Contacts of the helix formed by residues 539 - 560 (chain I) in PDB entry 3AOI
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 539 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538I SER* 1.3 75.8 + - - +
540I LEU* 1.3 58.9 + - + +
541I ASN 2.8 8.4 + - - -
542I ASP* 3.1 29.0 + - - +
543I LEU* 3.5 9.1 - - - +
598I ARG* 3.6 25.5 + - - +
600I LEU* 5.0 4.9 - - + +
601I ARG* 4.3 34.3 + - + +
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Residues in contact with LEU 540 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520I LEU* 5.1 9.0 - - + -
525I ARG* 3.5 34.8 - - + -
538I SER* 2.7 19.4 + - - +
539I ASP* 1.3 70.8 - - + +
541I ASN* 1.3 60.9 + - - +
542I ASP 3.4 0.2 - - - -
543I LEU* 3.3 17.9 + - + +
544I TYR* 3.1 38.6 + - + -
581I LEU* 5.5 2.0 - - + +
601I ARG* 3.9 18.6 - - + +
602I SER* 4.7 0.4 - - - -
603I LEU* 3.9 37.0 - - + +
606I ILE* 5.2 13.9 - - + -
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Residues in contact with ASN 541 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I THR* 5.6 2.5 - - + -
44I LEU* 3.7 19.2 - - + +
45I PHE* 5.1 11.9 - - + -
525I ARG* 2.6 42.1 + - - +
538I SER 2.7 37.5 + - - +
539I ASP 2.8 0.4 + - - -
540I LEU* 1.3 74.1 - - - +
542I ASP* 1.3 62.8 + - - +
544I TYR* 2.9 5.9 + - - +
545I ARG* 2.8 41.7 + - + +
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Residues in contact with ASP 542 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539I ASP* 3.1 19.1 + - - +
541I ASN* 1.3 82.3 + - - +
543I LEU* 1.3 60.9 + - - +
545I ARG* 3.4 27.8 + - - +
546I ARG* 3.1 23.9 + - - +
592I THR* 4.4 8.8 + - - -
598I ARG* 5.0 3.6 + - - -
600I LEU* 4.0 23.8 - - + +
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Residues in contact with LEU 543 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539I ASP 3.5 7.2 - - - +
540I LEU* 3.3 32.3 - - + +
542I ASP* 1.3 72.0 - - - +
544I TYR* 1.3 65.5 + - - +
546I ARG* 3.2 14.3 - - - +
547I LEU* 3.2 21.8 + - - +
577I ALA* 5.5 0.5 - - - +
580I ALA* 4.7 17.7 - - + +
581I LEU* 4.3 27.0 - - + +
584I ASN* 4.7 2.9 - - - +
590I PRO* 5.1 1.1 - - + -
600I LEU* 3.3 47.1 - - + +
601I ARG 3.9 16.6 - - - +
602I SER* 4.9 4.9 - - - -
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Residues in contact with TYR 544 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094H ALA* 4.9 2.1 + - - +
44I LEU* 4.4 14.1 - - + -
93I ILE* 4.3 13.9 - - + -
517I VAL* 4.6 0.9 - - + -
518I PRO 3.0 20.9 + - - -
519I VAL* 3.8 30.5 - - + -
520I LEU* 3.2 29.5 + - + +
525I ARG* 4.7 9.0 - - - -
540I LEU* 3.1 37.1 + - + -
541I ASN* 2.9 11.9 + - - +
543I LEU* 1.3 75.6 - - - +
545I ARG* 1.3 63.0 + - - +
546I ARG 3.3 0.2 + - - -
547I LEU* 3.4 5.1 + - + +
548I ILE* 2.8 32.2 + - + +
581I LEU* 3.3 37.4 - - + +
603I LEU* 4.6 12.0 - - + +
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Residues in contact with ARG 545 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I PRO* 4.4 21.1 + - + +
31I THR* 3.6 31.0 - - + -
44I LEU* 4.4 8.7 - - + -
541I ASN* 2.8 20.8 + - - +
542I ASP* 3.5 27.8 + - - +
544I TYR* 1.3 77.7 - - - +
546I ARG* 1.3 65.3 + - - +
