Contacts of the helix formed by residues 576 - 604 (chain A) in PDB entry 4IM0
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 ALA 576 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A GLU* 5.0 2.4 + - - -
574A ARG* 3.6 17.6 - - - +
575A LEU* 1.3 75.2 - - - +
577A TYR* 1.3 56.7 + - - +
578A ASN* 3.2 1.9 + - + +
579A GLU* 3.2 22.7 + - - +
580A GLU* 2.8 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A ARG* 5.0 0.4 - - - +
575A LEU 3.9 0.2 + - - -
576A ALA* 1.3 72.8 - - - +
578A ASN* 1.3 80.6 + - - +
580A GLU* 3.2 20.2 - - - +
581A GLN* 3.1 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A ALA* 3.3 1.8 - - + +
577A TYR* 1.3 92.0 - - - +
579A GLU* 1.3 79.8 + - - +
581A GLN* 3.0 7.9 + - - +
582A ILE* 3.0 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A ASP* 5.9 0.7 - - - +
572A GLU* 6.1 0.2 - - - +
575A LEU* 3.5 24.6 - - + +
576A ALA* 3.2 26.1 + - - +
578A ASN* 1.3 84.2 - - - +
580A GLU* 1.3 56.3 + - - +
582A ILE* 3.8 16.0 - - + +
583A HIS* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A TYR* 3.5 35.1 - - + +
575A LEU* 3.9 14.5 - - + +
576A ALA 2.8 13.4 + - - +
577A TYR* 3.2 25.9 - - - +
578A ASN 3.0 0.2 - - - -
579A GLU* 1.3 75.9 - - - +
581A GLN* 1.3 75.5 + - - +
583A HIS* 3.2 5.2 + - - +
584A LYS* 3.0 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A TYR* 3.1 35.8 + - + +
578A ASN* 3.0 11.2 + - - +
580A GLU* 1.3 90.8 - - - +
582A ILE* 1.3 54.1 + - + +
584A LYS* 2.9 14.9 + - + +
585A PHE* 2.7 61.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ASN* 3.0 30.6 + - + +
579A GLU* 3.8 16.4 - - + +
581A GLN* 1.3 75.3 - - + +
583A HIS* 1.3 63.0 + - - +
585A PHE* 3.4 15.7 + - + +
586A ASP* 3.0 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A TYR* 3.8 20.8 - + - -
408A LEU* 3.8 21.6 - - + +
411A ASP* 3.0 33.2 + - + +
566A PHE* 3.2 45.5 - + + -
569A ASP* 3.1 25.4 + - + +
575A LEU* 3.8 11.7 - - + -
579A GLU 3.0 19.6 + - - +
580A GLU* 3.3 5.4 - - - +
582A ILE* 1.3 77.3 - - - +
584A LYS* 1.3 59.4 + - - +
586A ASP* 3.6 0.8 + - - -
587A LYS* 3.2 21.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A TYR* 3.5 29.6 - - + -
580A GLU* 3.0 20.2 + - + +
581A GLN* 2.9 16.9 + - + +
583A HIS* 1.3 77.0 - - + +
585A PHE* 1.3 65.1 + - + +
587A LYS* 3.3 23.3 - - + +
588A GLN* 3.4 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A GLN* 2.7 49.8 + - + -
582A ILE* 3.6 16.6 - - + +
584A LYS* 1.3 75.4 - - + +
586A ASP* 1.3 59.2 + - - +
588A GLN* 3.1 12.2 + - + +
589A LYS* 3.0 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A ILE* 3.7 37.1 - - + +
565A GLN* 5.8 3.6 - - - +
566A PHE* 4.6 4.0 - - + -
582A ILE* 3.0 32.4 + - - +
583A HIS* 4.1 3.8 - - - +
585A PHE* 1.3 73.6 - - - +
587A LYS* 1.3 60.6 + - - +
588A GLN 3.2 0.2 - - - -
