Contacts of the helix formed by residues 534 - 554 (chain B) in PDB entry 3MBK
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 SER 534 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491B TRP* 3.5 5.3 + - - -
493B LYS* 4.1 7.9 - - - +
532B SER 3.5 2.0 + - - -
533B GLU* 1.3 78.6 - - - +
535B TYR* 1.3 64.6 + - - +
536B ASP* 3.5 9.1 + - - +
537B THR* 3.0 30.6 + - - -
538B TYR 2.9 18.2 + - - -
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Residues in contact with TYR 535 (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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491B TRP* 3.5 42.3 - + + +
534B SER* 1.3 72.5 - - - +
536B ASP* 1.3 77.4 + - - +
538B TYR* 3.1 5.7 + + - +
539B ILE* 2.9 49.6 + - + +
581B PRO* 4.1 6.0 - - + +
582B GLN 2.7 35.8 + - - -
583B ASN* 4.2 0.9 - - - -
584B SER* 3.6 30.1 - - - -
587B PHE* 3.6 43.7 - + + +
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Residues in contact with ASP 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B SER* 3.2 8.4 + - - +
535B TYR* 1.3 93.2 - - - +
537B THR* 1.3 57.8 + - - +
539B ILE* 4.6 3.8 - - - +
540B ASN* 2.9 46.4 + - - +
581B PRO* 5.7 5.0 - - - +
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Residues in contact with THR 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B ALA* 5.6 3.8 - - + -
533B GLU* 3.7 22.9 - - + +
534B SER* 3.0 29.4 + - - -
536B ASP* 1.3 76.1 - - - +
538B TYR* 1.3 61.5 + - - +
540B ASN* 3.5 5.4 + - - +
541B ARG* 2.9 28.6 + - + +
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Residues in contact with TYR 538 (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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488B LEU 5.2 0.4 + - - -
489B PHE 3.4 21.9 + - - -
490B GLU* 3.9 3.6 - - - -
491B TRP* 3.5 39.9 - + + -
533B GLU* 3.7 14.8 + - - +
534B SER 2.9 6.3 + - - -
535B TYR* 3.1 8.3 + + - +
537B THR* 1.3 77.0 - - - +
539B ILE* 1.3 71.1 + - + +
541B ARG* 3.4 22.5 - - - +
542B SER* 2.8 43.3 + - - -
567B SER* 2.7 44.7 + - - -
568B SER* 3.8 7.3 + - - -
571B ALA* 3.6 17.9 - - + +
572B CYS* 6.0 0.2 - - - -
587B PHE* 4.1 9.6 - + - -
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Residues in contact with ILE 539 (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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535B TYR* 2.9 60.3 + - + +
536B ASP* 4.0 4.7 - - - +
538B TYR* 1.3 80.9 - - + +
540B ASN* 1.3 64.2 + - - +
542B SER* 3.2 7.2 + - - -
543B PHE 3.0 18.5 + - - -
570B GLU* 5.9 0.7 - - + -
571B ALA* 3.9 30.1 - - + +
574B CYS* 5.3 5.2 - - + -
575B GLN* 3.3 20.9 - - + +
581B PRO* 3.7 25.8 - - + -
587B PHE* 4.1 11.9 - - + -
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Residues in contact with ASN 540 (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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536B ASP* 2.9 34.0 + - - +
537B THR* 3.9 5.4 - - - +
539B ILE* 1.3 78.7 - - - +
541B ARG* 1.3 57.8 + - - +
543B PHE* 3.3 6.4 + - + +
544B GLN* 2.9 27.9 + - - +
575B GLN* 3.1 29.5 + - - +
581B PRO* 5.6 1.0 - - - +
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Residues in contact with ARG 541 (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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486B PRO 4.0 0.2 + - - -
487B GLY 2.8 33.1 + - - +
489B PHE* 2.9 16.9 + - - -
490B GLU 3.0 22.6 + - - -
492B THR* 4.0 3.4 - - - +
524B ILE* 3.8 20.4 - - + -
529B LEU* 3.5 29.1 - - - +
533B GLU* 2.8 42.7 + - - -
537B THR* 2.9 19.2 + - + +
538B TYR* 3.4 19.0 - - - +
540B ASN* 1.3 76.4 - - - +
542B SER* 1.3 59.5 + - - +
544B GLN* 4.0 11.7 - - - +
545B VAL* 2.9 36.9 + - - +
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Residues in contact with SER 542 (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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487B GLY 4.7 8.7 + - - -
488B LEU* 5.7 1.1 - - - +
538B TYR* 2.8 39.5 + - - -
539B ILE 3.4 6.5 - - - -
541B ARG* 1.3 79.3 - - - +
543B PHE* 1.3 59.4 + - - +
545B VAL* 4.2 2.0 - - - +
546B THR* 2.7 33.2 + - - -
571B ALA* 3.3 34.7 - - - +
572B CYS* 4.0 9.2 - - - -
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Residues in contact with PHE 543 (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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539B ILE 3.0 5.7 + - - -
540B ASN* 3.5 8.1 - - - +
542B SER* 1.3 76.3 - - - +
544B GLN* 1.3 62.7 + - - +
546B THR* 3.3 5.6 + - - -
547B LYS* 3.0 65.7 + - + +
571B ALA 4.0 5.2 + - - +
572B CYS 5.0 2.2 - - - -
575B GLN* 3.1 55.2 - - + +
576B LEU* 3.6 31.2 - - + -
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Residues in contact with GLN 544 (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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523B HIS 4.7 3.8 + - - -
524B ILE* 3.9 32.1 - - - +
540B ASN 2.9 16.9 + - - +
541B ARG* 3.6 10.0 - - - +
