Contacts of the helix formed by residues 584 - 599 (chain A) in PDB entry 1W6J
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 CYS 584 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578A GLU* 4.2 5.4 - - - -
579A GLY* 3.0 44.9 + - - -
582A GLY 3.2 4.5 - - - -
583A VAL* 1.3 74.9 + - - +
585A PHE* 1.3 82.4 + - - +
586A THR* 3.5 1.4 + - - -
587A TYR* 3.4 2.2 + - - +
588A GLY 3.0 15.8 + - - -
631A GLU* 2.9 20.4 + - - +
635A SER* 3.8 13.9 - - - -
636A CYS* 3.9 23.8 - - - -
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Residues in contact with PHE 585 (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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572A ARG* 3.4 31.9 - - - -
576A SER* 3.6 17.9 - - - -
577A TRP 3.4 12.3 - - - +
578A GLU* 3.6 22.2 - - + -
584A CYS* 1.3 86.0 - - + +
586A THR* 1.3 60.0 + - - +
587A TYR 3.2 2.0 - - - -
589A THR* 2.6 37.1 + - - -
618A PHE* 4.1 16.2 - + + -
631A GLU* 2.9 21.8 + - - +
635A SER 3.9 1.8 - - - -
639A ARG 3.5 21.5 - - - -
640A ARG* 3.2 27.1 - - - -
641A TYR* 3.8 22.9 - - + -
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Residues in contact with THR 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A PHE* 1.3 75.8 - - - +
587A TYR* 1.3 59.2 + - - +
589A THR* 4.0 0.5 - - - -
590A TRP* 3.1 29.8 + - - +
619A LEU* 4.3 22.2 - - + +
629A TRP* 4.3 7.9 - - + -
631A GLU* 2.7 23.6 + - - +
641A TYR* 4.0 24.2 - - + +
651A ASN* 3.0 45.1 + - + +
654A TRP* 3.6 11.7 - - - +
655A ALA* 4.5 3.3 - - + -
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Residues in contact with TYR 587 (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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387A TRP* 4.0 22.7 - - - -
391A PHE* 5.3 1.0 - + - -
532A GLU* 3.5 33.4 - - + +
579A GLY* 4.3 0.7 - - - -
581A TRP* 3.8 12.6 + - + +
582A GLY* 3.4 38.8 - - - +
584A CYS 3.4 9.6 + - - +
585A PHE 3.2 0.4 - - - -
586A THR* 1.3 79.7 + - - +
588A GLY* 1.3 66.4 + - - +
590A TRP* 3.4 10.3 + + - +
591A PHE* 3.3 47.8 + + - -
654A TRP* 3.4 54.1 - + + -
707A TYR* 4.2 10.3 + + - -
711A PHE* 5.7 0.9 - + - -
1733A R71 4.6 1.0 - - - +
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Residues in contact with GLY 588 (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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531A VAL* 4.0 9.5 - - - +
532A GLU* 4.7 3.4 - - - -
577A TRP* 3.4 28.2 - - - +
578A GLU 4.2 2.0 - - - -
579A GLY* 4.0 12.3 - - - -
584A CYS 3.0 9.9 + - - -
587A TYR* 1.3 81.6 - - - +
589A THR* 1.3 57.5 + - - +
591A PHE* 3.3 5.4 + - - +
592A GLY 3.0 21.5 + - - -
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Residues in contact with THR 589 (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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575A GLY 4.3 2.2 - - - +
576A SER* 3.4 9.9 - - - -
577A TRP* 3.1 36.2 + - + -
585A PHE 2.6 23.8 + - - -
586A THR 4.2 2.0 - - - -
588A GLY* 1.3 73.6 - - - +
590A TRP* 1.3 59.7 + - - +
592A GLY* 3.8 0.2 - - - -
593A LEU* 2.9 31.1 + - + +
615A ALA* 4.2 19.5 - - + +
618A PHE* 4.8 2.0 - - + -
619A LEU* 4.1 32.1 - - + -
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Residues in contact with TRP 590 (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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391A PHE* 4.6 7.0 - + - -
586A THR 3.1 20.4 + - - +
587A TYR* 3.6 9.0 - + - +
589A THR* 1.3 76.1 - - - +
591A PHE* 1.3 99.1 + + - +
593A LEU* 3.3 1.8 + - - +
594A GLU* 2.9 63.7 + - + +
619A LEU* 5.7 1.5 - - - +
654A TRP* 3.6 44.6 - + + +
