Contacts of the helix formed by residues 549 - 570 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547C LYS 3.6 4.4 + - - +
548C PHE* 1.3 77.2 - - - +
550C MET* 1.3 66.7 + - - +
551C ILE* 3.3 20.1 - - + +
552C LYS* 3.1 9.0 + - + +
553C LEU* 3.0 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 550 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C GLU* 1.3 74.9 - - - +
551C ILE* 1.3 56.9 + - - +
553C LEU* 3.3 20.2 + - + -
554C ILE* 2.9 53.2 + - + +
650C MET* 3.9 23.8 - - - +
682C ARG* 4.9 5.2 - - + -
684C ASN* 3.5 57.7 - - - +
685C CYS* 4.1 5.4 - - + +
686C PRO* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 551 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C GLU* 4.3 22.0 - - + +
550C MET* 1.3 78.5 - - - +
552C LYS* 1.3 59.9 + - + +
554C ILE* 3.3 15.1 + - + -
555C ASP* 2.8 30.4 + - + +
718C ALA* 4.7 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 552 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C PHE* 3.8 24.2 - - + -
549C GLU* 3.1 20.4 + - + +
551C ILE* 1.3 80.2 - - + +
553C LEU* 1.3 61.5 + - - +
555C ASP* 2.7 32.1 + - + +
556C ILE* 2.8 49.5 + - + +
559C GLN* 3.6 3.6 - - - +
584C LEU* 5.5 2.0 - - - -
587C ASP 4.3 17.5 - - - -
588C LEU* 3.4 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 553 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C LEU* 4.6 3.1 - - + -
548C PHE* 3.6 36.6 - - + +
549C GLU 3.0 19.5 + - - +
550C MET* 3.3 33.8 + - + +
552C LYS* 1.3 75.5 - - - +
554C ILE* 1.3 61.8 + - - +
556C ILE* 3.2 4.8 + - - +
557C ALA* 2.9 22.7 + - - +
649C LEU* 3.6 37.6 - - + +
650C MET* 4.2 15.3 - - + -
682C ARG* 3.6 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 554 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C MET* 2.9 41.8 + - + +
551C ILE* 3.3 12.8 + - + +
553C LEU* 1.3 75.5 - - - +
555C ASP* 1.3 58.5 + - - +
557C ALA* 3.3 6.5 + - - +
558C ARG* 2.8 28.0 + - + +
650C MET* 4.4 0.4 - - + -
686C PRO* 4.5 5.6 - - + -
689C MET* 3.9 18.4 - - + -
714C ILE* 3.6 23.8 - - + +
717C LEU* 3.9 22.0 - - + -
718C ALA* 4.1 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 555 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551C ILE* 2.8 21.5 + - + +
552C LYS* 2.7 24.6 + - + +
554C ILE* 1.3 78.8 - - - +
556C ILE* 1.3 57.7 + - - +
558C ARG* 3.0 32.0 + - - +
559C GLN* 2.7 53.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 556 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C LEU* 3.9 28.7 - - + -
548C PHE* 3.8 37.5 - - + -
552C LYS* 2.8 36.1 + - - +
553C LEU* 3.6 5.8 - - - +
555C ASP* 1.3 74.1 - - - +
557C ALA* 1.3 60.5 + - - +
559C GLN* 4.9 0.9 - - - +
560C THR* 2.6 37.8 + - - +
582C ILE* 5.0 0.9 - - + -
584C LEU* 3.8 25.4 - - + -
590C VAL* 3.9 20.5 - - + +
649C LEU* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 557 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C LEU 2.9 13.0 + - - +
554C ILE* 3.6 11.2 - - - +
556C ILE* 1.3 76.6 - - - +
558C ARG* 1.3 57.5 + - - +
560C THR* 3.3 7.1 + - - -
561C ALA* 2.9 30.1 + - - +
642C PHE* 3.7 5.9 - - - -
646C LEU* 3.7 29.4 - - + -
649C LEU* 4.0 9.8 - - + +
650C MET* 5.2 0.7 - - + -
689C MET* 4.5 5.6 - - + -
714C ILE* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 558 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B GLY* 5.9 0.4 - - - -
512C ASN* 4.7 2.2 + - - -
554C ILE* 2.8 18.5 + - + +
555C ASP* 3.0 31.8 + - - +
557C ALA* 1.3 76.7 - - - +
559C GLN* 1.3 81.8 + - - +
561C ALA* 3.1 5.8 + - - +
562C GLN* 2.8 58.1 + - - +
711C LEU* 3.9 5.9 - - + +
714C ILE* 3.8 24.2 - - + +
715C GLU* 4.0 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 559 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512C ASN* 3.3 27.1 + - - +
552C LYS* 3.6 3.8 - - - +
555C ASP* 2.7 43.4 + - - +
556C ILE 4.8 0.2 - - - +
558C ARG* 1.3 94.4 - - - +
560C THR* 1.3 66.9 + - - +
562C GLN* 2.9 20.1 + - - +
563C GLY 3.0 10.2 + - - -
588C LEU 3.1 18.4 + - - -
589C THR* 3.3 8.8 - - - +
590C VAL* 2.9 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 560 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C ILE* 2.6 28.5 + - - +
557C ALA* 3.5 6.0 - - - -
559C GLN* 1.3 75.2 - - - +
561C ALA* 1.3 63.6 + - - +
563C GLY 3.1 2.6 + - - -
564C MET* 3.0 30.4 + - + +
577C LEU* 4.7 3.8 - - + -
582C ILE* 3.6 30.9 - - + +
