Contacts of the helix formed by residues 419 - 434 (chain B) in PDB entry 4LEY
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 CYS 419 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LEU* 3.2 19.2 - - - +
409B LYS* 4.9 3.6 - - - +
417B ALA 4.9 2.2 - - - +
418B PHE* 1.3 74.1 - - - +
420B SER* 1.3 66.9 + - - +
421B TYR* 3.2 23.4 + - - -
422B HIS* 3.2 35.3 + - - +
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Residues in contact with SER 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B SER* 5.5 0.2 + - - -
402B LYS* 4.0 35.0 + - - -
405B LEU* 4.0 10.4 - - - +
406B GLU* 6.5 1.1 - - - -
419B CYS* 1.3 73.5 - - - +
421B TYR* 1.3 61.7 + - - +
422B HIS 3.1 0.4 - - - -
423B VAL* 3.1 8.9 + - - +
424B LYS* 2.9 26.7 + - - +
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Residues in contact with TYR 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLU* 2.7 39.8 + - - -
419B CYS* 3.2 16.5 - - - -
420B SER* 1.3 81.5 + - - +
422B HIS* 1.3 55.1 + + + +
424B LYS* 3.7 19.5 - - + -
425B THR* 2.5 56.1 + - + -
428B PHE* 5.1 4.4 - + - -
467B HIS* 3.5 39.7 + + - -
468B TYR* 5.5 1.6 + - - +
469B PHE* 4.4 4.0 - - - -
475B LEU* 4.3 11.0 - - + -
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Residues in contact with HIS 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LEU* 5.7 0.7 - - + -
417B ALA 3.6 16.8 - - - -
418B PHE* 3.7 11.3 - - + +
419B CYS* 3.2 44.7 + - - +
420B SER 3.1 0.4 - - - -
421B TYR* 1.3 75.8 - + + +
423B VAL* 1.3 59.7 + - + +
425B THR* 3.5 0.6 + - - -
426B ALA* 2.9 31.4 + - - +
456B PHE* 3.8 15.9 - - + -
465B LEU* 3.5 17.0 - - + +
475B LEU* 4.1 29.5 + - + +
476B PHE* 4.0 15.5 - + + -
481B ILE* 4.1 17.2 - - + +
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Residues in contact with VAL 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LEU* 3.5 22.4 - - + -
401B MET* 3.5 47.3 - - + +
402B LYS* 4.0 10.1 - - + +
405B LEU* 3.9 28.3 - - + -
420B SER* 3.1 10.7 + - - +
422B HIS* 1.3 78.6 - - - +
424B LYS* 1.3 56.7 + - - +
426B ALA* 3.5 2.2 + - - +
427B ILE* 2.9 29.8 + - + +
452B LEU* 5.1 1.2 - - - +
456B PHE* 4.3 16.2 - - + -
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Residues in contact with LYS 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B GLY* 5.3 4.6 - - - -
202B GLU* 2.8 38.9 + - - -
368B SER* 5.7 0.8 - - - +
371B GLU* 2.8 31.1 + - - +
375B LEU* 4.1 5.8 - - - -
398B LEU* 4.1 17.9 - - + -
402B LYS* 4.8 8.7 - - - +
420B SER 2.9 14.6 + - - +
421B TYR* 3.7 22.2 - - + +
422B HIS 3.3 0.2 - - - -
423B VAL* 1.3 77.6 - - - +
425B THR* 1.3 56.6 + - - +
427B ILE* 3.2 11.3 - - + +
428B PHE* 2.9 57.9 + - + -
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Residues in contact with THR 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B TYR* 2.5 46.1 + - + -
422B HIS 3.8 4.3 - - - -
424B LYS* 1.3 72.5 - - - +
426B ALA* 1.3 67.2 + - - +
428B PHE* 3.1 14.1 + - - +
429B HIS* 3.0 33.1 + - + +
465B LEU* 4.3 8.3 - - + -
466B ASP 3.2 28.5 - - - +
467B HIS* 4.4 0.2 - - - -
468B TYR* 4.0 15.5 - - + +
475B LEU* 3.8 10.3 - - + +
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Residues in contact with ALA 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B HIS 2.9 18.2 + - - +
423B VAL* 3.7 4.0 - - - +
425B THR* 1.3 77.9 - - - +
427B ILE* 1.3 56.0 + - - +
429B HIS 3.1 2.3 + - - -
430B MET* 2.9 23.4 + - - +
452B LEU* 4.2 6.5 - - + -
455B PHE* 3.2 32.0 - - + -
456B PHE* 3.7 24.9 - - + -
459B CYS* 5.1 0.7 - - - -
465B LEU* 4.0 12.1 - - + +
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Residues in contact with ILE 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ARG 3.7 3.6 - - - +
