Contacts of the helix formed by residues 362 - 384 (chain A) in PDB entry 1LDK
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 ASP 362 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A ALA* 3.5 16.4 - - - +
360A LEU 2.6 11.5 + - - +
361A ASN* 1.3 76.2 - - - +
363A PRO* 1.3 66.9 - - - +
364A LYS* 3.3 6.7 + - - +
365A MET* 2.7 51.8 + - + +
366A TYR* 3.5 10.9 + - - +
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Residues in contact with PRO 363 (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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360A LEU 4.7 0.2 - - - +
361A ASN 4.0 2.9 - - - +
362A ASP* 1.3 86.4 - - - +
364A LYS* 1.3 64.8 + - - +
366A TYR* 3.5 5.9 - - - +
367A VAL* 3.4 22.1 + - - +
421B LEU* 3.5 16.2 - - + +
424B ARG* 3.5 60.3 - - + +
425B TYR* 4.2 9.4 - - - +
428B SER* 5.8 3.4 - - - -
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Residues in contact with LYS 364 (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 ASP* 3.2 5.1 + - - +
363A PRO* 1.3 73.8 - - - +
365A MET* 1.3 64.7 + - - +
366A TYR 2.9 2.5 - - - -
367A VAL* 2.3 29.3 + - - +
368A GLN* 2.6 28.3 + - + +
425B TYR* 3.3 48.6 - - + +
428B SER* 5.6 4.5 - - - +
429B LEU* 5.7 1.3 - - + -
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Residues in contact with MET 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A CYS* 3.8 25.1 - - + -
359A ALA* 4.6 15.9 - - + +
362A ASP* 2.7 42.9 + - + +
364A LYS* 1.3 76.6 - - - +
366A TYR* 1.3 49.4 + - - +
368A GLN* 3.2 8.2 - - - +
369A THR* 2.6 48.3 + - - +
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Residues in contact with TYR 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ILE* 4.7 16.8 - - + -
355A CYS* 5.9 1.6 - - - -
360A LEU* 5.5 5.8 - - - +
362A ASP 3.5 7.3 + - - +
363A PRO 3.5 10.3 - - - +
364A LYS 2.7 3.2 + - - -
365A MET* 1.3 73.9 - - - +
367A VAL* 1.3 84.3 + - + +
368A GLN 2.8 2.5 + - - -
369A THR* 3.0 16.3 + - - -
370A VAL* 3.1 35.4 + - + +
403A ILE* 3.2 17.1 + - + -
406A ASN* 4.7 5.3 + - + +
408A VAL* 3.1 45.9 - - + +
409A THR* 5.4 0.2 + - - -
418B SER* 2.6 39.0 + - - -
421B LEU* 4.0 18.2 - - + -
422B LEU* 5.4 1.6 - - + -
452B VAL* 6.2 2.9 - - + -
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Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PRO 3.4 15.9 - - - +
364A LYS 2.3 15.3 + - - +
366A TYR* 1.3 90.8 - - + +
368A GLN* 1.3 68.2 + - - +
370A VAL* 3.2 8.2 - - - +
371A LEU* 3.1 21.0 + - + +
422B LEU* 3.3 44.2 - - + +
425B TYR* 3.6 40.6 - - + -
449B VAL* 5.0 0.9 - - + -
452B VAL* 3.9 14.5 - - + +
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Residues in contact with GLN 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LYS* 2.6 34.9 + - + +
365A MET* 3.2 13.9 - - + +
367A VAL* 1.3 78.0 - - - +
369A THR* 1.3 57.2 + - - +
371A LEU* 2.4 35.6 + - - +
372A ASP* 3.0 32.9 + - - +
425B TYR* 4.3 12.7 + - + +
448B GLN* 4.4 14.3 + - - +
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Residues in contact with THR 369 (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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351A ALA* 3.7 15.0 - - + +
352A ILE* 3.6 41.3 - - + +
355A CYS* 3.3 19.0 - - - -
365A MET* 2.6 31.4 + - - +
366A TYR* 3.4 7.9 - - - -