590C VAL* 3.9 18.7 - - - +
592C ILE* 3.5 14.3 - - + +
642C PHE* 3.8 23.8 - - + -
645C VAL* 5.2 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 561 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557C ALA 2.9 13.2 + - - +
558C ARG 3.1 8.9 + - - +
560C THR* 1.3 77.2 - - - +
562C GLN* 1.3 52.4 + - - +
564C MET* 3.2 1.2 + - - +
565C ASP* 2.7 36.7 + - - +
642C PHE* 4.0 10.5 - - + -
707C PHE* 3.9 27.8 - - + -
710C ILE* 4.4 2.9 - - + -
711C LEU* 4.1 17.0 - - + -
714C ILE* 4.3 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 562 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B HIS* 3.3 18.6 - - - +
478B GLY* 3.1 34.7 - - - +
510C HIS* 3.9 7.2 + - + -
512C ASN* 3.5 14.1 - - - +
558C ARG* 2.8 40.6 + - - +
559C GLN* 2.9 12.1 + - - +
561C ALA* 1.3 77.3 - - - +
563C GLY* 1.3 56.9 + - - +
565C ASP* 3.5 4.2 - - - +
566C TYR* 3.1 25.5 + - - +
711C LEU* 3.4 31.6 - - - +
715C GLU* 3.9 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 563 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510C HIS* 4.4 1.8 - - - -
512C ASN* 4.0 19.5 - - - +
513C ILE* 3.7 16.1 - - - +
559C GLN 3.0 9.7 + - - -
560C THR 3.1 3.3 + - - -
562C GLN* 1.3 74.3 - - - +
564C MET* 1.3 60.8 + - - +
566C TYR* 3.3 7.3 + - - +
567C LEU* 2.9 32.2 + - - +
592C ILE* 4.0 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 564 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560C THR* 3.0 23.6 + - + +
561C ALA 3.6 2.9 - - - +
563C GLY* 1.3 75.3 - - - +
565C ASP* 1.3 65.8 + - - +
567C LEU* 3.1 16.9 + - + +
568C HIS* 2.9 41.8 + - - +
574C HIS* 4.3 10.3 - - + -
577C LEU* 3.9 27.1 - - + -
592C ILE* 4.0 16.2 - - + -
638C ASP* 3.6 35.7 - - + +
707C PHE* 3.4 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 565 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B HIS* 2.8 33.7 + - - -
561C ALA 2.7 21.9 + - - +
562C GLN 3.5 5.2 - - - +
564C MET* 1.3 71.9 - - - +
566C TYR* 1.3 62.1 + - - +
568C HIS* 3.3 2.7 + - - +
569C ALA* 3.0 23.2 + - - +
707C PHE* 3.8 14.5 - - + +
708C PRO* 3.4 28.8 - - - +
711C LEU* 3.6 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 566 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B TRP* 3.9 8.1 - - - -
476B TRP* 4.1 23.8 - + - -
477B HIS* 3.9 23.8 - + + -
517B MET 4.8 1.7 + - - -
507C LYS 3.5 9.0 + - - -
508C THR* 4.0 14.1 - - + -
509C ARG* 3.0 41.9 + - - -
510C HIS* 3.4 40.4 - + + -
513C ILE* 4.2 9.9 - - + -
562C GLN 3.1 11.5 + - - +
563C GLY 3.5 7.2 - - - +
565C ASP* 1.3 81.2 + - - +
567C LEU* 1.3 67.9 + - + +
569C ALA* 3.4 2.3 + - - +
570C LYS* 3.3 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 567 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C THR* 3.9 19.7 - - + -
513C ILE* 3.8 22.7 - - + -
563C GLY 2.9 19.4 + - - +
564C MET* 3.1 26.7 + - + +
566C TYR* 1.3 77.8 - - + +
568C HIS* 1.3 64.6 + - + +
570C LYS* 3.1 8.2 + - - +
572C ILE* 2.9 48.3 + - + +
574C HIS* 4.2 18.6 - - + -
592C ILE* 4.7 0.9 - - + -
595C PHE* 3.7 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 568 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564C MET* 2.9 22.2 + - + +
565C ASP* 3.8 5.8 - - - +
567C LEU* 1.3 73.8 - - + +
569C ALA* 1.3 54.9 + - - +
570C LYS 2.9 4.5 - - - -
571C SER* 2.6 28.1 + - - -
572C ILE 3.2 18.2 - - - -
635C PHE* 3.3 64.2 - + + +
638C ASP* 3.1 24.4 + - + +
639C VAL* 4.7 0.8 - - + +
706C LEU* 5.4 1.4 - - - +
707C PHE* 3.5 37.8 + + + +
708C PRO* 6.1 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 569 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B HIS* 3.5 36.3 - - + +
565C ASP* 3.0 11.8 + - - +
566C TYR 3.8 3.6 - - - +
568C HIS* 1.3 76.3 - - - +
570C LYS* 1.3 60.5 + - + +
571C SER* 3.3 2.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 570 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ASP 4.7 12.0 + - - -
450B TRP* 4.6 15.8 - - - +
451B GLU 6.0 0.2 + - - -
452B ILE* 6.1 0.4 - - - +
476B TRP* 4.3 20.6 - - + -
477B HIS* 6.2 0.2 - - - +
517B MET 5.5 0.4 + - - -
507C LYS* 3.3 44.2 - - + +
566C TYR* 3.3 37.9 + - + +
567C LEU* 3.1 8.3 + - - +
568C HIS 2.8 1.4 + - - -
569C ALA* 1.3 80.3 - - + +
571C SER* 1.3 69.8 + - - +
572C ILE* 3.2 19.1 + - + +
600C VAL* 4.8 2.6 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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