Contacts of the helix formed by residues 581 - 601 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B PHE 4.3 0.2 - - - +
580B ASN* 1.3 116.1 + - - +
582B THR* 1.3 65.9 + - - +
583B MET* 2.9 17.5 + - + +
584B SER* 3.4 13.6 + - - -
585B GLN* 4.4 1.4 + - - +
595C LYS* 4.5 20.4 + - - +
599C GLY* 5.3 11.8 - - - -
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Residues in contact with THR 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B ARG* 1.3 73.5 - - - +
583B MET* 1.3 54.7 + - - +
584B SER 3.2 0.4 - - - -
585B GLN* 2.9 13.7 + - + +
586B LEU* 2.3 61.6 + - - +
688B LYS* 5.8 2.9 - - - -
691B LEU* 5.8 3.4 - - + -
695B LYS* 5.2 13.0 - - - +
596C ASP* 5.3 2.3 + - - -
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Residues in contact with MET 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B ASN* 6.0 4.5 - - + -
580B ASN* 4.3 7.6 - - - +
581B ARG* 2.9 15.7 - - + +
582B THR* 1.3 79.6 + - - +
584B SER* 1.3 53.4 + - - +
586B LEU* 2.7 11.8 + - - -
587B SER* 2.4 41.6 + - - +
596C ASP* 6.0 2.0 - - - +
599C GLY 6.0 1.1 - - - +
600C PHE* 5.3 17.3 - - + -
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Residues in contact with SER 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B ASN* 2.7 32.6 + - - +
579B PHE* 3.0 25.1 - - - -
580B ASN* 3.3 1.6 + - - -
581B ARG 3.4 8.8 + - - +
582B THR 3.2 0.4 - - - -
583B MET* 1.3 78.0 - - - +
585B GLN* 1.3 69.7 + - - +
587B SER* 3.5 16.3 + - - -
588B THR* 4.0 5.7 + - - -
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Residues in contact with GLN 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B ARG 4.4 1.1 + - - +
582B THR* 2.9 15.0 + - + +
584B SER* 1.3 78.8 - - - +
586B LEU* 1.3 59.0 + - + +
587B SER 2.9 4.3 - - - -
588B THR* 2.6 43.9 + - - -
589B THR* 3.6 4.0 + - - +
691B LEU* 4.9 13.6 - - + +
694B GLN* 5.0 15.1 + - - +
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Residues in contact with LEU 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B THR* 2.3 64.1 + - - +
583B MET* 2.7 13.4 + - - +
585B GLN* 1.3 66.0 - - + +
587B SER* 1.3 54.4 + - - -
589B THR* 2.2 41.3 + - + +
590B MET* 4.0 2.1 + - - +
684B TYR* 3.4 27.4 - - + +
688B LYS* 4.4 9.2 - - + +
691B LEU* 3.5 26.9 - - + -
596C ASP* 3.7 25.1 - - - +
600C PHE* 5.4 13.1 - - + -
603C MET* 5.6 0.3 - - - +
675C MET* 5.4 2.4 - - - +
679C ILE* 5.6 3.1 - - + -
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Residues in contact with SER 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B TRP* 5.4 5.5 - - - -
574B PHE* 4.9 14.7 - - - -
578B ASN* 5.1 9.2 + - - +
583B MET* 2.4 31.2 + - - +
584B SER* 3.5 11.7 - - - -
585B GLN 2.9 0.4 + - - -
586B LEU* 1.3 70.6 - - - +
588B THR* 1.3 64.9 + - - +
589B THR 3.1 0.4 - - - -
590B MET* 3.6 5.5 + - - +
591B SER* 3.0 20.5 + - - -
1007B PLM 5.3 3.1 - - - +
603C MET* 4.4 20.4 - - - -
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Residues in contact with THR 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B TRP* 5.9 0.8 - - + -
584B SER 4.1 6.1 + - - -
585B GLN* 2.6 31.1 + - - -
587B SER* 1.3 70.4 - - - +
589B THR* 1.3 57.4 + - - +
591B SER* 3.0 12.7 + - - +
592B ARG* 2.8 30.5 + - + +
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Residues in contact with THR 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585B GLN 4.1 1.3 - - - +
586B LEU* 2.2 49.9 + - + +
588B THR* 1.3 74.4 - - - +
590B MET* 1.3 60.0 + - - +
592B ARG* 2.7 32.1 + - - +
593B CYS* 3.5 4.5 + - - +
683B THR* 5.5 2.4 + - - -
684B TYR* 3.7 32.4 - - + -
687B VAL* 3.6 31.4 - - + +
691B LEU* 4.7 9.2 - - + -
675C MET* 4.9 5.2 - - - +
679C ILE* 5.9 0.3 - - - +
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Residues in contact with MET 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B LEU 4.9 1.1 - - - +
587B SER* 3.6 7.1 + - - +
589B THR* 1.3 81.8 + - - +
591B SER* 1.3 61.8 + - - +
593B CYS* 3.0 42.1 - - - -
594B ALA* 4.3 2.4 + - + +
1007B PLM 5.1 9.4 - - - +
603C MET* 4.7 12.1 - - + -
671C ILE* 3.6 21.1 - - + -
674C ASN* 2.4 37.2 - - - +
675C MET* 3.5 24.3 - - + +
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Residues in contact with SER 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B TRP* 3.1 36.0 - - - -
587B SER 3.0 15.9 + - - -
588B THR* 3.1 22.1 - - - +
589B THR 3.0 0.8 - - - -
590B MET* 1.3 78.5 - - - +
592B ARG* 1.3 60.3 + - - +
593B CYS 3.5 0.2 + - - -
594B ALA* 4.3 6.8 + - - +
595B LYS* 5.2 1.4 + - - +
1007B PLM 5.5 4.4 + - - -
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Residues in contact with ARG 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B THR* 2.8 11.9 + - + +
589B THR 2.7 21.8 + - - +
591B SER* 1.3 73.0 - - - +
593B CYS* 1.3 65.9 + - - +
594B ALA 3.4 0.2 + - - -
595B LYS* 3.7 49.7 + - - +
683B THR* 5.3 10.8 - - + -
687B VAL* 4.5 22.0 - - + -
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Residues in contact with CYS 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B THR 3.5 4.7 + - - +
590B MET* 3.0 49.7 + - - +
592B ARG* 1.3 81.1 - - - +
594B ALA* 1.3 84.6 + - - +
595B LYS 2.7 2.8 + - - -
596B ASP* 2.8 21.8 + - - +
597B LEU* 3.6 10.2 + - + -
679B ILE 5.2 5.4 - - - +
680B ILE* 5.8 5.8 - - + -
683B THR* 4.5 21.8 - - - +
674C ASN* 4.2 5.8 - - - +
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Residues in contact with ALA 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B MET* 4.3 2.9 + - + +
591B SER 4.3 4.8 + - - +
592B ARG 3.4 1.0 + - - -
593B CYS* 1.3 89.4 - - - +
595B LYS* 1.3 57.3 + - - +
596B ASP 3.0 0.2 - - - -
597B LEU* 2.6 12.6 + - + +
598B PHE* 2.3 54.5 + - + +
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Residues in contact with LYS 595 (chain B).
