Contacts of the helix formed by residues 581 - 601 (chain A) in PDB entry 5MKF
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 ARG 581 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579A PHE 4.3 0.5 - - - +
580A ASN* 1.3 112.6 + - - +
582A THR* 1.3 66.2 + - - +
583A MET* 2.8 24.0 + - + +
584A SER* 3.4 13.2 + - - -
585A GLN* 4.4 1.2 + - - +
595B LYS* 4.6 20.4 + - - +
599B GLY* 5.3 11.8 - - - -
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Residues in contact with THR 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A ARG* 1.3 73.3 - - - +
583A MET* 1.3 54.0 + - - +
584A SER 3.2 0.2 - - - -
585A GLN* 2.9 13.2 + - + +
586A LEU* 2.3 62.5 + - - +
688A LYS* 5.8 3.1 - - - -
691A LEU* 5.8 4.5 - - + -
695A LYS* 5.2 12.8 - - - +
596B ASP* 5.3 1.6 + - - -
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Residues in contact with MET 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ASN* 4.3 23.1 - - + +
580A ASN* 2.6 40.4 - - - +
581A ARG* 3.0 18.5 - - + +
582A THR* 1.3 79.0 + - - +
584A SER* 1.3 56.0 + - - +
586A LEU* 2.4 15.9 + - - -
587A SER* 2.4 44.3 + - - +
596B ASP* 6.0 1.1 - - - +
599B GLY 4.6 12.3 - - - +
600B PHE* 5.3 17.5 - - + +
602B ILE* 4.5 20.4 - - + -
603B MET* 5.7 4.7 - - + -
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Residues in contact with SER 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ASN* 2.7 33.0 + - - +
579A PHE* 3.0 25.7 - - - -
580A ASN* 3.3 1.6 + - - -
581A ARG 3.4 8.0 + - - -
582A THR 3.2 0.4 - - - -
583A MET* 1.3 79.7 - - - +
585A GLN* 1.3 68.9 + - - +
587A SER* 3.5 17.3 + - - -
588A THR* 4.0 5.9 + - - -
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Residues in contact with GLN 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A ARG 5.5 0.9 - - - +
582A THR* 2.9 15.2 + - + +
584A SER* 1.3 79.0 - - - +
586A LEU* 1.3 60.9 + - + +
587A SER 2.9 4.7 - - - -
588A THR* 2.6 43.4 + - - -
589A THR* 3.6 3.6 + - - +
691A LEU* 4.9 13.9 - - + +
694A GLN* 4.9 15.8 + - - +
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Residues in contact with LEU 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A THR* 2.3 63.5 + - - +
583A MET* 2.4 13.9 + - - +
585A GLN* 1.3 67.5 - - + +
587A SER* 1.3 55.1 + - - -
589A THR* 2.2 41.9 + - + +
590A MET* 4.0 2.4 + - - +
684A TYR* 3.4 26.0 - - + +
688A LYS* 4.4 9.4 - - + +
691A LEU* 3.5 27.1 - - + -
596B ASP* 3.7 26.2 - - - +
600B PHE* 5.4 13.3 - - + -
603B MET* 5.7 0.5 - - - +
675B MET* 5.5 1.2 - - - +
679B ILE* 5.7 2.5 - - + -
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Residues in contact with SER 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A TRP* 5.4 4.4 - - - -
574A PHE* 4.9 15.6 - - - -
578A ASN* 5.1 9.4 + - - -
583A MET* 2.4 32.5 + - - +
584A SER* 3.5 14.1 + - - -
585A GLN 2.9 0.2 + - - -
586A LEU* 1.3 69.6 - - - +
588A THR* 1.3 63.5 + - - +
589A THR 3.1 0.7 - - - -
590A MET* 3.6 5.2 + - - +
591A SER* 3.0 20.1 + - - -
1007A PLM 5.2 4.0 - - - +
603B MET* 4.5 17.8 - - - -
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Residues in contact with THR 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A TRP* 5.9 1.5 - - - -
584A SER 4.1 5.9 + - - -
585A GLN* 2.6 31.1 + - - -
587A SER* 1.3 70.8 - - - +
589A THR* 1.3 56.9 + - - -
591A SER* 3.0 12.5 + - - +
592A ARG* 2.8 31.3 + - + +
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Residues in contact with THR 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585A GLN 4.1 2.0 - - - +
586A LEU* 2.2 49.8 + - + +
588A THR* 1.3 75.4 - - - +
590A MET* 1.3 58.9 + - - +
592A ARG* 2.7 31.6 + - - +
593A CYS* 3.5 4.7 + - - +
683A THR* 5.5 2.3 + - - -
684A TYR* 3.7 31.5 - - + -
687A VAL* 3.6 30.3 - - + +
691A LEU* 4.7 9.6 - - + -
675B MET* 5.1 5.4 - - - +
679B ILE* 5.9 0.5 - - - +
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Residues in contact with MET 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A LEU 4.9 1.3 - - - +
587A SER* 3.6 6.7 + - - +
588A THR 3.5 0.2 - - - -
589A THR* 1.3 82.5 + - - +
591A SER* 1.3 62.0 + - - +
593A CYS* 3.0 41.6 - - - -
594A ALA* 4.3 2.7 + - + +
1007A PLM 5.0 10.8 - - + +
603B MET* 4.6 15.0 - - + -
671B ILE* 3.5 18.4 - - + -
674B ASN* 2.5 36.3 - - - +
675B MET* 3.5 23.9 - - + +
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Residues in contact with SER 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A TRP* 3.1 35.9 - - - -
587A SER 3.0 16.5 + - - -
