Contacts of the helix formed by residues 549 - 570 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547G LYS 5.0 2.5 - - - +
548G PHE* 1.3 78.2 - - - +
550G MET* 1.3 65.7 + - - +
551G ILE* 3.4 22.0 - - + +
552G LYS* 3.2 13.5 + - + +
553G LEU* 3.1 19.0 + - - +
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Residues in contact with MET 550 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548G PHE 4.0 0.4 + - - -
549G GLU* 1.3 71.8 - - - +
551G ILE* 1.3 66.7 + - - +
553G LEU* 3.1 22.2 + - + -
554G ILE* 3.1 37.8 + - + +
650G MET* 4.1 21.5 - - - +
682G ARG* 4.7 5.4 - - + +
684G ASN* 3.2 57.4 - - + +
685G CYS* 4.3 1.8 - - + -
686G PRO* 4.1 18.4 - - + -
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Residues in contact with ILE 551 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549G GLU* 3.8 26.7 - - + +
550G MET* 1.3 76.9 - - - +
552G LYS* 1.3 62.1 + - + +
554G ILE* 3.4 13.0 + - - +
555G ASP* 3.1 24.3 + - - +
718G ALA 5.9 2.9 - - - +
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Residues in contact with LYS 552 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548G PHE* 4.1 22.0 - - + -
549G GLU* 3.2 23.5 + - + +
550G MET 3.1 0.6 - - - -
551G ILE* 1.3 81.2 - - + +
553G LEU* 1.3 65.8 + - - +
554G ILE 3.1 1.8 - - - -
555G ASP* 3.0 39.1 + - + +
556G ILE* 3.0 27.8 + - + +
559G GLN* 4.5 0.8 - - - +
584G LEU* 5.5 4.7 - - - -
587G ASP 4.3 14.8 - - - -
588G LEU* 3.6 27.3 + - - +
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Residues in contact with LEU 553 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541G LEU* 4.7 4.3 - - + -
548G PHE* 3.5 40.6 - - + +
549G GLU 3.1 15.3 + - - +
550G MET* 3.1 26.5 + - + +
552G LYS* 1.3 74.4 - - - +
554G ILE* 1.3 61.4 + - - +
556G ILE* 3.6 8.5 + - + +
557G ALA* 3.2 21.7 + - - +
649G LEU* 3.8 36.1 - - + +
650G MET* 3.7 15.2 - - + +
682G ARG* 3.8 25.6 - - - +
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Residues in contact with ILE 554 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550G MET* 3.1 40.0 + - + +
551G ILE* 3.5 11.2 - - - +
553G LEU* 1.3 76.0 - - - +
555G ASP* 1.3 54.9 + - - +
557G ALA* 3.2 6.5 + - - +
558G ARG* 2.7 34.6 + - + +
650G MET* 5.2 3.1 - - + -
686G PRO* 4.7 2.9 - - + -
689G MET* 4.9 12.8 - - + -
714G ILE* 3.9 22.7 - - + +
717G LEU* 4.2 24.7 - - + -
718G ALA* 4.1 25.4 - - + +
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Residues in contact with ASP 555 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551G ILE 3.1 12.0 + - - +
552G LYS* 3.0 32.6 + - + +
554G ILE* 1.3 78.3 - - - +
556G ILE* 1.3 51.5 + - - +
558G ARG* 2.9 35.7 + - - +
559G GLN* 2.6 61.1 + - - +
588G LEU 4.4 0.2 - - - +
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Residues in contact with ILE 556 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537G LEU* 3.7 33.2 - - + -
548G PHE* 4.1 27.1 - - + -
552G LYS* 3.0 29.2 + - + +
553G LEU* 3.7 11.7 - - - +
554G ILE 3.3 0.2 - - - -
555G ASP* 1.3 74.5 - - - +
557G ALA* 1.3 55.1 + - - +
559G GLN* 3.5 1.9 + - - +
560G THR* 2.7 41.2 + - - +
582G ILE* 5.1 0.2 - - + -
584G LEU* 4.0 32.8 - - + -
590G VAL* 3.9 18.4 - - + +
645G VAL* 6.1 0.2 - - + -
649G LEU* 3.8 11.9 - - + -
