Contacts of the helix formed by residues 564 - 580 (chain B) in PDB entry 5MJ6
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 564 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560B LYS 3.3 8.7 - - - +
563B LEU* 1.3 80.7 - - - +
565B GLU* 1.3 71.0 + - - +
566B ASP* 2.6 26.1 + - - +
567B VAL* 3.6 24.5 - - - +
568B PHE* 3.3 17.7 + - - +
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Residues in contact with GLU 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B TYR* 4.3 5.2 + - + +
496B PHE* 3.5 20.4 - - + -
500B LYS* 3.1 30.8 + - - -
560B LYS* 3.1 37.0 + - + -
564B SER* 1.3 76.7 + - - +
566B ASP* 1.3 61.0 + - - +
568B PHE* 3.6 6.9 - - + +
569B GLN* 3.1 23.9 + - - +
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Residues in contact with ASP 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B SER* 2.6 17.9 + - - +
565B GLU* 1.3 72.3 - - - +
567B VAL* 1.3 65.5 + - + +
568B PHE 3.2 1.1 - - - -
569B GLN* 3.1 24.2 + - - +
570B HIS* 3.0 26.1 + - + +
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Residues in contact with VAL 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B LEU* 4.0 17.3 - - + -
564B SER* 3.4 28.5 + - - +
566B ASP* 1.3 78.1 - - + +
568B PHE* 1.3 63.6 + - - +
569B GLN 3.2 0.2 + - - -
570B HIS* 3.4 9.8 + - + -
571B ALA* 3.1 22.3 + - - +
593B PHE* 5.1 2.9 - - + -
596B VAL* 3.7 19.4 - - + +
597B THR* 3.8 28.7 - - + -
1125B NAG 5.8 3.6 - - - +
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Residues in contact with PHE 568 (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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407B TYR* 3.8 16.8 - - - -
489B PHE* 4.2 18.6 - + - -
492B PHE* 3.6 35.0 - + - -
493B MET* 5.2 3.1 - - - -
556B LEU* 3.7 27.4 - - + -
559B LEU* 4.7 0.7 - - + -
560B LYS* 3.5 29.8 - - + -
563B LEU* 5.0 1.3 - - + +
564B SER 3.3 17.9 + - - +
565B GLU* 3.6 7.2 - - - +
566B ASP 3.2 0.2 - - - -
567B VAL* 1.3 80.7 - - - +
569B GLN* 1.3 62.2 + - - +
571B ALA* 3.5 2.6 + - - +
572B VAL* 3.1 35.4 + - + +
593B PHE* 3.7 33.9 - + - -
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Residues in contact with GLN 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B ASN 4.6 1.2 + - - -
407B TYR* 3.0 67.4 + - + +
409B GLU* 3.6 18.0 + - - +
565B GLU 3.1 12.2 + - - +
566B ASP* 3.1 21.5 + - - +
568B PHE* 1.3 79.5 - - - +
570B HIS* 1.3 60.2 + - + +
572B VAL* 3.1 5.9 + - - +
573B VAL* 2.8 28.3 + - + +
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Residues in contact with HIS 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B GLU* 5.7 2.0 - - - +
566B ASP* 3.0 31.8 + - + +
567B VAL* 4.2 6.7 - - + -
569B GLN* 1.3 78.2 - - + +
571B ALA* 1.3 61.9 + - - +
573B VAL* 3.7 14.8 - - + -
574B LEU* 2.9 33.0 + - + +
596B VAL* 3.2 38.3 - - + +
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Residues in contact with ALA 571 (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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567B VAL 3.1 18.1 + - - +
568B PHE 3.5 5.2 - - - +
570B HIS* 1.3 77.0 - - - +
572B VAL* 1.3 58.5 + - - +
574B LEU* 3.6 1.8 - - - +
575B TYR* 2.9 31.3 + - - +
589B LEU* 6.4 0.4 - - - -
592B SER* 3.9 6.5 - - - +
593B PHE* 3.7 47.6 - - + +
596B VAL* 3.8 14.0 - - + +
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Residues in contact with VAL 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B TYR* 4.7 7.4 - - + +
408B PHE* 3.9 23.1 - - + -
471B PHE* 3.9 20.0 - - + -
489B PHE* 3.9 22.7 - - + -
493B MET* 5.9 0.9 - - - -
568B PHE* 3.1 37.0 + - + +
569B GLN* 3.1 11.1 + - - +
571B ALA* 1.3 80.0 - - + +
573B VAL* 1.3 62.3 + - + +
575B TYR* 3.4 8.5 + - - +
576B LEU* 3.0 30.9 + - + +
