Contacts of the helix formed by residues 549 - 570 (chain F) in PDB entry 4MNE
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 GLU 549 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547F LYS 3.8 2.7 + - - +
548F PHE* 1.3 77.5 - - - +
550F MET* 1.3 64.6 + - - +
551F ILE* 3.3 19.3 - - + +
552F LYS* 3.1 16.9 + - + +
553F LEU* 3.2 11.4 + - - +
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Residues in contact with MET 550 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548F PHE 4.0 0.4 + - - -
549F GLU* 1.3 73.0 - - - +
551F ILE* 1.3 59.1 + - - +
553F LEU* 3.3 17.5 + - + +
554F ILE* 3.0 37.1 + - + +
650F MET* 3.9 24.5 - - - +
682F ARG* 5.0 7.0 - - + -
684F ASN* 3.2 61.3 - - - +
685F CYS* 3.6 12.3 - - + +
686F PRO* 3.8 22.0 - - + -
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Residues in contact with ILE 551 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549F GLU* 4.4 19.5 - - + +
550F MET* 1.3 78.9 - - - +
552F LYS* 1.3 64.8 + - + +
554F ILE* 3.5 18.2 + - + +
555F ASP* 3.2 22.2 + - - +
718F ALA* 6.6 0.4 - - - -
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Residues in contact with LYS 552 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548F PHE* 3.7 32.8 - - + -
549F GLU* 3.1 16.8 + - + +
550F MET 3.1 0.2 - - - -
551F ILE* 1.3 83.2 - - + +
553F LEU* 1.3 59.1 + - - +
554F ILE 3.1 1.1 - - - -
555F ASP* 2.9 23.5 + - + +
556F ILE* 2.9 40.4 + - + +
584F LEU* 4.2 7.0 - - - +
587F ASP 3.7 15.7 + - - -
588F LEU* 3.3 36.3 + - - +
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Residues in contact with LEU 553 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541F LEU* 4.7 1.6 - - + -
548F PHE* 3.6 38.6 - - + +
549F GLU 3.2 10.0 + - - +
550F MET* 3.4 29.2 - - + +
552F LYS* 1.3 78.8 - - - +
554F ILE* 1.3 61.4 + - - +
556F ILE* 3.4 8.8 + - + +
557F ALA* 3.0 22.7 + - - +
649F LEU* 3.6 35.5 - - + +
650F MET* 3.7 20.0 - - + +
682F ARG* 3.5 27.4 - - - +
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Residues in contact with ILE 554 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550F MET* 3.0 33.1 + - + +
551F ILE* 3.7 18.8 - - + +
552F LYS 3.1 0.2 - - - -
553F LEU* 1.3 77.0 - - - +
555F ASP* 1.3 54.0 + - - +
557F ALA* 3.2 7.2 + - - +
558F ARG* 2.8 33.2 + - + +
650F MET* 5.0 2.5 - - + -
686F PRO* 4.0 19.3 - - + -
689F MET* 4.3 17.7 - - + -
714F ILE* 4.0 23.5 - - + +
717F LEU* 3.5 30.5 - - + -
718F ALA* 6.2 2.9 - - + -
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Residues in contact with ASP 555 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551F ILE 3.2 11.1 + - - +
552F LYS* 2.9 34.0 + - + +
554F ILE* 1.3 79.4 - - - +
556F ILE* 1.3 55.2 + - - +
558F ARG* 2.3 49.0 + - - +
559F GLN* 2.7 52.5 + - - +
588F LEU 3.9 0.5 - - - +
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Residues in contact with ILE 556 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537F LEU* 4.1 32.1 - - + -
548F PHE* 4.2 22.7 - - + -
552F LYS* 2.9 34.2 + - + +
553F LEU* 3.6 18.2 - - + +
554F ILE 3.3 0.2 - - - -
555F ASP* 1.3 72.6 - - - +
557F ALA* 1.3 65.1 + - - +
559F GLN* 3.5 1.0 + - - +
560F THR* 2.8 33.3 + - - +