589A LYS* 3.5 30.1 + - - +
590A LEU* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL* 3.8 22.0 - - + +
403A HIS 2.3 31.2 + - - +
404A PRO* 3.4 14.6 + - + +
405A ARG 3.2 19.0 + - - -
406A TYR* 4.0 1.9 - - - +
411A ASP* 3.3 32.3 + - - +
414A MET* 4.1 17.4 - - + +
566A PHE* 4.0 10.5 - - + -
583A HIS* 3.2 15.5 + - + +
584A LYS* 3.3 18.4 - - + +
585A PHE 3.1 0.2 - - - -
586A ASP* 1.3 78.6 - - - +
588A GLN* 1.3 69.1 + - - +
590A LEU* 3.4 19.0 - - - +
591A TYR* 3.5 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL* 5.1 11.3 - - - +
404A PRO* 5.5 8.7 - - - +
584A LYS 3.7 12.8 + - - +
585A PHE* 3.1 11.5 + - + +
587A LYS* 1.3 87.7 + - - +
589A LYS* 1.3 59.4 - - - +
591A TYR* 3.3 17.2 + - - +
592A TYR* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A ILE* 4.2 9.9 - - + -
585A PHE* 3.0 26.9 + - - +
586A ASP* 3.2 33.7 + - - +
588A GLN* 1.3 74.3 - - - +
590A LEU* 1.3 58.5 + - - +
592A TYR* 3.2 11.5 + - + +
593A HIS* 2.8 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A MET* 4.3 14.4 - - + -
415A ALA* 3.6 36.6 - - + -
418A ILE* 4.0 10.3 - - + -
419A THR* 4.1 4.5 - - - +
559A MET* 3.6 55.5 - - + +
562A ILE* 4.0 19.7 - - + +
566A PHE* 4.4 5.4 - - + -
586A ASP 2.8 15.6 + - - +
587A LYS 3.4 9.9 - - - +
589A LYS* 1.3 73.3 - - - +
591A TYR* 1.3 57.0 - - - +
593A HIS* 3.2 4.8 + - - +
594A ALA* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A LEU* 5.0 11.7 - - + -
400A PRO 5.7 4.5 - - - -
401A LYS* 6.2 4.3 - - + -
402A VAL* 4.2 29.2 - - + -
418A ILE* 4.2 15.7 - - + -
587A LYS 3.5 8.0 + - - +
588A GLN* 3.3 18.1 + - - +
589A LYS 3.3 0.2 - - - -
590A LEU* 1.3 80.6 - - - +
592A TYR* 1.3 63.6 + - + +
594A ALA* 3.7 0.5 - - - +
595A THR* 2.9 60.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A GLN 2.9 17.3 + - - +
589A LYS* 3.2 12.5 + - + +
591A TYR* 1.3 85.3 - - + +
593A HIS* 1.3 83.6 + + - +
595A THR* 4.0 4.5 - - - -
596A LYS* 2.8 57.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LEU* 3.8 28.9 - - + +
558A CYS* 3.7 38.2 - - + +
559A MET* 3.7 16.4 - - + -
562A ILE* 4.4 10.6 - - + +
589A LYS* 2.8 43.8 + - + +
590A LEU* 3.6 5.6 - - - +
592A TYR* 1.3 93.0 - + - +
594A ALA* 1.3 57.8 + - - +
596A LYS* 3.4 4.1 + - - +
597A ALA* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A LEU* 3.6 15.0 - - + -
418A ILE* 3.5 28.9 - - + -
422A VAL* 4.0 5.1 - - + +
559A MET* 3.7 18.1 - - + -
590A LEU 2.9 16.8 + - - +
591A TYR 3.7 2.0 - - - +
593A HIS* 1.3 76.0 - - - +
595A THR* 1.3 65.5 + - - +
597A ALA* 3.2 2.1 + - - +
598A MET* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A LEU* 3.8 10.7 - - - +
591A TYR* 2.9 50.1 + - + +
592A TYR* 4.0 6.1 - - - -
594A ALA* 1.3 74.5 - - - +
596A LYS* 1.3 63.3 + - - +
598A MET* 3.9 2.5 - - - +
