Contacts of the helix formed by residues 419 - 434 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A LEU* 3.4 16.4 - - - +
409A LYS* 4.1 7.6 - - - +
417A ALA 5.1 1.6 - - - +
418A PHE* 1.3 75.8 - - - +
420A SER* 1.3 67.9 + - - +
421A TYR* 3.2 23.6 - - - -
422A HIS* 3.2 41.3 + - - +
423A VAL 4.0 0.2 + - - -
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Residues in contact with SER 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER* 5.4 0.3 + - - -
402A LYS* 4.0 34.1 + - - +
405A LEU* 4.2 10.0 - - - +
406A GLU* 6.1 3.4 - - - -
419A CYS* 1.3 72.1 - - - +
421A TYR* 1.3 60.8 + - - +
422A HIS 3.2 0.2 - - - -
423A VAL* 3.3 10.4 + - - +
424A LYS* 3.0 26.7 + - - +
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Residues in contact with TYR 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A GLU* 2.8 39.0 + - - -
419A CYS* 3.2 16.2 - - - -
420A SER* 1.3 78.0 + - - +
422A HIS* 1.3 61.3 + + - +
424A LYS* 3.9 21.1 - - + -
425A THR* 2.9 50.9 + - - -
428A PHE* 5.4 4.5 - + - -
467A HIS* 3.2 40.2 + + - -
468A TYR* 5.5 2.1 + - - +
469A PHE* 4.8 2.4 - - - -
475A LEU* 4.3 10.8 - - + -
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Residues in contact with HIS 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A LEU* 5.6 0.4 - - + -
417A ALA 3.5 25.4 - - - -
418A PHE* 3.6 9.4 - - - +
419A CYS* 3.2 36.7 + - - +
420A SER 3.2 0.2 - - - -
421A TYR* 1.3 82.0 - + + +
423A VAL* 1.3 56.3 + - + +
425A THR* 3.6 0.8 + - - -
426A ALA* 3.0 27.4 + - - +
456A PHE* 3.9 15.2 - - + -
465A LEU* 3.6 18.5 - - + +
475A LEU* 4.1 31.0 + - + +
476A PHE* 3.7 25.7 - + + -
481A ILE* 4.1 6.5 - - + +
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Residues in contact with VAL 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LEU* 3.9 10.1 - - + -
401A MET* 3.8 29.9 - - + +
402A LYS* 3.9 25.6 - - + +
405A LEU* 3.6 35.9 - - + -
419A CYS 4.1 0.7 - - - +
420A SER* 3.3 12.1 + - - +
422A HIS* 1.3 72.5 - - - +
424A LYS* 1.3 62.8 + - - +
426A ALA* 3.6 8.3 - - - +
427A ILE* 2.9 30.0 + - - +
452A LEU* 5.1 1.9 - - - +
456A PHE* 4.4 17.0 - - + -
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Residues in contact with LYS 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLY* 5.4 3.8 - - - -
202A GLU* 2.7 40.0 + - - +
368A SER* 5.6 1.2 - - - +
371A GLU* 2.6 31.0 + - - +
375A LEU* 4.2 4.3 - - - -
398A LEU* 4.3 16.8 - - + -
420A SER 3.0 17.2 + - - +
421A TYR* 3.6 22.0 - - + +
422A HIS 3.3 0.2 - - - -
423A VAL* 1.3 76.3 - - - +
425A THR* 1.3 65.6 + - - +
427A ILE* 3.2 11.0 - - + +
428A PHE* 3.0 51.5 + - + -
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Residues in contact with THR 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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421A TYR* 2.9 41.4 + - - -
422A HIS 3.7 4.7 - - - -
424A LYS* 1.3 75.6 - - - +
426A ALA* 1.3 63.5 + - - +
428A PHE* 3.1 14.1 + - - +
429A HIS* 3.0 37.1 + - + +
465A LEU* 3.8 11.7 - - + -
466A ASP 3.2 28.3 - - - +
468A TYR* 4.2 12.3 + - + +
475A LEU* 3.8 8.3 - - + +
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Residues in contact with ALA 426 (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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422A HIS 3.0 19.8 + - - +
423A VAL* 3.6 6.3 - - - +
425A THR* 1.3 76.9 - - - +
427A ILE* 1.3 55.4 + - - +
429A HIS 3.2 1.9 + - - -
430A MET* 2.9 25.1 + - - +
452A LEU* 4.3 9.6 - - + -
455A PHE* 3.5 31.2 - - + -
456A PHE* 3.7 23.6 - - + -
465A LEU* 4.2 7.2 - - + +
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Residues in contact with ILE 427 (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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394A ARG 3.7 4.5 - - - +
