Contacts of the helix formed by residues 566 - 584 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562A LEU 3.5 9.6 - - - +
563A GLU 3.9 10.8 - - - +
564A GLU 3.3 11.4 - - - +
565A TYR* 1.3 84.6 - - - +
567A MET* 1.3 70.6 + - + +
568A MET 2.9 0.2 - - - -
569A ARG* 2.8 34.4 + - + +
570A ARG* 3.5 7.1 + - - +
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Residues in contact with MET 567 (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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565A TYR* 3.2 2.9 + - + -
566A PRO* 1.3 91.8 - - + +
568A MET* 1.3 65.1 + - + +
569A ARG 3.2 0.2 - - - -
570A ARG* 3.3 54.5 + - - +
571A ALA* 3.6 9.7 + - - +
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Residues in contact with MET 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LEU* 3.6 48.2 - - + +
467A ASN 5.8 0.9 - - - +
468A ALA* 4.1 15.9 - - + -
469A ASP* 5.8 1.1 - - - -
472A PHE* 3.3 43.3 - - + -
562A LEU* 4.1 4.9 - - + -
565A TYR* 3.1 17.9 - - + +
566A PRO 2.9 0.6 - - - -
567A MET* 1.3 82.9 - - + +
569A ARG* 1.3 62.7 + - - +
570A ARG 3.3 0.4 - - - -
571A ALA* 3.4 17.7 - - + +
572A PHE* 3.2 27.5 + - - -
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Residues in contact with ARG 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LEU 4.9 2.0 + - - -
533A LEU* 3.8 38.7 + - + +
535A LYS* 5.7 5.7 - - - +
558A PHE* 5.0 3.4 - - - -
559A ASN* 3.7 20.6 + - - -
562A LEU* 4.0 35.4 + - + +
565A TYR 3.6 2.0 + - - +
566A PRO* 2.8 19.5 + - + +
568A MET* 1.3 77.1 - - - +
570A ARG* 1.3 64.5 + - + +
571A ALA 3.1 0.2 - - - -
572A PHE* 3.0 4.6 + - - +
573A GLU* 2.9 54.8 + - - +
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Residues in contact with ARG 570 (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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566A PRO 3.5 6.3 + - - +
567A MET* 3.3 57.4 + - - +
568A MET 3.3 0.6 - - - -
569A ARG* 1.3 78.4 - - + +
571A ALA* 1.3 57.1 + - - +
573A GLU* 3.7 18.9 - - - +
574A THR* 2.9 37.7 + - - +
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Residues in contact with ALA 571 (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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464A LEU* 4.0 12.4 - - + +
567A MET 3.6 6.1 + - - +
568A MET* 3.4 39.3 - - + +
569A ARG 3.1 0.2 - - - -
570A ARG* 1.3 80.3 - - - +
572A PHE* 1.3 63.0 + - - +
574A THR* 3.9 4.1 - - - -
575A VAL* 3.4 24.8 + - - +
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Residues in contact with PHE 572 (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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464A LEU* 3.4 34.3 - - + -
472A PHE* 4.4 4.9 - + - -
476A MET* 4.1 22.7 - - + -
501A MET* 4.7 4.3 - - + -
503A PHE* 4.9 4.7 - + - -
526A TYR* 3.9 36.5 + + - -
529A GLU* 4.2 16.3 - - + +
533A LEU* 4.2 19.7 - - + +
558A PHE* 4.2 19.5 - + - -
562A LEU* 4.2 19.3 - - + -
568A MET* 3.2 21.9 + - + -
569A ARG* 3.0 7.0 + - - +
571A ALA* 1.3 78.7 - - - +
573A GLU* 1.3 64.4 + - - +
575A VAL* 3.2 6.2 + - - +
576A ALA* 3.0 21.1 + - - +
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Residues in contact with GLU 573 (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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533A LEU* 4.1 25.7 - - + +
569A ARG* 2.9 44.7 + - - +
570A ARG* 3.7 24.1 + - - +
572A PHE* 1.3 76.4 - - - +
574A THR* 1.3 56.8 + - - +
576A ALA* 3.2 3.7 + - - +
577A ILE* 2.8 41.8 + - + +
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Residues in contact with THR 574 (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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570A ARG* 2.9 19.1 + - - +
571A ALA* 3.9 6.1 - - - -
573A GLU* 1.3 76.5 - - - +
575A VAL* 1.3 65.6 + - + +
577A ILE* 3.3 9.0 + - - +
578A ASP* 3.1 34.9 + - - +
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Residues in contact with VAL 575 (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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464A LEU* 5.7 2.5 - - + -
526A TYR* 3.6 25.1 - - + +
529A GLU* 4.7 0.9 - - - +
571A ALA 3.4 13.2 + - - +
572A PHE 3.2 4.7 + - - +
574A THR* 1.3 79.3 - - + +