548I ILE* 3.3 8.4 + - - +
549I ASN* 2.8 37.3 + - - +
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Residues in contact with ARG 546 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542I ASP 3.1 12.3 + - - +
543I LEU* 3.2 22.0 - - - +
545I ARG* 1.3 81.8 - - - +
547I LEU* 1.3 66.8 + - - +
549I ASN* 2.9 13.5 + - - +
550I ARG* 2.7 59.1 + - - +
577I ALA* 5.0 8.7 - - + +
580I ALA* 5.4 8.5 - - + -
590I PRO* 4.9 17.6 - - - +
591I VAL 5.0 10.7 + - - +
593I ASN* 5.5 4.9 + - - -
600I LEU* 5.8 4.3 - - - +
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Residues in contact with LEU 547 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I ILE* 4.4 12.8 - - + -
95I LEU* 5.4 2.7 - - + -
517I VAL* 3.8 40.2 - - + -
543I LEU 3.2 8.3 + - - +
544I TYR* 3.7 8.3 - - + +
546I ARG* 1.3 79.0 - - - +
548I ILE* 1.3 65.9 + - + +
550I ARG* 3.3 1.0 + - - +
551I ASN* 2.7 32.5 + - + +
574I LEU* 4.0 8.5 - - + +
577I ALA* 3.2 16.5 - - + +
578I VAL* 3.2 44.9 - - + +
581I LEU* 4.1 16.2 - - + -
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Residues in contact with ILE 548 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I VAL* 3.6 23.3 - - + +
27I GLU 4.5 0.9 - - - +
28I LYS* 3.8 9.2 - - - +
29I PRO* 3.5 33.9 - - + -
44I LEU* 5.1 9.9 - - + -
93I ILE* 3.3 36.1 - - + -
519I VAL* 5.2 0.2 - - + -
544I TYR* 2.8 29.5 + - + +
545I ARG* 3.5 7.9 - - - +
547I LEU* 1.3 76.5 - - - +
549I ASN* 1.3 63.5 + - - +
551I ASN* 3.4 7.9 + - - +
552I ASN* 2.8 39.0 + - - +
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Residues in contact with ASN 549 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I LYS* 5.4 1.6 - - - +
29I PRO* 3.2 34.7 - - - +
545I ARG* 2.8 26.8 + - - +
546I ARG* 2.9 11.8 + - - +
548I ILE* 1.3 70.5 - - - +
550I ARG* 1.3 56.5 + - + +
552I ASN* 2.8 8.0 + - - +
553I ARG* 2.6 37.2 + - - +
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Residues in contact with ARG 550 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546I ARG* 2.7 50.9 + - - +
547I LEU* 4.0 2.7 - - - +
549I ASN* 1.3 76.0 - - + +
551I ASN* 1.3 63.6 + - - +
553I ARG* 3.7 12.2 - - - +
554I LEU* 2.8 27.8 + - - +
570I GLU* 4.8 9.6 - - + +
573I MET* 3.1 71.1 + - + +
574I LEU* 4.5 13.9 - - + +
576I GLU* 4.4 8.3 + - - +
577I ALA* 4.6 10.2 - - + +
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Residues in contact with ASN 551 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I ILE* 3.1 33.3 - - + +
94I GLU 3.6 16.5 - - - +
95I LEU* 3.8 16.2 - - + -
96I ALA* 3.9 3.1 + - - +
547I LEU* 2.7 26.3 + - + +
548I ILE* 3.7 5.9 + - - +
550I ARG* 1.3 72.4 - - - +
552I ASN* 1.3 74.0 + - - +
554I LEU* 3.6 7.7 - - - +
555I LYS* 3.1 39.4 + - - +
574I LEU* 3.9 20.3 - - + +
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Residues in contact with ASN 552 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I GLU* 3.3 31.4 + - - +
28I LYS* 5.3 4.8 - - + +
29I PRO* 5.2 5.4 - - + -
548I ILE* 2.8 29.7 + - - +
549I ASN* 2.8 9.6 + - - +
551I ASN* 1.3 86.3 + - - +
553I ARG* 1.3 66.1 + - - +
554I LEU 2.9 1.8 - - - -
555I LYS* 3.0 30.1 + - - +