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Residues in contact with ALA 557 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553G LEU 3.2 11.4 + - - +
554G ILE* 3.2 11.8 + - - +
556G ILE* 1.3 77.4 - - - +
558G ARG* 1.3 59.2 + - - +
560G THR* 3.3 3.4 + - - -
561G ALA* 2.8 30.8 + - - +
642G PHE* 3.6 9.1 - - - -
646G LEU* 3.8 26.2 - - + -
649G LEU* 4.0 9.6 - - + -
650G MET* 5.9 0.4 - - + -
689G MET* 4.9 6.5 - - + -
714G ILE* 3.9 12.3 - - + -
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Residues in contact with ARG 558 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554G ILE* 2.7 20.2 + - + +
555G ASP* 2.9 33.0 + - - +
557G ALA* 1.3 73.2 - - - +
559G GLN* 1.3 78.2 + - - +
561G ALA* 3.1 5.9 + - - +
562G GLN* 2.8 51.5 + - - +
711G LEU* 3.9 12.8 - - + +
714G ILE* 3.8 24.8 - - + +
715G GLU* 4.3 21.2 + - + +
718G ALA* 5.7 6.1 - - - -
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Residues in contact with GLN 559 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512G ASN* 3.0 24.9 + - - +
552G LYS* 4.5 1.0 - - - +
555G ASP* 2.6 46.5 + - - +
556G ILE* 3.9 1.3 - - - +
558G ARG* 1.3 92.1 - - - +
560G THR* 1.3 65.7 + - - +
562G GLN* 3.2 9.3 - - - +
563G GLY 3.0 18.4 + - - -
588G LEU 3.3 18.4 + - - -
589G THR* 3.3 7.4 + - - +
590G VAL* 2.6 45.2 + - + +
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Residues in contact with THR 560 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556G ILE* 2.7 29.5 + - - +
557G ALA* 3.7 4.7 - - - -
559G GLN* 1.3 72.2 - - - +
561G ALA* 1.3 63.4 + - - +
563G GLY 3.2 1.9 + - - -
564G MET* 2.9 27.2 + - + +
577G LEU* 4.6 5.4 - - + -
582G ILE* 3.6 35.1 - - + +
590G VAL* 3.8 14.6 - - - +
592G ILE* 3.7 16.3 - - + +
642G PHE* 4.0 22.2 - - + -
645G VAL* 5.4 2.5 - - + +
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Residues in contact with ALA 561 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557G ALA 2.8 13.6 + - - +
558G ARG 3.2 10.1 - - - +
560G THR* 1.3 75.8 - - - +
562G GLN* 1.3 54.6 + - - +
564G MET* 2.9 2.9 + - - +
565G ASP* 2.7 35.0 + - - +
642G PHE* 3.9 12.9 - - + -
707G PHE* 4.0 21.0 - - + -
710G ILE* 4.3 4.3 - - + -
711G LEU* 4.0 19.1 - - + -
714G ILE* 4.2 9.9 - - + -
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Residues in contact with GLN 562 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477F HIS* 3.1 28.8 + - - +
478F GLY* 3.3 22.7 - - - +
510G HIS* 3.7 9.6 - - + -
512G ASN* 3.4 16.8 - - - +
558G ARG* 2.8 31.7 + - - +
559G GLN* 3.2 13.5 - - - +
561G ALA* 1.3 72.9 - - - +
563G GLY* 1.3 57.7 + - - +
565G ASP* 3.7 2.3 + - - +
566G TYR* 3.0 25.5 + - - +
711G LEU* 3.8 29.9 - - + +
715G GLU* 4.3 6.4 - - - +
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Residues in contact with GLY 563 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510G HIS* 4.2 4.7 - - - -
512G ASN* 3.7 21.5 - - - +
513G ILE* 3.6 7.6 - - - +
559G GLN 3.0 8.1 + - - -
560G THR 3.7 2.7 - - - -
562G GLN* 1.3 77.5 - - - +
564G MET* 1.3 59.6 + - - +
566G TYR* 3.2 3.0 + - - +
567G LEU* 2.9 31.7 + - - +
592G ILE* 4.0 12.6 - - - -
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Residues in contact with MET 564 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560G THR* 2.9 23.2 + - + +