368A GLN* 1.3 71.3 - - - +
370A VAL* 1.3 65.8 + - - +
372A ASP* 3.6 9.0 + - - +
373A VAL* 3.4 19.8 + - - +
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Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ILE* 4.8 7.2 - - + -
366A TYR* 3.2 43.1 - - + +
367A VAL* 3.2 9.0 - - + +
368A GLN 2.8 1.2 + - - -
369A THR* 1.3 72.8 - - - +
371A LEU* 1.3 72.6 + - - +
373A VAL* 3.2 8.7 + - - +
374A HIS* 3.0 20.8 + - + +
402A PHE* 3.5 37.6 - - + -
403A ILE* 4.1 21.3 - - + -
452B VAL* 5.0 12.6 - - + -
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Residues in contact with LEU 371 (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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367A VAL* 3.6 12.1 - - + +
368A GLN* 2.4 23.2 + - - +
370A VAL* 1.3 76.6 - - - +
372A ASP* 1.3 67.3 + - - +
374A HIS* 2.7 21.3 + - + +
375A LYS* 2.8 36.2 + - + +
425B TYR* 5.8 3.4 - - + -
448B GLN* 3.1 57.7 - - + +
449B VAL* 4.3 0.9 - - - +
451B VAL* 4.4 11.7 - - + -
452B VAL* 3.3 30.3 - - + -
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Residues in contact with ASP 372 (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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368A GLN* 3.0 27.9 + - - +
369A THR* 3.6 11.5 - - - +
371A LEU* 1.3 77.4 - - - +
373A VAL* 1.3 68.6 + - + +
375A LYS* 2.6 24.1 + - - +
376A LYS* 3.1 10.2 + - - +
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Residues in contact with VAL 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ILE* 4.5 5.6 - - + +
347A GLN* 4.4 2.5 - - + +
348A GLY* 3.7 39.0 - - - +
351A ALA* 3.8 16.4 - - + -
369A THR* 3.5 14.6 - - + +
370A VAL* 3.2 7.0 + - - +
372A ASP* 1.3 80.7 - - + +
374A HIS* 1.3 67.8 + - - +
376A LYS* 3.1 13.3 + - - +
377A TYR* 3.3 36.5 + - + -
399A CYS* 6.6 0.2 - - - -
402A PHE* 5.0 6.1 - - + -
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Residues in contact with HIS 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ILE* 6.5 0.2 - - - -
370A VAL* 3.0 14.1 + - + +
371A LEU* 2.7 19.8 + - + +
373A VAL* 1.3 74.6 - - - +
375A LYS* 1.3 73.7 + - + -
377A TYR* 3.3 2.2 + - - +
378A ASN* 2.8 53.6 + - + +
395A LEU* 3.5 23.5 - - + +
399A CYS* 4.0 17.7 - - - -
402A PHE* 5.5 1.7 - - + -
451B VAL* 3.5 37.0 - - + +
455B TYR* 3.9 25.0 - + + -
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Residues in contact with LYS 375 (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 LEU* 2.8 41.8 + - + +
372A ASP* 2.6 18.6 + - - +
374A HIS* 1.3 84.0 + - + +
376A LYS* 1.3 53.8 + - - +
378A ASN* 4.5 6.9 + - + +
379A ALA* 2.7 38.7 + - - +
448B GLN* 4.0 15.8 - - - +
451B VAL* 5.0 10.9 - - - +
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Residues in contact with LYS 376 (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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314A ASP* 2.9 41.5 + - - -
316A ASN* 5.9 4.0 - - - +
347A GLN* 4.7 7.4 - - - +
372A ASP 3.1 6.4 + - - +
373A VAL* 3.1 11.2 + - - +
375A LYS* 1.3 77.4 - - - +
377A TYR* 1.3 95.3 + - + +
379A ALA* 2.9 22.6 - - - +
380A LEU* 2.9 14.0 + - + +
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Residues in contact with TYR 377 (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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311A LEU* 4.2 13.9 + - + -
