Contacts of the helix formed by residues 491 - 510 (chain D) in PDB entry 4YJL
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 491 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489D THR* 3.1 16.9 + - + +
490D ASN* 1.3 75.3 - - - +
492D HIS* 1.3 60.4 + - - +
493D TYR* 3.2 13.8 - - - +
494D SER* 2.9 38.1 + - - -
495D ILE* 2.9 26.0 + - - +
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Residues in contact with HIS 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A LYS* 3.8 22.4 - - - +
490D ASN* 3.0 19.0 + - + -
491D ASP* 1.3 71.7 + - - +
493D TYR* 1.3 57.1 + - - +
495D ILE* 3.9 11.7 - - + +
496D THR* 2.8 35.7 + - - +
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Residues in contact with TYR 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A ASP 4.3 1.8 - - - -
435A LYS* 3.5 48.1 + - + +
441D PRO* 3.7 18.4 - - + -
442D VAL* 3.4 48.2 - - + +
445D GLN* 3.9 2.3 - - - -
446D ILE 3.3 11.1 + - - -
447D CYS* 3.0 36.8 + - + +
448D PRO* 3.7 5.0 - - - +
491D ASP* 3.2 13.3 + - - +
492D HIS* 1.3 77.8 - - - +
494D SER* 1.3 64.8 + - - +
496D THR* 3.8 2.1 - - - -
497D LEU* 3.0 29.6 + - + +
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Residues in contact with SER 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D PRO* 5.5 2.2 - - - -
482D ASP* 2.7 26.4 + - - -
486D TYR* 5.5 2.9 - - - -
489D THR* 3.5 15.4 - - - +
491D ASP* 2.9 24.7 + - - -
493D TYR* 1.3 75.5 - - - +
495D ILE* 1.3 64.2 + - - +
497D LEU* 3.4 12.0 - - - +
498D ARG* 3.0 47.0 + - - +
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Residues in contact with ILE 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489D THR* 3.7 15.7 - - + +
490D ASN* 3.4 40.6 - - - +
491D ASP 2.9 11.3 + - - +
492D HIS* 3.9 11.0 - - + +
493D TYR 3.3 0.2 - - - -
494D SER* 1.3 74.4 - - - +
496D THR* 1.3 65.4 + - - +
498D ARG* 3.3 9.8 + - - +
499D ARG* 3.0 36.5 + - + +
535D SER* 4.7 2.5 - - - +
537D SER* 3.6 35.9 - - - +
540D LEU* 4.5 12.2 - - + +
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Residues in contact with THR 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A GLY 5.5 2.2 - - - +
431A MET* 4.2 1.8 - - - -
435A LYS* 3.3 22.9 - - + -
447D CYS* 3.4 24.5 - - - -
492D HIS* 2.8 21.7 + - - +
493D TYR 3.8 0.7 - - - -
495D ILE* 1.3 77.7 - - - +
497D LEU* 1.3 61.6 + - - +
499D ARG* 3.1 22.4 + - - +
500D TYR* 2.9 47.9 + - + +
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Residues in contact with LEU 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441D PRO* 3.6 37.7 - - + -
446D ILE* 4.1 13.2 - - + -
447D CYS* 3.7 13.2 - - - -
450D VAL* 3.6 22.8 - - + +
478D LEU* 4.8 12.8 - - + +
479D LEU* 5.4 2.7 - - - -
482D ASP* 4.1 18.6 - - + +
493D TYR* 3.0 26.1 + - + +
494D SER* 3.4 12.6 - - - +
496D THR* 1.3 77.1 - - - +
498D ARG* 1.3 73.4 + - + +
501D ALA* 2.9 33.2 + - + +
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Residues in contact with ARG 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479D LEU* 3.7 27.4 - - + +