397A CYS* 4.2 4.5 - - + -
398A LEU* 3.6 47.8 - - + +
423A VAL 2.9 17.4 + - - +
424A LYS* 3.2 13.7 - - + +
426A ALA* 1.3 73.6 - - - +
428A PHE* 1.3 63.9 + - + +
430A MET* 3.7 1.7 - - + +
431A TRP* 2.9 79.8 + - + +
440A TRP* 4.7 6.1 - - + -
452A LEU* 3.8 27.1 - - + +
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Residues in contact with PHE 428 (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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331A TRP* 5.1 1.1 - + - -
371A GLU* 3.9 29.8 - - + -
374A ILE* 4.0 15.9 - - + -
375A LEU* 3.7 14.6 - - + -
421A TYR* 5.4 4.3 - + - -
424A LYS* 3.0 50.3 + - + -
425A THR* 3.1 14.8 + - - +
427A ILE* 1.3 77.0 - - + +
429A HIS* 1.3 57.1 + - - +
431A TRP* 3.1 36.9 + + - +
432A THR* 2.9 30.3 + - - -
468A TYR* 3.6 42.3 + + + -
469A PHE* 4.9 2.7 - + - -
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Residues in contact with HIS 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A PRO* 5.4 6.0 - - + +
425A THR* 3.0 36.4 + - + +
426A ALA 3.5 6.7 - - - +
428A PHE* 1.3 75.8 - - - +
430A MET* 1.3 58.6 + - - +
432A THR* 3.4 4.6 + - - +
433A GLN* 2.9 28.8 + - - +
455A PHE* 3.7 19.5 - + + -
465A LEU* 4.2 11.2 - - + -
466A ASP* 2.8 36.8 + - + +
467A HIS 4.9 0.2 - - - -
468A TYR* 3.5 30.5 - + - -
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Residues in contact with MET 430 (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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426A ALA 2.9 13.2 + - - +
427A ILE* 3.7 9.2 - - - +
428A PHE 3.2 0.2 - - - -
429A HIS* 1.3 76.9 - - - +
431A TRP* 1.3 61.2 + - - +
433A GLN* 3.2 42.5 + - + +
434A ASP* 2.8 37.6 + - - +
440A TRP* 3.9 15.9 - - + -
451A LYS* 4.3 25.1 - - + +
452A LEU* 3.8 26.7 - - + -
455A PHE* 3.5 39.9 - - + -
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Residues in contact with TRP 431 (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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331A TRP* 3.4 48.1 - + + -
374A ILE* 4.7 3.8 - - + -
375A LEU* 4.0 26.9 - - + -
378A HIS* 5.2 7.4 - + + -
394A ARG* 3.4 44.7 - - + +
395A LYS* 5.4 0.7 - - + -
398A LEU* 4.7 3.4 - - + -
427A ILE* 2.9 54.2 + - + +
428A PHE* 3.4 38.1 - + - +
430A MET* 1.3 73.6 - - - +
432A THR* 1.3 63.8 + - - +
434A ASP 3.2 21.5 - - - +
435A PRO* 3.2 9.2 - - - +
440A TRP* 3.3 30.0 - + - -
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Residues in contact with THR 432 (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 PRO* 3.1 30.8 + - + +
331A TRP* 4.0 11.0 - - + +
428A PHE 2.9 10.2 + - - -
429A HIS* 3.7 6.5 - - - +
430A MET 3.3 0.2 - - - -
431A TRP* 1.3 72.7 - - - +
433A GLN* 1.3 66.6 + - - +
435A PRO* 3.5 13.9 - - - +
468A TYR* 2.1 38.4 + - - -
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Residues in contact with GLN 433 (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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429A HIS 2.9 16.9 + - - +
430A MET* 3.2 32.9 - - + +
431A TRP 3.3 0.2 - - - -
432A THR* 1.3 79.1 - - - +
434A ASP* 1.3 73.7 + - - +
435A PRO* 3.2 8.0 - - - +
439A GLN* 5.0 0.7 + - - -
451A LYS* 4.2 15.0 - - - +
455A PHE* 4.8 6.8 - - - -
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Residues in contact with ASP 434 (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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394A ARG* 4.1 1.0 + - - -
430A MET* 2.8 19.6 + - - +
431A TRP 3.2 7.7 - - - +
433A GLN* 1.3 96.1 + - - +
435A PRO* 1.4 63.0 - - - +
436A GLN 3.5 0.3 + - - -
439A GLN* 3.2 34.2 + - + +
440A TRP* 2.9 34.0 + - - +
451A LYS* 3.0 35.7 + - - +
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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