 26.8 + - - +
411A PRO* 3.4 6.5 - - + +
412A SER 3.1 0.4 - - - -
413A PHE* 1.3 74.9 - - - +
415A GLN* 1.3 54.8 + - - +
416A SER 3.2 0.2 - - - -
417A VAL* 2.8 24.7 + - + -
418A ALA* 2.6 34.9 + - + +
438A LEU* 4.4 20.2 - - + +
439A VAL* 6.0 1.1 - - - -
442A GLN* 3.5 36.3 - - + -
460A ALA* 3.6 22.2 - - + +
464A VAL* 4.0 26.5 - - + -
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Residues in contact with GLN 415 (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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366A TYR* 4.8 11.9 - - + -
369A PHE* 3.5 17.3 - - + -
411A PRO 2.9 23.3 + - - +
412A SER* 3.5 7.2 - - - +
414A LEU* 1.3 74.4 - - - +
416A SER* 1.3 57.5 + - - +
418A ALA* 2.8 31.3 + - - +
419A SER 3.2 5.7 + - - -
456A VAL* 4.7 15.0 + - + +
459A ARG* 5.2 4.0 - - - +
460A ALA* 4.6 19.8 - - - +
463A LYS* 2.6 36.7 + - - +
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Residues in contact with SER 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLY* 3.7 31.8 - - - -
366A TYR* 3.9 9.5 + - - -
369A PHE* 3.1 23.1 - - - -
388A LEU* 5.5 2.1 - - - +
412A SER 2.5 22.3 + - - -
413A PHE* 2.7 19.6 + - - -
415A GLN* 1.3 78.7 - - - +
417A VAL* 1.3 54.7 + - - +
420A VAL* 2.9 32.9 + - - +
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Residues in contact with VAL 417 (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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388A LEU* 3.5 16.8 - - + -
389A ILE* 5.9 3.8 - - + -
392A CYS* 3.3 28.7 - - + -
413A PHE 2.8 24.8 + - - +
414A LEU* 2.8 33.3 + - + +
416A SER* 1.3 72.6 - - - +
418A ALA* 1.3 52.6 + - - +
420A VAL* 3.1 9.2 - - + +
421A LEU* 2.7 59.2 + - + +
438A LEU* 3.9 14.8 - - + -
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Residues in contact with ALA 418 (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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414A LEU* 2.6 14.5 + - + +
415A GLN* 2.8 18.2 + - - +
417A VAL* 1.3 73.4 - - - +
419A SER* 1.3 56.2 + - - +
421A LEU* 3.1 14.8 + - - +
422A LEU* 2.9 25.3 + - - +
460A ALA* 4.8 3.6 - - - +
463A LYS* 3.3 35.2 - - + +
464A VAL* 4.3 14.0 - - + +
467A ALA* 5.1 2.4 - - - +
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Residues in contact with SER 419 (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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369A PHE* 3.0 36.3 - - - -
372A PRO 4.6 3.7 - - - +
373A CYS* 4.6 15.6 - - - -
415A GLN 3.2 4.4 + - - -
418A ALA* 1.3 76.1 - - - +
420A VAL* 1.3 64.8 + - - +
422A LEU* 2.9 38.0 + - - +
423A TYR* 3.8 10.4 - - - -
463A LYS* 3.0 17.3 + - - -
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Residues in contact with VAL 420 (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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365A GLY 5.0 0.4 - - - +
368A LEU* 3.0 37.9 - - + +
369A PHE* 4.4 1.6 - - - +
372A PRO* 5.0 6.3 - - + -
376A ILE* 5.3 0.3 - - - +
384A MSE 5.0 5.6 - - + +
385A TYR* 3.1 42.7 - - + +
388A LEU* 4.0 27.4 - - + -
389A ILE* 5.3 1.3 - - + -
416A SER 2.9 19.1 + - - +
417A VAL* 3.1 20.0 - - + +
419A SER* 1.3 78.0 - - - +
421A LEU* 1.3 59.1 + - + +
422A LEU 3.4 2.4 + - - -
423A TYR* 3.9 11.4 + - - +
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Residues in contact with LEU 421 (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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385A TYR* 3.0 38.6 - - + +
389A ILE* 4.6 7.2 - - + -
414A LEU* 5.2 0.2 - - + -
417A VAL* 2.7 45.7 + - + +
418A ALA* 3.1 6.5 + - - +
420A VAL* 1.3 68.4 - - - +
422A LEU* 1.3 52.5 + - - +
423A TYR 2.7 21.9 + - - +
424A LEU* 4.2 14.1 - - + +
435A LEU* 4.8 15.7 - - + -
438A LEU* 6.1 0.4 - - + -
464A VAL* 3.5 35.0 - - + +
467A ALA* 3.5 19.4 - - + +
468A LEU* 5.5 5.8 - - + -
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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