482D ASP* 2.9 45.5 + - + +
483D CYS* 3.6 14.9 - - - +
486D TYR* 3.8 3.6 - - - +
487D GLY 2.9 29.1 + - - -
488D LEU* 4.5 3.4 - - - +
489D THR* 3.8 10.8 + - - +
494D SER* 3.0 30.3 + - - +
495D ILE* 3.6 7.1 - - - +
497D LEU* 1.3 79.1 - - + +
499D ARG* 1.3 59.0 + - - +
501D ALA* 3.7 1.4 - - - +
502D GLY* 2.9 26.5 + - - -
532D GLN* 2.8 36.8 + - - -
540D LEU* 3.9 24.0 - - + +
544D ILE* 5.2 0.7 - - - +
801D EDO 3.7 6.3 + - - -
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Residues in contact with ARG 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495D ILE* 3.0 28.1 + - - +
496D THR* 3.1 31.9 + - - +
498D ARG* 1.3 77.0 - - - +
500D TYR* 1.3 73.9 + - + +
502D GLY 3.2 1.2 + - - -
503D MET* 2.9 45.2 + - - +
537D SER* 4.6 0.2 - - - -
539D ASP* 3.9 23.0 + - - +
540D LEU* 3.8 37.7 - - + +
543D VAL* 3.5 16.2 - - + +
506I TYR* 5.6 2.6 + - - -
508I PHE* 6.4 0.2 - - - -
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Residues in contact with TYR 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A GLU* 4.1 7.8 - - + +
429A PRO 3.7 15.2 + - - -
430A GLY 5.2 0.3 - - - -
431A MET* 3.6 25.1 - - - +
447D CYS* 3.9 8.1 - - - -
450D VAL* 3.7 25.1 - - + +
451D CYS* 3.5 35.2 - - + -
454D MET* 3.7 34.6 - - + +
496D THR* 2.9 40.8 + - + +
499D ARG* 1.3 87.1 + - + +
501D ALA* 1.3 64.8 + - - +
503D MET* 3.3 17.9 + - + +
504D ALA* 3.1 20.4 + - - +
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Residues in contact with ALA 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D VAL* 4.1 15.6 - - + +
475D ILE* 3.6 21.6 - - + +
478D LEU* 5.1 2.5 - - + -
479D LEU* 4.2 22.9 - - + +
497D LEU* 2.9 19.3 + - + +
498D ARG* 3.7 4.5 - - - +
500D TYR* 1.3 74.7 - - - +
502D GLY* 1.3 59.4 + - - +
504D ALA* 3.2 6.5 + - - +
505D LEU* 3.0 32.5 + - - +
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Residues in contact with GLY 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479D LEU* 4.5 5.8 - - - +
498D ARG 2.9 13.8 + - - -
501D ALA* 1.3 77.4 - - - +
503D MET* 1.3 56.2 + - - +
505D LEU* 3.3 7.5 + - - -
506D THR* 2.9 31.0 + - - -
543D VAL* 3.5 21.1 - - - -
544D ILE* 5.3 2.5 - - - -
547D VAL* 3.3 13.5 - - - +
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Residues in contact with MET 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454D MET* 3.6 35.2 - - + -
458D PHE* 4.6 4.7 - - + -
499D ARG* 2.9 33.1 + - - +
500D TYR* 3.6 25.4 - - + +
502D GLY* 1.3 72.7 - - - +
504D ALA* 1.3 60.4 + - - +
506D THR* 3.3 5.0 + - - -
507D ASN* 3.0 33.9 + - - +
543D VAL* 3.6 6.0 - - + +
506I TYR* 3.5 57.7 - - + +
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Residues in contact with ALA 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D VAL 5.4 0.4 - - - +
453D LEU* 4.5 1.6 - - + +
454D MET* 4.1 14.3 - - - +
457D SER* 3.6 21.7 + - - +
475D ILE* 3.9 26.9 - - + -
500D TYR 3.1 12.9 + - - +
501D ALA* 3.5 8.1 - - - +
503D MET* 1.3 76.0 - - - +
505D LEU* 1.3 59.0 + - - +
507D ASN* 3.1 3.1 + - - +
508D LEU* 2.8 35.4 + - + +