589B LEU* 6.2 0.9 - - - -
593B PHE* 5.2 3.1 - - + -
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Residues in contact with VAL 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B TYR 4.0 16.4 - - - +
408B PHE* 3.9 21.1 - - - +
409B GLU* 4.0 26.7 - - - +
569B GLN* 2.8 27.9 + - + +
570B HIS* 3.9 11.2 - - + -
571B ALA 3.3 0.4 - - - -
572B VAL* 1.3 75.0 - - + +
574B LEU* 1.3 63.7 + - - +
576B LEU* 3.3 3.8 + - - +
577B HIS* 2.9 52.4 + - + +
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Residues in contact with LEU 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B HIS* 2.9 18.8 + - + +
571B ALA* 3.6 3.1 - - - +
573B VAL* 1.3 77.9 - - - +
575B TYR* 1.3 58.3 + - - +
577B HIS* 3.3 6.4 + - - +
578B ASN* 2.9 29.5 + - + +
592B SER* 4.3 10.5 - - - +
595B GLU* 3.7 28.7 - - + +
596B VAL* 3.7 26.2 - - + -
1N NAG 3.3 28.7 - - + +
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Residues in contact with TYR 575 (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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471B PHE* 3.9 32.3 - + - -
475B VAL* 4.2 15.5 - - + -
485B LEU* 4.6 8.8 + - - +
489B PHE* 4.9 1.8 - + - -
571B ALA 2.9 17.9 + - - +
572B VAL* 3.4 8.1 - - - +
574B LEU* 1.3 73.8 - - - +
576B LEU* 1.3 70.7 + - + +
578B ASN* 4.7 0.2 - - - -
579B HIS* 3.2 46.3 + - - +
584B ILE* 2.8 36.4 - - + +
588B ASP* 4.1 2.0 - - + -
589B LEU* 3.6 50.6 - - + +
592B SER* 3.5 23.3 + - - +
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Residues in contact with LEU 576 (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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408B PHE* 3.7 44.9 - - + +
410B ILE* 3.7 16.2 - - + -
470B TRP* 4.0 26.9 - - + +
471B PHE* 4.1 28.3 - - + -
474B LEU* 4.9 3.4 - - + -
475B VAL* 3.9 23.2 - - + +
572B VAL* 3.0 20.7 + - + +
573B VAL* 3.9 3.1 - - - +
575B TYR* 1.3 79.3 - - + +
577B HIS* 1.3 57.0 + - - +
580B SER* 2.9 34.1 + - - -
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Residues in contact with HIS 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B GLU* 4.0 10.0 + - + -
410B ILE* 3.5 32.1 - - + +
573B VAL* 2.9 45.9 + - + +
574B LEU* 3.6 6.0 - - - +
576B LEU* 1.3 75.1 - - - +
578B ASN* 1.3 66.5 + - - +
579B HIS 3.3 0.5 + - - -
580B SER* 3.8 10.6 + - - -
1131B BR 3.7 28.9 - - + +
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Residues in contact with ASN 578 (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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574B LEU* 2.9 22.9 + - + +
575B TYR* 4.7 0.4 - - - -
577B HIS* 1.3 74.5 - - - +
579B HIS* 1.3 80.2 + - + +
580B SER 3.9 1.0 + - - +
582B ALA* 5.7 0.2 - - - +
592B SER* 5.5 0.8 + - - -
595B GLU* 4.8 0.4 + - - -
1N NAG 1.4 72.5 + - + +
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Residues in contact with HIS 579 (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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475B VAL* 3.4 16.6 - - + +
575B TYR* 3.2 31.8 + + - +
578B ASN* 1.3 103.1 - - + +
580B SER* 1.3 68.9 + - - +
581B TYR 3.4 0.3 + - - -
582B ALA* 3.1 24.3 + - + +
583B SER 4.5 9.0 - - - +
584B ILE* 3.6 29.8 - - + +
588B ASP* 4.0 34.5 - - + +
592B SER* 4.5 4.3 - - - -
1N NAG 3.3 21.7 + - - -
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Residues in contact with SER 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B ILE* 4.4 6.8 - - - +
474B LEU* 3.5 25.4 - - - +
475B VAL* 4.0 2.2 - - - -
576B LEU 2.9 21.7 + - - -
577B HIS* 3.8 7.4 + - - -
578B ASN 3.6 2.5 + - - +
579B HIS* 1.3 77.0 - - - +
581B TYR* 1.3 85.4 + - - +
582B ALA* 3.2 4.5 + - - +
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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