314A ASP* 5.7 0.2 - - - -
340A LEU* 4.5 6.1 - - + -
343A HIS* 3.1 32.7 + + - -
344A ILE* 3.3 46.9 - - + -
347A GLN* 3.3 19.7 + - + +
373A VAL* 3.3 33.4 + - + +
374A HIS* 4.1 2.0 - - - +
375A LYS 3.2 0.4 - - - -
376A LYS* 1.3 105.4 + - + +
378A ASN* 1.3 67.9 + - - +
379A ALA 3.0 0.4 - - - -
380A LEU* 3.7 21.2 - - + +
381A VAL* 2.9 27.9 + - + +
395A LEU* 3.9 6.1 - - + -
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Residues in contact with ASN 378 (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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374A HIS* 2.8 40.9 + - + +
375A LYS* 3.9 8.5 + - + +
377A TYR* 1.3 71.3 - - - +
379A ALA* 1.3 66.3 + - - +
381A VAL* 2.9 20.4 + - - +
382A MET* 3.3 36.4 + - - +
387A ASN* 5.1 2.6 + - - -
392A VAL* 5.7 3.4 - - - +
395A LEU* 3.1 24.4 - - + +
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Residues in contact with ALA 379 (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 LYS 2.7 21.4 + - - +
376A LYS* 2.9 14.6 - - - +
378A ASN* 1.3 77.4 - - - +
380A LEU* 1.3 49.3 + - - +
382A MET* 3.8 8.8 + - - +
383A SER* 2.7 31.4 + - - -
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Residues in contact with LEU 380 (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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311A LEU* 4.6 5.2 - - + -
316A ASN* 3.1 42.6 - - + +
319A LEU* 3.6 23.3 - - + -
340A LEU* 5.6 0.4 - - + -
376A LYS* 2.9 18.9 + - + +
377A TYR* 3.8 26.9 - - + +
378A ASN 3.2 0.4 - - - -
379A ALA* 1.3 73.3 - - - +
381A VAL* 1.3 59.7 + - - +
383A SER* 3.1 10.3 - - - +
384A ALA* 2.7 62.4 + - + +
385A PHE* 3.3 16.4 + - + -
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Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LEU* 4.8 6.5 - - + -
377A TYR* 2.9 17.2 + - + +
378A ASN* 2.9 16.9 + - - +
380A LEU* 1.3 73.4 - - - +
382A MET* 1.3 59.7 + - - +
385A PHE* 3.0 17.9 + - + -
386A ASN 3.0 9.7 + - - -
387A ASN* 2.8 44.4 + - - +
391A PHE* 4.1 26.9 - - + +
392A VAL* 4.0 23.1 - - + +
395A LEU* 3.7 17.9 - - + -
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Residues in contact with MET 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ASN* 3.3 39.7 + - - +
379A ALA* 4.1 8.1 - - - +
381A VAL* 1.3 74.3 - - - +
383A SER* 1.3 60.5 + - - +
386A ASN* 3.0 27.9 + - - -
387A ASN* 3.3 27.3 + - + +
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Residues in contact with SER 383 (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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316A ASN* 6.0 0.2 - - - +
379A ALA 2.7 22.4 + - - -
380A LEU* 3.1 12.8 - - - +
382A MET* 1.3 82.0 - - - +
384A ALA* 1.3 71.2 + - - +
386A ASN* 4.1 2.3 + - - +
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Residues in contact with ALA 384 (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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316A ASN* 5.1 2.7 - - + +
319A LEU* 4.9 0.7 - - + -
320A GLY* 3.9 24.9 - - - +
323A TYR* 3.7 15.5 - - - +
324A ASN* 4.2 3.6 + - - -
380A LEU* 2.7 45.9 + - + +
383A SER* 1.3 82.9 + - - +
385A PHE* 1.3 70.5 + - + +
386A ASN* 3.3 2.9 + - - +
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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