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Residues in contact with LEU 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D LEU* 3.9 35.7 - - + +
475D ILE* 3.9 18.8 - - + -
476D ALA* 4.0 17.7 - - + +
479D LEU* 3.8 29.2 - - + -
501D ALA 3.0 16.4 + - - +
502D GLY* 3.3 9.8 + - - +
504D ALA* 1.3 76.1 - - - +
506D THR* 1.3 59.5 + - - +
508D LEU* 3.8 3.9 - - + +
509D THR* 2.9 32.2 + - - +
519D LEU* 4.3 21.1 - - + -
525D CYS* 5.0 0.7 - - - -
529D LEU* 4.7 7.2 - - + -
547D VAL* 4.1 8.7 - - + -
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Residues in contact with THR 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502D GLY 2.9 17.1 + - - -
503D MET 3.5 8.5 - - - -
504D ALA 3.2 0.4 - - - -
505D LEU* 1.3 75.4 - - - +
507D ASN* 1.3 61.9 + - - +
509D THR* 3.1 11.0 + - - -
510D PHE* 3.2 4.0 + - - +
543D VAL 4.0 0.9 + - - -
546D SER* 3.6 21.0 - - - +
547D VAL* 3.2 24.7 + - - +
550D ASN* 2.8 35.1 + - - +
504I ALA 3.6 3.8 - - - +
505I LEU 4.5 0.2 - - - +
506I TYR* 3.5 34.6 - - + +
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Residues in contact with ASN 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457D SER* 2.9 41.8 + - - +
458D PHE* 3.3 39.4 - - - +
463D ARG* 3.3 18.1 + - - -
503D MET 3.0 15.4 + - - +
504D ALA 3.1 2.7 + - - +
506D THR* 1.3 74.2 - - - +
508D LEU* 1.3 59.9 + - - +
509D THR 3.5 0.7 + - - -
510D PHE* 3.5 16.2 + - - +
505I LEU* 3.5 17.7 - - + +
506I TYR* 2.8 29.3 + - - +
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Residues in contact with LEU 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457D SER* 4.7 2.5 - - - -
463D ARG* 4.0 27.8 - - + +
466D MET* 3.9 35.2 - - + -
467D ASN* 3.9 18.3 + - - +
471D GLY 4.3 0.2 - - - -
472D LEU* 3.8 46.7 - - + +
475D ILE* 4.0 12.3 - - + -
504D ALA 2.8 25.4 + - - +
505D LEU* 4.0 2.0 - - + +
506D THR 3.3 0.2 - - - -
507D ASN* 1.3 73.6 - - - +
509D THR* 1.3 58.5 + - - +
510D PHE 3.5 0.4 - - - -
512D ASP* 3.5 8.9 - - - +
515D ASN* 2.8 28.2 + - - +
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Residues in contact with THR 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D LEU* 3.9 17.9 - - + -
505D LEU 2.9 20.0 + - - +
506D THR* 3.1 11.6 + - - -
508D LEU* 1.3 78.8 - - - +
510D PHE* 1.3 66.4 + - - +
511D GLY 3.1 3.3 + - - -
512D ASP 3.2 5.3 + - - -
515D ASN* 4.2 14.6 - - - +
516D LYS* 3.1 27.2 - - - +
519D LEU* 4.2 7.6 - - + -
547D VAL* 4.8 3.4 + - + +
550D ASN* 3.3 22.1 + - - +
551D LEU* 4.0 21.5 - - + -
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Residues in contact with PHE 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463D ARG* 4.8 12.7 + - - -
506D THR 3.2 7.0 + - - +
507D ASN 3.7 14.4 - - - +
508D LEU 3.5 1.5 - - - +
509D THR* 1.3 74.5 - - - +
511D GLY* 1.3 62.7 + - - +
512D ASP* 3.0 10.6 + - - +
550D ASN* 3.8 5.8 - - - +
503I ASP* 3.5 32.8 - - - -
504I ALA* 3.5 33.4 - - - +
505I LEU* 3.7 33.4 - - + +
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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