588A THR* 3.1 21.4 - - - +
589A THR 3.0 0.8 - - - -
590A MET* 1.3 76.6 - - - +
592A ARG* 1.3 61.7 + - - +
594A ALA* 4.3 7.1 + - - +
595A LYS* 5.2 1.6 + - - +
1007A PLM 5.5 4.7 + - - -
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Residues in contact with ARG 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A THR* 2.8 12.2 + - + +
589A THR 2.7 21.1 + - - +
591A SER* 1.3 74.0 - - - +
593A CYS* 1.3 65.1 + - - +
594A ALA 3.4 0.3 + - - -
595A LYS* 3.7 48.7 + - - +
683A THR* 5.3 11.0 - - + -
687A VAL* 4.5 22.7 - - + -
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Residues in contact with CYS 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589A THR 3.5 4.1 + - - +
590A MET* 3.0 51.5 + - - +
592A ARG* 1.3 81.6 - - - +
594A ALA* 1.3 73.4 + - - +
595A LYS 2.7 14.0 + - - -
596A ASP* 2.8 21.5 + - - +
597A LEU* 3.6 10.5 + - + -
679A ILE* 5.2 6.3 - - + +
680A ILE* 5.8 4.9 - - + -
683A THR* 4.5 22.4 - - - +
674B ASN* 4.2 6.3 - - - +
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Residues in contact with ALA 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590A MET* 4.3 2.2 + - + +
591A SER 4.3 4.6 + - - +
592A ARG 3.4 1.2 + - - -
593A CYS* 1.3 89.6 - - - +
595A LYS* 1.3 56.3 + - - +
597A LEU* 2.6 13.5 + - + +
598A PHE* 2.3 54.7 + - + +
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Residues in contact with LYS 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A ARG* 5.0 15.2 - - - +
591A SER 5.2 2.1 + - - +
592A ARG* 3.7 46.4 + - - +
593A CYS 2.7 5.5 + - - -
594A ALA* 1.3 74.1 - - - +
596A ASP* 1.3 59.4 + - - +
598A PHE* 4.9 3.6 - - - -
599A GLY* 4.5 5.4 + - - -
581D ARG* 4.6 17.5 + - - +
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Residues in contact with ASP 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A ARG 4.7 0.2 + - - -
593A CYS 2.8 11.6 + - - +
594A ALA 3.1 1.1 - - - -
595A LYS* 1.3 81.0 - - - +
597A LEU* 1.3 58.1 + - - +
599A GLY 3.7 0.9 + - - -
600A PHE* 3.0 30.3 + - - +
679A ILE* 3.2 31.4 - - + +
683A THR* 6.1 4.0 - - + -
582D THR* 5.3 2.1 + - - -
583D MET* 6.1 0.9 - - - +
586D LEU* 3.8 20.0 - - - +
684D TYR* 3.6 15.4 + - - -
688D LYS* 5.0 5.5 + - - +
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Residues in contact with LEU 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A CYS* 3.6 8.7 + - + +
594A ALA* 2.6 17.5 + - - +
596A ASP* 1.3 74.6 - - + +
598A PHE* 1.3 57.1 + - - +
599A GLY 3.1 1.8 - - - -
600A PHE* 2.5 49.9 + - + -
601A ALA* 2.7 26.6 + - + +
675A MET* 5.8 1.8 - - + +
676A PHE* 4.7 28.7 - - + -
679A ILE* 5.3 12.8 - - + -
680A ILE* 5.6 9.9 - - + -
666B PHE* 6.2 4.3 - - + -
670B PHE* 6.5 0.9 - - + -
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Residues in contact with PHE 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A PHE* 5.4 17.9 - + - -
594A ALA* 2.3 47.9 + - + +
595A LYS* 4.9 3.1 - - - -
597A LEU* 1.3 70.1 - - - +
599A GLY* 1.3 61.6 + - - +
601A ALA* 4.1 8.7 + - - +
602A ILE 5.3 0.5 + - - -
1008A PLM 6.1 7.2 - - + -
1009A PLM 5.8 2.6 - - - +
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Residues in contact with GLY 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A ALA 3.8 1.4 + - - -
595A LYS 4.5 5.5 + - - -
596A ASP 3.7 5.5 + - - -
597A LEU 3.1 0.2 - - - -
598A PHE* 1.3 83.9 - - - +
600A PHE* 1.3 62.7 + - - +
601A ALA 3.5 0.2 - - - -
602A ILE* 3.3 17.7 - - - +
581D ARG* 5.3 11.7 - - - -
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Residues in contact with PHE 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A ASP* 3.0 28.0 + - - +
597A LEU* 2.5 36.9 + - + +
599A GLY* 1.3 70.1 - - - +
601A ALA* 1.3 53.2 + - - +
602A ILE* 2.6 22.3 + - - +
603A MET* 2.7 66.2 + - + +
604A PHE* 4.5 11.7 - - + -
675A MET* 3.3 37.2 - - + -
676A PHE* 5.3 2.0 - + - -
679A ILE* 5.3 7.9 - - + -
583D MET* 5.4 12.6 - - + -
586D LEU* 5.4 12.1 - - + -
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Residues in contact with ALA 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A LEU* 2.7 25.3 + - + +
598A PHE* 4.1 6.7 + - - +
599A GLY 3.5 1.0 - - - -
600A PHE* 1.3 79.7 - - - +
602A ILE* 1.3 50.5 + - - +
603A MET 3.2 0.7 - - - -
604A PHE* 3.5 9.0 + - + +
605A PHE* 2.8 36.7 + - + +
676A PHE* 6.0 4.0 - - + -
1008A PLM 5.4 3.8 - - + -
1009A PLM 5.3 10.5 - - + -
666B PHE* 4.6 21.8 - - + -
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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