556I LYS* 3.1 37.1 + - - +
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Residues in contact with ARG 553 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549I ASN 2.6 18.9 + - - +
550I ARG* 3.7 11.2 - - - +
552I ASN* 1.3 73.5 - - - +
554I LEU* 1.3 57.0 - - - +
556I LYS* 3.6 8.6 + - - +
557I LEU* 2.9 36.2 + - + +
570I GLU* 3.0 34.4 + - - -
573I MET* 3.4 19.6 - - - +
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Residues in contact with LEU 554 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I ALA* 3.4 29.8 - - + +
550I ARG 2.8 16.7 + - - +
551I ASN* 3.6 4.5 - - - +
553I ARG* 1.3 74.6 - - - +
555I LYS* 1.3 58.3 + - - +
556I LYS 3.1 1.6 - - - -
557I LEU* 2.8 19.1 + - + -
558I LEU* 2.6 60.9 + - + +
567I ILE* 4.8 4.3 - - + -
570I GLU* 4.4 18.3 - - + +
571I LYS* 4.0 22.4 - - + -
574I LEU* 3.4 32.5 - - + -
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Residues in contact with LYS 555 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I GLU* 4.1 13.9 + - - -
27I GLU* 4.5 14.1 + - - +
93I ILE* 6.0 0.2 - - - +
94I GLU* 3.5 28.0 + - - +
96I ALA* 4.8 11.9 - - + +
551I ASN* 3.1 30.0 - - - +
552I ASN* 3.0 22.5 + - - +
554I LEU* 1.3 78.5 - - - +
556I LYS* 1.3 65.8 + - + +
558I LEU* 3.2 28.2 + - + +
559I ALA* 3.5 8.3 + - - +
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Residues in contact with LYS 556 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I LYS* 4.9 14.8 - - - +
552I ASN* 3.1 35.9 + - - +
553I ARG* 3.9 7.9 - - - +
554I LEU 3.1 0.6 - - - -
555I LYS* 1.3 76.7 - - + +
557I LEU* 1.3 55.3 + - - +
558I LEU 3.0 9.6 + - - -
559I ALA* 4.7 3.1 - - - +
560I GLN* 3.1 47.5 + - + +
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Residues in contact with LEU 557 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553I ARG* 2.9 29.2 + - + +
554I LEU* 2.8 12.6 + - + +
556I LYS* 1.3 75.5 - - - +
558I LEU* 1.3 57.8 + - - +
560I GLN* 4.6 5.8 - - - +
561I GLY 3.2 26.9 - - - +
566I ILE* 3.1 37.9 - - + +
567I ILE* 3.6 16.0 - - + +
570I GLU* 3.3 45.1 - - + +
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Residues in contact with LEU 558 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I ALA* 4.3 13.5 - - + -
97I THR* 6.0 0.2 - - - +
554I LEU* 2.6 51.4 - - + +
555I LYS* 3.2 22.9 - - + +
556I LYS 3.0 0.4 - - - -
557I LEU* 1.3 82.0 - - - +
559I ALA* 1.3 63.5 + - + +
560I GLN 3.5 0.4 - - - -
561I GLY* 4.6 2.4 + - - -
562I ALA* 4.2 16.6 + - + +
567I ILE* 4.3 18.6 - - + -
571I LYS* 4.7 4.0 - - - -
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Residues in contact with ALA 559 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555I LYS 3.5 8.0 + - - +
556I LYS* 3.5 5.0 + - - +
558I LEU* 1.3 80.5 - - + +
560I GLN* 1.3 67.0 + - + +
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Residues in contact with GLN 560 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556I LYS* 3.1 35.7 + - + +
557I LEU* 5.0 4.9 - - - +
559I ALA* 1.3 82.7 - - + +
561I GLY* 1.3 59.8 + - - +
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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