582F ILE* 5.2 1.6 - - + -
584F LEU* 4.0 25.4 - - + -
590F VAL* 4.1 22.8 - - + +
649F LEU* 4.1 6.7 - - + -
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Residues in contact with ALA 557 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553F LEU 3.0 14.2 + - - +
554F ILE* 3.5 9.9 - - - +
556F ILE* 1.3 76.3 - - - +
558F ARG* 1.3 62.7 + - - +
560F THR* 4.5 1.6 - - - -
561F ALA* 3.0 24.1 + - - +
642F PHE* 3.6 9.8 - - + -
645F VAL* 6.2 0.4 - - - -
646F LEU* 3.6 31.0 - - + -
649F LEU* 3.8 10.2 - - + +
689F MET* 4.4 6.5 - - + -
714F ILE* 4.2 12.1 - - + -
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Residues in contact with ARG 558 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554F ILE* 2.8 20.3 + - + +
555F ASP* 2.3 51.7 + - - +
557F ALA* 1.3 73.0 - - - +
559F GLN* 1.3 76.2 + - - +
561F ALA* 3.5 3.7 + - - +
562F GLN* 2.8 34.9 + - - +
711F LEU* 3.7 13.9 - - + +
714F ILE* 4.0 31.1 - - + +
715F GLU* 5.4 11.7 - - + -
718F ALA* 6.3 2.7 - - - -
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Residues in contact with GLN 559 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512F ASN* 3.3 29.2 + - - +
555F ASP* 2.7 47.2 + - - +
558F ARG* 1.3 93.1 - - - +
560F THR* 1.3 66.6 + - - +
562F GLN* 3.2 10.3 + - + +
563F GLY 3.1 16.8 + - - -
588F LEU 3.3 13.3 + - - -
589F THR* 3.4 8.2 - - - +
590F VAL* 2.9 41.3 + - + +
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Residues in contact with THR 560 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556F ILE* 2.8 25.0 + - - +
557F ALA* 3.8 4.9 - - - -
559F GLN* 1.3 79.0 - - - +
561F ALA* 1.3 55.9 + - - +
563F GLY* 3.1 3.3 + - - -
564F MET* 2.8 36.7 + - + +
577F LEU* 4.7 5.4 - - + -
582F ILE* 3.7 33.9 - - + +
590F VAL* 3.8 15.6 - - - +
592F ILE* 3.7 16.3 - - + +
642F PHE* 4.1 19.7 - - + -
645F VAL* 5.3 3.8 - - + +
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Residues in contact with ALA 561 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557F ALA 3.0 17.0 + - - +
558F ARG* 3.6 6.3 - - - +
560F THR* 1.3 77.0 - - - +
562F GLN* 1.3 52.8 + - - +
564F MET* 3.7 0.2 - - - +
565F ASP* 2.7 37.6 + - - +
642F PHE* 3.8 10.4 - - + -
707F PHE* 3.7 29.0 - - + -
710F ILE* 4.1 10.1 - - + -
711F LEU* 4.0 15.9 - - + -
714F ILE* 4.8 1.6 - - + -
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Residues in contact with GLN 562 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510F HIS* 3.6 11.4 - - + +
512F ASN* 3.2 17.5 - - - +
558F ARG* 2.8 24.5 + - + +
559F GLN* 3.2 13.9 - - + +
561F ALA* 1.3 76.7 - - - +
563F GLY* 1.3 56.2 + - - +
565F ASP* 3.6 1.9 - - - +
566F TYR* 3.2 22.9 + - - +
711F LEU* 3.7 26.9 - - - +
715F GLU* 5.4 3.4 + - - -
477G HIS* 3.0 22.2 - - - +
478G GLY* 3.2 29.0 + - - +
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Residues in contact with GLY 563 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510F HIS* 4.3 1.3 - - - -
512F ASN* 3.9 19.9 - - - +
513F ILE* 3.7 11.6 - - - +
559F GLN 3.1 9.9 + - - -
560F THR 3.1 2.7 + - - -
562F GLN* 1.3 75.1 - - - +
564F MET* 1.3 61.2 + - - +
566F TYR* 3.3 7.0 + - - +
567F LEU* 2.9 32.9 + - - +
592F ILE* 4.0 8.7 - - - -