561G ALA 3.5 1.8 - - - +
563G GLY* 1.3 74.1 - - - +
565G ASP* 1.3 65.7 + - - +
567G LEU* 3.1 16.7 + - + +
568G HIS* 2.9 37.2 + - + +
574G HIS* 4.2 9.2 - - + -
577G LEU* 4.1 29.2 - - + -
592G ILE* 3.8 19.3 - - + -
638G ASP* 3.4 43.1 - - + +
707G PHE* 3.5 32.5 - - + -
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Residues in contact with ASP 565 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477F HIS* 2.7 33.3 + - - +
561G ALA 2.7 19.4 + - - +
562G GLN* 3.7 11.4 + - - +
564G MET* 1.3 73.0 - - - +
566G TYR* 1.3 60.3 + - - +
568G HIS* 4.1 3.2 - - - +
569G ALA* 3.2 22.3 + - - +
707G PHE* 3.6 20.2 - - + +
708G PRO* 3.4 28.7 - - - +
711G LEU* 3.7 20.0 - - + +
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Residues in contact with TYR 566 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450F TRP* 3.9 4.5 - - - -
476F TRP* 4.2 22.0 - + - -
477F HIS* 4.0 22.4 - + + -
517F MET 5.1 1.2 + - - -
507G LYS 3.6 3.8 + - - -
508G THR* 4.0 15.0 - - + -
509G ARG 2.9 42.3 + - - -
510G HIS* 3.4 41.3 - + + +
513G ILE* 4.0 10.5 - - + -
562G GLN 3.0 15.7 + - - +
563G GLY* 3.5 7.0 - - - +
564G MET 3.1 0.4 - - - -
565G ASP* 1.3 76.3 + - - +
567G LEU* 1.3 71.4 + - + +
568G HIS 3.3 0.2 + - - -
569G ALA* 3.5 1.9 + - - +
570G LYS* 3.3 49.2 + - + +
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Residues in contact with LEU 567 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508G THR* 3.8 18.8 - - + -
513G ILE* 3.7 20.2 - - + -
563G GLY 2.9 15.7 + - - +
564G MET* 3.1 23.7 + - + +
566G TYR* 1.3 77.7 - - + +
568G HIS* 1.3 63.5 + - + +
570G LYS* 3.3 6.4 + - - +
571G SER 3.2 4.2 + - - -
572G ILE* 3.0 46.4 + - + +
574G HIS* 3.9 22.0 - - + +
592G ILE* 4.9 1.6 - - + -
595G PHE* 3.6 39.9 - - + -
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Residues in contact with HIS 568 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564G MET* 2.9 19.8 + - + +
565G ASP* 4.2 4.3 - - - +
567G LEU* 1.3 76.8 - - + +
569G ALA* 1.3 58.8 + - - +
571G SER* 2.6 26.0 + - - -
572G ILE 3.2 21.8 - - - -
635G PHE* 3.3 67.6 - + + +
638G ASP* 2.9 25.6 + - + +
639G VAL* 5.4 0.2 - - - +
706G LEU* 5.6 0.8 - - - +
707G PHE* 3.3 37.6 + + + +
708G PRO* 6.4 1.3 - - + -
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Residues in contact with ALA 569 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477F HIS* 3.3 37.9 - - + +
565G ASP* 3.2 10.4 + - - +
566G TYR 3.8 3.1 - - - +
568G HIS* 1.3 78.6 - - - +
570G LYS* 1.3 57.1 + - + +
571G SER* 3.4 7.3 + - - -
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Residues in contact with LYS 570 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449F ASP 3.6 19.0 + - - +
450F TRP* 3.2 35.2 - - - +
476F TRP* 4.7 13.4 - - - -
477F HIS* 6.2 0.4 - - - +
517F MET 5.1 0.8 + - - -
507G LYS* 3.5 27.3 + - + +
566G TYR* 3.3 40.3 + - + +
567G LEU* 3.3 9.0 + - - +
568G HIS 3.1 0.8 - - - -
569G ALA* 1.3 77.1 - - + +
571G SER* 1.3 69.7 + - - +
572G ILE* 3.3 21.0 + - + +
600G VAL* 5.0 2.9 - - - +
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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