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* 4.6 18.5 + - - +
504B ARG* 5.0 14.8 - - - +
591B SER 5.2 1.4 + - - +
592B ARG* 3.7 46.3 + - - +
593B CYS 2.7 5.3 + - - -
594B ALA* 1.3 74.3 - - - +
596B ASP* 1.3 59.5 + - - +
598B PHE* 4.9 3.8 - - - -
599B GLY* 4.5 5.4 + - - -
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Residues in contact with ASP 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A THR* 5.3 1.4 + - - -
583A MET* 6.0 1.4 - - - +
586A LEU* 3.7 20.5 - - - +
684A TYR* 3.5 16.3 + - - -
688A LYS* 5.0 4.9 + - - +
592B ARG 4.7 0.2 + - - -
593B CYS 2.8 11.0 + - - +
594B ALA 3.1 1.1 - - - -
595B LYS* 1.3 81.4 - - - +
597B LEU* 1.3 57.8 + - - +
599B GLY* 3.7 1.6 + - - -
600B PHE* 3.0 30.5 + - - +
679B ILE* 3.2 31.5 - - + +
683B THR* 6.1 4.3 - - + -
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Residues in contact with LEU 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593B CYS* 3.6 9.2 + - + +
594B ALA* 2.6 17.1 + - - +
596B ASP* 1.3 74.8 - - + +
598B PHE* 1.3 56.3 + - - +
599B GLY 3.1 2.2 - - - -
600B PHE* 2.5 50.0 + - + -
601B ALA* 2.7 26.3 + - + +
675B MET* 5.8 1.6 - - + +
676B PHE* 4.7 28.7 - - + -
679B ILE* 5.3 13.5 - - + -
680B ILE* 5.6 9.4 - - + -
666C PHE* 6.0 5.8 - - + -
670C PHE* 6.4 2.0 - - + -
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Residues in contact with PHE 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B PHE* 5.4 16.4 - + - -
594B ALA* 2.3 48.0 + - + +
595B LYS* 4.9 3.1 - - - -
597B LEU* 1.3 70.3 - - - +
599B GLY* 1.3 60.9 + - - +
601B ALA* 4.1 9.4 + - - +
602B ILE 5.3 0.7 + - - -
1008B PLM 6.0 8.1 - - + +
1009B PLM 5.8 3.6 - - - +
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Residues in contact with GLY 599 (chain B).
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* 5.3 11.4 - - - -
583A MET* 4.6 11.9 - - - +
594B ALA 3.8 1.6 + - - -
595B LYS 4.5 4.6 + - - -
596B ASP 3.7 5.5 + - - -
597B LEU 3.1 0.4 - - - -
598B PHE* 1.3 83.7 - - - +
600B PHE* 1.3 63.3 + - - +
601B ALA 3.5 0.2 - - - -
602B ILE* 3.3 17.5 - - - +
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Residues in contact with PHE 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583A MET* 5.3 17.7 - - + -
586A LEU* 5.4 12.8 - - + -
596B ASP* 3.0 27.2 + - - +
597B LEU* 2.5 36.1 + - + +
599B GLY* 1.3 70.5 - - - +
601B ALA* 1.3 52.7 + - - +
602B ILE* 2.6 21.0 + - - +
603B MET* 2.7 68.1 + - + -
604B PHE* 4.5 11.9 - - + -
675B MET* 3.3 37.5 - - + -
676B PHE* 5.3 1.8 - + - -
679B ILE* 5.3 7.0 - - + -
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Residues in contact with ALA 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B LEU* 2.7 24.4 + - + +
598B PHE* 4.1 7.3 + - - +
599B GLY 3.5 1.4 - - - -
600B PHE* 1.3 80.0 - - - +
602B ILE* 1.3 50.3 + - - +
603B MET 3.2 0.6 + - - -
604B PHE* 3.5 8.8 + - + +
605B PHE* 2.8 36.8 + - + +
676B PHE* 6.0 4.3 - - + -
1008B PLM 5.4 4.3 - - + -
1009B PLM 5.3 9.2 - - + -
666C PHE* 4.6 22.2 - - + -
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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