Contacts of the helix formed by residues 566 - 583 (chain B) in PDB entry 3U0Z
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 PRO 566 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562B LEU 3.5 9.8 - - - +
563B GLU 3.9 11.7 - - - +
564B GLU 3.3 11.9 - - - +
565B TYR* 1.3 84.4 - - - +
567B MET* 1.3 70.2 + - + +
568B MET 2.9 0.2 - - - -
569B ARG* 2.8 36.2 + - + +
570B ARG* 3.5 6.8 + - - +
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Residues in contact with MET 567 (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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565B TYR* 3.2 3.1 + - + +
566B PRO* 1.3 91.1 - - + +
568B MET* 1.3 65.6 + - + +
569B ARG 3.3 0.2 - - - -
570B ARG* 3.4 52.6 + - - +
571B ALA* 3.5 9.9 + - - +
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Residues in contact with MET 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B LEU* 3.7 40.8 - - + +
467B ASN 5.8 1.1 - - - +
468B ALA* 4.1 17.3 - - + -
469B ASP* 5.8 1.1 - - - -
472B PHE* 3.3 42.4 - - + -
562B LEU* 4.1 4.5 - - + -
565B TYR* 3.1 18.8 - - + +
566B PRO 2.9 0.2 - - - -
567B MET* 1.3 83.4 - - + +
569B ARG* 1.3 64.0 + - - +
570B ARG 3.3 0.4 - - - -
571B ALA* 3.4 21.9 - - + +
572B PHE* 3.2 28.4 + - - -
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Residues in contact with ARG 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B LEU 5.0 1.8 + - - -
533B LEU* 3.8 37.5 + - + +
535B LYS* 5.3 7.5 - - - +
558B PHE* 4.9 1.8 - - - -
559B ASN* 3.6 22.0 + - - -
562B LEU* 4.1 36.5 + - + +
565B TYR 3.7 2.0 + - - +
566B PRO* 2.8 20.0 + - + +
568B MET* 1.3 76.5 - - - +
570B ARG* 1.3 64.4 + - + +
572B PHE* 3.0 3.8 + - - +
573B GLU* 2.9 54.1 + - + +
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Residues in contact with ARG 570 (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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566B PRO 3.5 5.4 + - - +
567B MET* 3.4 55.2 + - - +
568B MET 3.3 0.4 - - - -
569B ARG* 1.3 77.6 - - + +
571B ALA* 1.3 57.4 + - - +
573B GLU* 3.7 18.8 - - - +
574B THR* 2.9 36.4 + - - +
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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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464B LEU* 4.0 11.8 - - + +
567B MET 3.5 6.3 + - - +
568B MET* 3.4 37.6 + - + +
569B ARG 3.1 0.4 - - - -
570B ARG* 1.3 80.0 - - - +
572B PHE* 1.3 62.4 + - - +
574B THR* 3.8 4.4 - - - -
575B VAL* 3.4 24.4 + - - +
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Residues in contact with PHE 572 (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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464B LEU* 3.4 34.3 - - + -
472B PHE* 4.4 4.5 - + - -
476B MET* 4.1 21.5 - - + -
501B MET* 4.6 6.7 - - + -
503B PHE* 4.9 1.8 - + - -
526B TYR* 3.9 35.6 + + - -
529B GLU* 4.2 15.3 - - + +
533B LEU* 4.2 19.7 - - + -
558B PHE* 4.2 20.0 - + - -
562B LEU* 4.2 23.8 - - + -
568B MET* 3.2 20.8 + - + -
569B ARG 3.0 7.6 + - - +
571B ALA* 1.3 77.0 - - - +
573B GLU* 1.3 66.2 - - - +
575B VAL* 3.2 6.2 + - - +
576B ALA* 3.0 21.7 + - - +
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Residues in contact with GLU 573 (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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533B LEU* 4.1 25.0 - - + +
569B ARG* 2.9 43.2 + - - +
570B ARG* 3.3 24.6 + - - +
572B PHE* 1.3 76.2 - - - +
574B THR* 1.3 56.6 + - - +
576B ALA* 3.2 4.9 + - - +
577B ILE* 2.9 41.8 + - + +
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Residues in contact with THR 574 (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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570B ARG* 2.9 19.5 + - - +
571B ALA* 3.8 6.3 - - - -
573B GLU* 1.3 76.1 - - - +
575B VAL* 1.3 64.9 + - + +
577B ILE* 3.3 9.9 + - - +
578B ASP* 3.1 35.5 + - - +