599A THR* 2.8 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 596 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LEU* 3.6 32.9 - - + +
592A TYR* 2.8 61.9 + - + +
593A HIS* 3.6 5.8 + - - +
595A THR* 1.3 80.3 - - - +
597A ALA* 1.3 61.4 + - - +
599A THR* 3.7 5.3 - - - -
600A HIS* 3.1 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A VAL* 4.0 25.6 - - + -
425A ALA* 6.2 0.7 - - + -
552A LEU* 3.3 25.8 - - + +
555A LEU* 3.8 19.3 - - + +
593A HIS 3.0 17.5 + - - +
594A ALA 3.2 4.9 + - - +
596A LYS* 1.3 76.5 - - - +
598A MET* 1.3 59.3 + - - +
600A HIS* 3.2 2.2 + - - -
601A PHE* 2.8 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 598 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ILE 3.7 23.1 - - - +
398A SER* 5.3 2.7 - - - -
399A LEU* 3.8 30.1 - - + +
421A VAL* 4.6 4.7 - - + -
422A VAL* 4.6 9.2 - - + -
425A ALA* 3.8 25.4 - - + -
594A ALA 3.0 20.6 + - - +
595A THR* 3.9 4.5 - - - +
597A ALA* 1.3 72.5 - - - +
599A THR* 1.3 60.5 + - - +
601A PHE* 3.2 22.7 + - + +
602A THR* 2.8 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A THR* 2.8 30.7 + - - +
596A LYS* 3.7 6.5 - - - -
598A MET* 1.3 76.9 - - - +
600A HIS* 1.3 58.6 + - - +
602A THR* 3.8 5.4 - - - -
603A ASP* 2.8 56.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ASN* 2.7 33.4 + - - +
551A LYS* 4.0 28.1 - - + +
552A LEU* 4.2 23.3 - - + -
555A LEU* 5.7 3.1 - - + -
596A LYS* 3.1 13.0 + - + +
597A ALA* 3.5 8.1 - - - +
599A THR* 1.3 79.9 - - - +
601A PHE* 1.3 58.0 + - - +
603A ASP* 5.0 0.7 - - - -
604A GLU* 2.9 50.9 + - + +
605A CYS* 3.2 9.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TYR* 4.4 11.9 - + - -
396A LYS* 6.3 1.6 - - + -
425A ALA* 3.3 38.4 - - + -
428A ILE* 3.9 21.5 - - + -
429A ALA* 3.8 25.8 - - + -
432A LEU* 4.4 2.7 - - + -
552A LEU* 4.6 7.4 - - + -
597A ALA 2.8 16.6 + - - +
598A MET* 3.2 20.8 + - + +
600A HIS* 1.3 78.2 - - - +
602A THR* 1.3 66.4 + - + +
605A CYS* 3.1 16.4 + - + +
606A VAL* 2.7 59.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A MET* 2.8 33.9 + - + +
599A THR* 3.3 5.0 + - - -
601A PHE* 1.3 88.9 - - + +
603A ASP* 1.3 80.9 + - - +
606A VAL* 3.6 13.0 - - + +
607A LYS* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A THR* 2.8 40.9 + - + +
600A HIS* 5.0 0.9 - - - -
602A THR* 1.3 86.6 + - - +
604A GLU* 1.3 60.5 + - + +
607A LYS* 3.3 28.2 - - + +
608A LYS* 5.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A THR* 4.0 0.9 - - - +
546A ASP* 5.6 3.5 - - - +
548A ASN* 3.7 28.6 + - - +
600A HIS* 2.9 37.0 + - + +
603A ASP* 1.3 83.7 - - + +
605A CYS* 1.3 63.5 + - - +
606A VAL 3.5 0.2 - - - -
607A LYS 4.3 0.4 - - - -
608A LYS* 3.0 66.5 + - + +
----------------------------------------------------------
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