543B PHE* 1.3 78.9 - - - +
545B VAL* 1.3 61.9 + - - +
547B LYS* 3.3 13.8 + - - +
548B GLU* 3.1 48.8 + - - +
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Residues in contact with VAL 545 (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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485B GLU* 3.5 33.9 - - + +
487B GLY* 3.7 13.7 - - - +
488B LEU* 4.4 8.5 - - + -
523B HIS* 4.7 5.4 - - + -
524B ILE* 3.1 42.6 - - + -
541B ARG 2.9 18.8 + - - +
542B SER* 4.2 2.7 - - - +
544B GLN* 1.3 74.1 - - - +
546B THR* 1.3 58.4 + - - +
548B GLU* 3.2 8.3 + - - +
549B ILE* 2.8 39.4 + - + +
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Residues in contact with THR 546 (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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375B LEU* 3.5 27.6 - - + -
488B LEU* 4.8 2.3 - - - +
542B SER 2.7 22.1 + - - -
543B PHE* 3.7 4.0 - - - -
545B VAL* 1.3 77.7 - - - +
547B LYS* 1.3 57.1 + - - +
549B ILE* 3.3 8.9 + - + +
550B ILE* 2.9 39.6 + - + +
562B ILE* 4.4 7.7 - - + +
572B CYS* 3.4 41.5 - - - +
576B LEU* 4.3 5.4 - - + -
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Residues in contact with LYS 547 (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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543B PHE* 3.0 67.1 + - + +
544B GLN* 3.6 14.1 - - - +
546B THR* 1.3 77.9 - - - +
548B GLU* 1.3 57.9 + - + +
550B ILE* 3.3 7.9 + - - +
551B SER* 2.9 30.8 + - - -
576B LEU* 4.9 10.3 - - + -
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Residues in contact with GLU 548 (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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523B HIS* 3.4 44.6 + - + +
544B GLN* 3.1 47.2 + - - +
545B VAL* 3.2 6.3 + - - +
547B LYS* 1.3 77.6 - - + +
549B ILE* 1.3 57.9 + - - +
551B SER* 3.8 5.5 - - - -
552B GLU* 3.0 31.9 + - - +
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Residues in contact with ILE 549 (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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375B LEU* 5.0 1.6 - - + -
456B TYR* 3.5 56.1 - - + -
485B GLU* 4.5 1.6 - - + -
488B LEU* 4.2 15.5 - - + -
523B HIS* 4.3 6.7 - - - +
545B VAL* 2.8 39.4 + - + +
546B THR* 3.6 5.6 - - - +
548B GLU* 1.3 74.9 - - - +
550B ILE* 1.3 66.9 + - + +
552B GLU* 3.3 8.3 + - - +
553B CYS* 3.2 24.8 + - - -
560B ILE* 3.8 18.4 - - + -
562B ILE* 4.3 16.2 - - + -
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Residues in contact with ILE 550 (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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373B ARG* 3.1 33.1 + - - +
375B LEU* 4.6 9.4 - - + -
546B THR* 2.9 29.1 + - + +
547B LYS* 3.7 6.3 - - - +
549B ILE* 1.3 74.5 - - - +
551B SER* 1.3 65.0 + - - +
553B CYS* 3.2 2.6 + - - +
554B LYS* 2.9 22.7 + - - +
560B ILE* 3.9 20.7 - - + +
576B LEU* 3.9 39.5 - - + -
611B TRP* 3.9 20.9 - - + +
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Residues in contact with SER 551 (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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547B LYS 2.9 17.9 + - - -
548B GLU* 3.8 7.6 - - - -
550B ILE* 1.3 78.1 - - - +
552B GLU* 1.3 61.6 + - - +
553B CYS 3.3 0.7 + - - -
554B LYS* 3.3 24.6 + - - +
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Residues in contact with GLU 552 (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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454B HIS* 5.7 0.2 + - - -
456B TYR* 2.6 35.0 + - - +
483B ARG* 4.4 9.3 + - - +
520B TYR* 3.6 9.6 - - - -
521B ARG 5.3 0.7 - - - +
523B HIS* 2.8 40.1 + - - +
548B GLU 3.0 15.5 + - - +
549B ILE* 3.5 3.7 - - - +
551B SER* 1.3 76.7 - - - +
553B CYS* 1.3 57.8 + - - +
554B LYS 3.5 0.2 - - - -
556B LYS* 3.4 30.5 + - - +
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Residues in contact with CYS 553 (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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454B HIS* 3.4 35.2 - - - +
456B TYR* 3.3 33.9 - - - -
483B ARG* 4.1 2.7 - - - -
549B ILE 3.2 15.6 + - - +
550B ILE 3.6 0.4 - - - +
552B GLU* 1.3 78.3 - - - +
554B LYS* 1.3 58.7 + - - +
555B SER 3.3 0.5 + - - -
556B LYS* 2.9 33.6 + - - +
557B GLY 3.6 8.3 - - - +
560B ILE* 3.6 23.1 - - + -
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Residues in contact with LYS 554 (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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373B ARG* 3.0 51.9 - - - +
550B ILE 2.9 12.2 + - - +
551B SER* 3.3 20.0 + - - +
553B CYS* 1.3 75.4 - - - +
555B SER* 1.3 87.2 + - - +
556B LYS* 3.1 13.3 + - - +
557B GLY 5.6 0.2 - - - -
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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
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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