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Residues in contact with MET 564 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560F THR* 2.8 21.9 + - + +
563F GLY* 1.3 78.5 - - - +
565F ASP* 1.3 60.4 - - - +
567F LEU* 3.2 12.4 + - + -
568F HIS* 3.0 39.0 + - + +
574F HIS* 4.2 11.9 - - + -
577F LEU* 3.9 30.3 - - + -
592F ILE* 3.6 20.4 - - + -
638F ASP* 3.6 39.3 - - + +
642F PHE* 5.0 0.2 - - + -
707F PHE* 3.4 36.3 - - + -
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Residues in contact with ASP 565 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561F ALA 2.7 20.5 + - - +
562F GLN* 3.6 8.9 - - - +
564F MET* 1.3 72.2 - - - +
566F TYR* 1.3 57.7 + - - +
568F HIS* 4.1 2.3 - - - +
569F ALA* 3.1 28.6 + - - +
707F PHE* 3.6 16.9 - - + +
708F PRO* 3.4 29.4 - - - +
711F LEU* 3.7 25.9 - - + +
477G HIS* 2.6 32.6 + - - +
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Residues in contact with TYR 566 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507F LYS 3.6 0.2 + - - -
508F THR* 4.0 12.6 - - + -
509F ARG* 3.1 33.8 + - - +
510F HIS* 3.3 49.6 - + + +
513F ILE* 4.1 10.1 - - + -
562F GLN 3.2 8.3 + - - +
563F GLY 3.4 8.1 - - - +
565F ASP* 1.3 78.3 - - - +
567F LEU* 1.3 69.8 + - + +
569F ALA* 3.1 8.2 + - + +
570F LYS* 3.0 56.6 + - + +
450G TRP* 4.0 4.0 - - - -
476G TRP* 4.1 24.1 - + - -
477G HIS* 4.2 18.6 - + + -
517G MET 5.1 1.0 + - - -
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Residues in contact with LEU 567 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508F THR* 3.7 27.8 - - + -
513F ILE* 3.6 24.5 - - + -
563F GLY 2.9 20.1 + - - +
564F MET* 3.2 26.2 + - - +
566F TYR* 1.3 76.3 - - + +
568F HIS* 1.3 60.1 + - + +
570F LYS* 2.9 17.1 + - - -
571F SER 3.1 0.2 + - - -
572F ILE* 3.0 40.0 + - + +
574F HIS* 4.2 17.3 - - + -
592F ILE* 4.8 1.3 - - + -
595F PHE* 3.9 27.6 - - + -
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Residues in contact with HIS 568 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564F MET* 3.0 22.9 + - + +
565F ASP* 4.3 3.6 - - - +
567F LEU* 1.3 79.4 - - + +
569F ALA* 1.3 58.3 + - - +
571F SER* 2.9 19.3 + - - +
572F ILE 3.2 19.1 - - - -
635F PHE* 3.3 73.6 - + + +
638F ASP* 3.0 26.2 + - + +
706F LEU* 5.3 1.4 - - - +
707F PHE* 3.5 30.8 + + + +
708F PRO* 6.4 1.3 - - + -
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Residues in contact with ALA 569 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D PRO* 5.6 5.7 - - - +
565F ASP* 3.1 21.3 + - - +
566F TYR* 3.1 8.3 + - + +
568F HIS* 1.3 76.6 - - - +
570F LYS* 1.3 63.3 + - + +
571F SER* 3.4 2.9 + - - -
477G HIS* 3.3 31.4 - - + +
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Residues in contact with LYS 570 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507F LYS* 3.1 41.4 - - + +
566F TYR* 3.0 40.3 + - + +
567F LEU* 2.9 9.4 + - - +
569F ALA* 1.3 82.7 + - + +
571F SER* 1.3 68.0 + - - +
572F ILE* 3.3 19.2 + - + +
600F VAL* 5.1 1.2 - - - +
449G ASP 4.3 12.8 + - - -
450G TRP* 3.8 19.8 - - - +
451G GLU 5.7 2.6 + - - -
476G TRP* 4.7 15.8 - - + -
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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