Contacts of the helix formed by residues 413 - 425 (chain A) in PDB entry 1SLY
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 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A LYS 5.4 1.0 + - - +
412A SER* 1.3 70.3 - - - +
414A THR* 1.3 60.7 + - - +
416A GLN* 3.1 25.5 + - - +
417A ALA* 3.2 21.0 + - - +
438A ALA 4.0 5.7 + - - -
439A GLY* 3.1 32.0 - - - +
440A LYS* 4.5 12.9 - - - +
441A LEU* 3.8 16.5 - - + +
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Residues in contact with THR 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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372A PRO* 4.3 5.9 - - + +
412A SER* 2.8 22.3 + - - -
413A LYS* 1.3 78.9 - - + +
415A GLU* 1.3 60.1 + - - +
417A ALA* 3.0 9.5 + - - +
418A GLN* 2.9 32.1 + - - +
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Residues in contact with GLU 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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376A ASP* 5.1 1.7 - - - +
378A ALA* 6.0 0.5 - - - +
379A LEU* 3.9 31.1 - - + +
411A LYS* 3.7 20.3 - - + +
412A SER* 3.0 26.5 + - - +
414A THR* 1.3 75.6 + - - +
416A GLN* 1.3 62.5 + - - +
417A ALA 3.1 1.3 - - - -
418A GLN* 3.6 20.1 - - - +
419A LEU* 2.8 37.2 + - - +
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Residues in contact with GLN 416 (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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408A VAL* 3.0 34.1 - - + +
409A LYS* 4.7 4.3 - - - +
411A LYS* 3.6 20.9 + - + +
412A SER 3.0 8.6 + - - +
413A LYS* 3.1 36.0 + - - +
415A GLU* 1.3 76.9 - - - +
417A ALA* 1.3 57.1 + - - +
419A LEU* 3.9 7.9 - - + +
420A ALA* 3.1 22.0 + - - +
435A ALA* 4.1 8.9 - - - +
438A ALA* 4.4 4.2 - - - +
439A GLY* 3.1 38.0 + - - -
441A LEU* 3.5 11.0 - - + +
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Residues in contact with ALA 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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371A ALA* 4.4 2.9 - - - +
372A PRO* 3.6 22.3 - - + +
413A LYS 3.2 15.0 + - - +
414A THR* 3.0 14.6 + - - +
416A GLN* 1.3 76.5 - - - +
418A GLN* 1.3 61.3 + - - +
420A ALA* 3.6 3.0 + - - +
421A ARG* 3.2 22.3 + - - +
441A LEU* 3.6 16.8 - - + +
444A HIS* 4.5 16.2 - - + +
447A GLU* 4.9 0.4 - - - +
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Residues in contact with GLN 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PRO* 3.8 17.7 - - + +
374A ASN* 2.6 47.9 + - - +
375A VAL* 3.5 28.6 - - + +
376A ASP* 3.5 15.9 + - - +
379A LEU* 4.1 7.7 - - + +
414A THR* 2.9 16.1 + - - +
415A GLU* 3.6 29.3 + - + +
417A ALA* 1.3 76.3 - - - +
419A LEU* 1.3 56.9 + - - +
421A ARG* 3.0 5.2 + - - +
422A TYR* 2.8 26.9 + - - +
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Residues in contact with LEU 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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375A VAL* 5.7 0.2 - - + -
379A LEU* 3.9 32.3 - - + -
380A THR* 5.2 2.9 - - - +
385A MET* 3.7 30.1 - - + -
404A TRP* 3.5 21.8 - - + -
407A LEU* 4.1 12.1 - - + +
408A VAL* 3.8 40.4 - - + -
411A LYS* 4.7 5.8 - - + -
415A GLU 2.8 29.5 + - - +
416A GLN* 3.9 7.4 - - - +
418A GLN* 1.3 71.2 - - - +
420A ALA* 1.3 62.0 + - - +
422A TYR* 3.6 5.1 - - + +
423A ALA 3.1 18.5 + - - -
435A ALA* 4.8 0.2 - - + -
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Residues in contact with ALA 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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416A GLN 3.1 19.3 + - - +
417A ALA* 3.7 7.4 - - - +
418A GLN 3.3 0.2 - - - -
419A LEU* 1.3 74.8 - - - +
421A ARG* 1.3 59.6 + - - +
423A ALA* 3.5 1.4 + - - +
424A PHE* 2.8 29.9 + - - +
432A SER* 3.5 13.1 + - - +
435A ALA* 3.8 19.2 - - + +
436A THR* 4.6 6.5 - - - +
441A LEU* 4.7 3.8 - - + -
447A GLU* 4.1 22.7 - - + +
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Residues in contact with ARG 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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371A ALA* 4.1 15.8 + - + +
372A PRO* 4.4 16.4 - - + +
375A VAL* 4.2 8.1 - - + -
417A ALA 3.2 11.0 + - - +
418A GLN* 3.0 8.6 + - - +
420A ALA* 1.3 81.0 - - - +
422A TYR* 1.3 50.7 + - - +
424A PHE* 3.1 28.5 + - - +
425A ASN* 2.8 67.6 + - - +
446A GLU* 3.3 21.6 + - - +
447A GLU* 3.1 27.0 + - - +
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Residues in contact with TYR 422 (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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375A VAL* 4.1 17.4 - - + +
380A THR* 3.9 38.8 + - + +
385A MET* 3.7 38.8 - - + +
389A ARG* 3.1 28.3 + - - -
404A TRP* 5.2 0.9 - + - -
418A GLN 2.8 18.4 + - - +
419A LEU* 3.6 8.3 - - - +
421A ARG* 1.3 67.6 - - - +
423A ALA* 1.3 67.1 + - - +
425A ASN* 3.0 22.5 + - + +
426A ASN* 3.0 38.3 + - - +
428A TRP* 4.3 7.6 - + - -
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Residues in contact with ALA 423 (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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404A TRP* 3.8 16.8 - - + -
419A LEU 3.1 14.7 + - - +
420A ALA 3.7 2.9 - - - +
422A TYR* 1.3 78.3 - - - +
424A PHE* 1.3 64.9 + - - +
426A ASN* 3.0 11.6 + - - -
428A TRP* 3.2 37.5 + - + +
431A LEU* 4.0 9.9 - - + -
432A SER* 3.8 22.0 - - - +
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Residues in contact with PHE 424 (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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420A ALA 2.8 18.7 + - - +
421A ARG* 3.1 51.6 - - - +
423A ALA* 1.3 71.9 - - - +
425A ASN* 1.3 62.8 + - - +
427A GLN* 3.3 16.1 + - - +
429A TRP* 4.3 13.1 + + - -
432A SER* 3.4 21.0 + - - +
446A GLU* 3.2 47.1 - - - -
447A GLU* 3.9 8.5 - - + -
450A PRO* 3.7 20.2 - - + -
451A LEU 5.3 1.6 - - - -
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Residues in contact with ASN 425 (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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375A VAL* 5.0 4.6 - - - +
421A ARG* 2.8 60.7 + - - +
422A TYR* 3.0 13.5 + - + +
424A PHE* 1.3 77.9 - - - +
426A ASN* 1.3 63.1 + - - +
427A GLN* 3.3 6.8 + - - +
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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