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Residues in contact with VAL 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B LEU* 5.7 3.1 - - + -
526B TYR* 3.5 26.5 - - + +
529B GLU* 4.6 0.7 - - - +
571B ALA 3.4 11.6 + - - +
572B PHE 3.2 5.1 + - - +
574B THR* 1.3 79.3 - - + +
576B ALA* 1.3 56.2 + - - +
578B ASP* 3.3 11.6 + - + +
579B ARG* 2.9 57.8 + - + +
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Residues in contact with ALA 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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529B GLU* 4.3 8.0 + - - +
530B ILE* 4.0 23.8 - - + -
533B LEU* 4.1 15.9 - - + -
572B PHE 3.0 13.1 + - - +
573B GLU* 3.2 10.5 + - - +
575B VAL* 1.3 74.0 - - - +
577B ILE* 1.3 67.1 + - + +
579B ARG* 3.1 7.6 + - - +
580B LEU* 3.0 32.0 + - + +
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Residues in contact with ILE 577 (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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573B GLU* 2.9 28.5 + - + +
574B THR* 3.3 7.4 + - - +
576B ALA* 1.3 72.9 - - + +
578B ASP* 1.3 65.7 + - - +
580B LEU* 3.3 9.3 + - + +
581B ASP* 3.0 27.9 + - + +
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Residues in contact with ASP 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 THR* 3.1 31.1 + - - +
575B VAL* 3.7 11.9 - - + +
576B ALA 3.2 0.2 - - - -
577B ILE* 1.3 79.7 - - - +
579B ARG* 1.3 60.1 + - + +
581B ASP* 4.0 5.1 - - - +
582B ARG* 3.3 44.7 + - - +
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Residues in contact with ARG 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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521B LEU* 4.0 12.3 - - - +
525B SER* 5.0 2.4 + - - -
526B TYR* 2.8 42.7 + - - +
529B GLU* 2.8 46.3 + - - -
530B ILE* 4.3 4.5 - - + -
575B VAL* 2.9 36.7 + - + +
576B ALA 3.1 5.6 + - - +
578B ASP* 1.3 78.5 - - + +
580B LEU* 1.3 61.5 + - - +
582B ARG* 3.4 12.5 + - - +
583B ILE* 3.4 10.0 + - - +
646B CMP 3.2 79.0 + - + +
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Residues in contact with LEU 580 (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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530B ILE* 4.0 25.8 - - + -
534B THR* 5.6 2.9 - - + -
539B THR* 4.0 33.2 - - + +
576B ALA* 3.0 23.8 + - + +
577B ILE* 4.0 9.0 - - + +
579B ARG* 1.3 73.1 - - - +
581B ASP* 1.3 60.1 + - - +
583B ILE* 3.6 10.5 - - + +
584B GLY 3.3 3.3 + - - -
585B LYS* 2.6 60.6 + - + +
586B LYS* 6.1 0.4 - - - -
587B ASN* 4.7 21.5 - - + +
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Residues in contact with ASP 581 (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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577B ILE* 3.0 21.9 + - + +
578B ASP* 4.0 6.5 - - - +
580B LEU* 1.3 78.5 - - - +
582B ARG* 1.3 60.4 + - - +
584B GLY* 3.3 12.2 + - - +
585B LYS 4.7 4.0 - - - -
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Residues in contact with ARG 582 (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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519B MET* 4.2 18.9 - - + +
578B ASP* 3.3 41.9 + - - +
579B ARG* 3.4 9.9 + - - +
580B LEU 3.3 0.2 - - - -
581B ASP* 1.3 77.3 - - - +
583B ILE* 1.3 60.3 + - + +
584B GLY 3.4 1.2 + - - -
646B CMP 3.2 34.2 + - - +
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Residues in contact with ILE 583 (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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511B VAL* 5.8 2.5 - - + -
513B THR* 4.4 13.1 - - - +
516B SER* 4.5 18.6 - - - -
519B MET* 3.9 26.7 - - - -
539B THR* 4.4 7.9 - - - +
540B ALA* 5.1 1.3 - - + -
579B ARG 3.4 12.1 - - - +
580B LEU* 3.6 16.6 - - + +
582B ARG* 1.3 79.8 - - - +
584B GLY* 1.3 63.6 + - - +
585B LYS* 3.3 33.8 + - + +
646B CMP 4.0 25.8 - - + +
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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