397B CYS* 4.0 3.8 - - + -
398B LEU* 3.4 50.7 - - + +
423B VAL 2.9 15.6 + - - +
424B LYS* 3.2 17.7 - - - +
426B ALA* 1.3 73.0 - - - +
428B PHE* 1.3 62.1 + - + +
430B MET* 4.2 2.5 - - + -
431B TRP* 2.9 78.2 + - + +
440B TRP* 5.1 2.5 - - + -
452B LEU* 3.8 29.8 - - + +
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Residues in contact with PHE 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B TRP* 4.5 1.6 - + - -
371B GLU* 3.7 33.2 - - + -
374B ILE* 4.3 13.7 - - + -
375B LEU* 3.7 24.0 - - + -
421B TYR* 5.1 3.8 - + - -
424B LYS* 2.9 46.1 + - + -
425B THR* 3.2 13.0 - - - +
427B ILE* 1.3 77.6 - - - +
429B HIS* 1.3 55.7 + - - +
431B TRP* 3.3 23.9 + + - +
432B THR* 2.6 35.1 + - - -
468B TYR* 3.7 42.2 + + + -
469B PHE* 4.4 7.0 - + - -
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Residues in contact with HIS 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TYR* 3.9 14.9 + - - +
499A ASN* 4.3 17.3 + - - -
327B PRO* 5.6 0.7 - - + -
425B THR* 3.0 31.1 + - + +
426B ALA 3.4 6.3 - - - +
428B PHE* 1.3 77.6 - - - +
430B MET* 1.3 56.6 + - - +
432B THR* 3.3 7.1 + - - -
433B GLN* 2.9 31.5 + - - +
455B PHE* 3.5 18.4 - + + -
465B LEU* 4.1 12.8 - - + -
466B ASP* 3.0 39.7 + - + +
467B HIS 4.8 0.2 - - - -
468B TYR* 3.5 28.0 - + - -
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Residues in contact with MET 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B ALA 2.9 8.0 + - - +
427B ILE* 3.7 7.0 - - - +
428B PHE 3.2 0.2 - - - -
429B HIS* 1.3 74.8 - - - +
431B TRP* 1.3 54.8 + - - +
433B GLN* 2.9 44.2 + - + +
434B ASP* 2.7 55.5 + - - +
440B TRP* 4.0 16.1 - - + -
451B LYS* 3.9 20.4 - - + -
452B LEU* 3.7 41.3 - - + -
455B PHE* 3.6 29.6 - - + -
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Residues in contact with TRP 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B TRP* 3.6 43.0 + + + -
374B ILE* 4.7 3.8 - - + -
375B LEU* 3.7 29.6 - - + -
378B HIS* 5.1 6.3 - + + -
394B ARG* 3.5 50.6 - - + +
395B LYS* 4.9 1.1 - - + -
398B LEU* 4.3 5.2 - - + -
427B ILE* 2.9 52.0 + - + +
428B PHE* 3.7 35.9 - + - +
430B MET* 1.3 75.4 - - - +
432B THR* 1.3 60.2 + - - +
434B ASP 3.3 21.3 - - - +
435B PRO* 3.5 8.1 - - - +
440B TRP* 3.5 27.4 - + - -
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Residues in contact with THR 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A LYS 5.7 0.2 - - - +
495A TYR* 3.9 26.2 - - + +
327B PRO* 3.1 36.1 - - + +
328B ILE* 4.7 2.9 - - - -
331B TRP* 4.0 13.4 - - + +
428B PHE 2.6 18.2 + - - -
429B HIS 3.5 6.5 - - - -
431B TRP* 1.3 79.5 - - - +
433B GLN* 1.3 59.7 + - - +
435B PRO* 3.8 12.4 - - - +
468B TYR* 2.4 30.2 + - - +
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Residues in contact with GLN 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A GLU* 5.2 1.7 - - - +
412A PHE* 5.1 6.9 - - - -
491A LYS* 5.5 2.6 - - - +
492A LYS* 3.3 26.1 + - + +
495A TYR* 3.4 45.6 + - + +
496A GLU* 6.0 0.2 - - - -
506A LYS* 4.8 11.4 + - - -
429B HIS 2.9 9.5 + - - +
430B MET* 2.9 33.3 + - + +
432B THR* 1.3 79.2 - - - +
434B ASP* 1.3 66.1 + - - +
435B PRO* 3.2 9.7 - - - +
451B LYS* 6.0 0.3 - - - -
455B PHE* 3.4 32.6 - - - -
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Residues in contact with ASP 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A LYS* 3.1 23.9 + - - -
394B ARG* 4.2 0.7 + - - -
430B MET* 2.7 27.8 + - - +
431B TRP 3.3 8.7 - - - +
433B GLN* 1.3 75.0 - - - +
435B PRO* 1.3 63.3 - - - +
436B GLN 3.3 1.8 - - - -
439B GLN* 3.6 28.7 + - + +
440B TRP* 2.6 48.3 + - + +
451B LYS* 3.6 27.8 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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