576A ALA* 1.3 56.2 + - - +
578A ASP* 3.3 12.6 + - + +
579A ARG* 2.9 52.0 + - + +
582A ARG* 5.8 2.9 - - - +
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Residues in contact with ALA 576 (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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529A GLU* 4.3 10.4 + - - +
530A ILE* 4.0 23.3 - - + +
533A LEU* 4.2 17.0 - - + -
572A PHE 3.0 13.4 + - - +
573A GLU* 3.3 10.1 - - - +
575A VAL* 1.3 74.2 - - - +
577A ILE* 1.3 66.4 + - + +
579A ARG* 3.2 5.0 + - - +
580A LEU* 2.9 31.7 + - + +
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Residues in contact with ILE 577 (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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573A GLU* 2.8 27.0 + - + +
574A THR* 4.0 6.7 - - - +
576A ALA* 1.3 74.3 - - + +
578A ASP* 1.3 59.9 + - - +
580A LEU* 3.3 11.4 + - + +
581A ASP* 2.9 33.8 + - + +
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Residues in contact with ASP 578 (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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574A THR* 3.1 29.8 + - - +
575A VAL* 3.6 11.2 - - + +
576A ALA 3.2 0.2 - - - -
577A ILE* 1.3 78.6 - - - +
579A ARG* 1.3 57.5 + - - +
581A ASP* 3.2 9.3 + - - +
582A ARG* 2.9 46.9 + - - +
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Residues in contact with ARG 579 (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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521A LEU* 4.0 11.9 - - - +
525A SER* 5.1 2.0 + - - -
526A TYR* 2.8 43.6 + - - +
527A PHE* 4.0 0.2 - - - +
529A GLU* 2.8 46.3 + - - -
530A ILE* 4.2 4.3 - - + -
575A VAL* 2.9 34.4 + - + +
576A ALA* 3.2 6.0 + - - +
578A ASP* 1.3 75.4 - - - +
580A LEU* 1.4 62.4 + - - +
582A ARG* 3.1 19.4 + - - +
583A ILE* 3.4 9.7 + - - +
646A CMP 3.2 80.0 + - + +
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Residues in contact with LEU 580 (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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530A ILE* 4.3 20.6 - - + -
534A THR* 5.6 3.4 - - + -
539A THR* 4.2 30.5 - - + +
576A ALA* 2.9 23.0 + - + +
577A ILE* 3.9 11.4 - - + +
579A ARG* 1.4 75.5 - - - +
581A ASP* 1.3 57.1 + - - +
583A ILE* 3.6 8.9 - - + +
584A GLY 3.0 7.8 + - - -
585A LYS* 2.9 63.4 + - + +
586A LYS* 5.3 0.7 - - - +
587A ASN* 4.5 24.2 - - + +
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Residues in contact with ASP 581 (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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577A ILE* 2.9 20.6 + - + +
578A ASP* 3.5 10.5 - - - +
579A ARG 3.2 0.2 - - - -
580A LEU* 1.3 79.1 - - - +
582A ARG* 1.3 61.0 + - - +
583A ILE 3.5 0.3 + - - -
584A GLY* 3.7 8.9 + - - -
585A LYS 5.1 1.6 - - - -
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Residues in contact with ARG 582 (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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519A MET* 3.6 23.9 - - + +
575A VAL* 5.8 3.0 - - - +
578A ASP* 2.9 37.3 + - - +
579A ARG* 3.1 18.1 + - - +
581A ASP* 1.3 76.5 - - - +
583A ILE* 1.3 61.2 + - - +
646A CMP 2.8 44.9 + - - +
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Residues in contact with ILE 583 (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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511A VAL* 5.6 2.9 - - + -
513A THR* 4.4 13.5 - - - +
516A SER* 4.6 19.1 - - - -
519A MET* 3.9 26.0 - - - -
539A THR* 4.4 7.4 - - - +
540A ALA* 5.2 1.1 - - + -
579A ARG 3.4 10.7 + - - +
580A LEU* 3.6 14.8 - - + +
582A ARG* 1.3 82.5 - - - +
584A GLY* 1.3 59.6 + - - +
585A LYS* 3.7 36.7 - - + +
646A CMP 4.1 24.9 - - + +
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Residues in contact with GLY 584 (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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580A LEU 3.0 5.7 + - - -
581A ASP* 3.7 7.8 + - - -
582A ARG 3.7 1.6 - - - -
583A ILE* 1.3 80.9 - - - +
585A LYS* 1.3 61.6 + - - +
586A LYS* 6.1 0.9 - - - -
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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