657A MET* 3.6 30.9 - - + +
658A GLY* 3.7 24.9 - - - -
711A PHE* 3.5 23.1 - + - -
714A TRP* 4.5 13.2 - + - -
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Residues in contact with PHE 591 (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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387A TRP* 5.3 4.7 - + - -
391A PHE* 4.7 10.5 - + - -
455A ASP* 6.4 0.4 - - + -
459A GLU* 4.4 14.8 - - - -
531A VAL* 4.4 2.0 - - - +
532A GLU* 3.5 51.6 - - + +
535A SER* 2.7 37.7 + - - -
536A ALA* 4.4 5.2 - - + -
539A GLN* 4.5 5.6 - - - -
587A TYR* 3.3 52.6 + + - -
588A GLY 3.3 9.0 + - - +
589A THR 3.3 0.4 - - - -
590A TRP* 1.3 110.9 - + - +
592A GLY* 1.3 61.1 + - - +
594A GLU* 3.3 3.8 + - + +
595A ALA 3.1 8.1 + - - -
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Residues in contact with GLY 592 (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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531A VAL* 4.1 11.6 - - - +
567A CYS* 5.4 0.9 - - - -
577A TRP* 3.9 31.0 - - - -
588A GLY 3.0 11.0 + - - -
589A THR 3.3 2.9 + - - -
590A TRP 3.3 0.2 - - - -
591A PHE* 1.3 73.4 - - - +
593A LEU* 1.3 65.7 + - - +
595A ALA* 3.3 4.4 + - - +
596A PHE* 3.2 29.3 + - - -
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Residues in contact with LEU 593 (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 TRP* 4.1 3.3 - - + -
589A THR* 2.9 23.8 + - + +
590A TRP 3.8 3.8 - - - +
592A GLY* 1.3 75.7 - - - +
594A GLU* 1.3 56.4 + - - +
596A PHE* 3.5 2.7 + - + +
597A ALA* 2.9 30.2 + - - +
612A VAL* 4.3 13.2 - - + -
615A ALA* 3.8 24.9 - - + -
616A CYS* 4.3 11.7 - - - -
619A LEU* 3.8 25.4 - - + -
658A GLY* 3.6 36.3 - - - +
659A LEU 4.2 0.4 - - - +
661A ALA* 4.8 1.3 - - - -
662A VAL* 3.8 28.1 - - + +
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Residues in contact with GLU 594 (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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535A SER* 4.0 1.1 - - - +
539A GLN* 3.5 34.1 - - - +
590A TRP* 2.9 51.3 + - + +
591A PHE* 3.7 5.4 - - + +
592A GLY 3.3 0.4 - - - -
593A LEU* 1.3 76.1 - - - +
595A ALA* 1.3 57.9 + - - +
597A ALA* 3.7 5.0 - - - +
598A CYS* 3.0 30.3 + - - +
661A ALA* 3.5 19.2 - - + +
718A ARG* 2.7 35.7 + - - -
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Residues in contact with ALA 595 (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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535A SER* 3.7 19.2 + - - +
538A MET* 4.1 11.7 - - + -
564A LEU* 4.2 3.4 - - + -
567A CYS* 3.9 23.1 - - + -
591A PHE 3.1 13.5 + - - +
592A GLY 3.6 8.5 - - - +
593A LEU 3.3 0.2 - - - -
594A GLU* 1.3 75.1 - - - +
596A PHE* 1.3 64.9 + - - +
598A CYS* 3.5 10.5 - - - -
599A MET* 3.3 29.5 + - - +
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Residues in contact with PHE 596 (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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564A LEU* 3.9 23.8 - - + -
567A CYS* 4.5 4.3 - - + -
568A ARG* 4.0 39.7 - - + -
577A TRP* 3.9 28.3 - + - -
592A GLY 3.2 22.7 + - - +
593A LEU* 3.9 5.4 - - - +
595A ALA* 1.3 78.7 - - - +
597A ALA* 1.3 59.5 + - - +
599A MET* 3.2 9.7 + - - +
600A GLY 3.3 0.2 + - - -
601A GLN* 2.9 47.8 + - + +
609A CYS* 4.1 3.4 - - - -
611A GLU* 3.7 33.7 - - + -
612A VAL* 3.9 25.8 - - + -
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Residues in contact with ALA 597 (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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593A LEU 2.9 19.3 + - - +
594A GLU* 3.7 6.5 - - - +
596A PHE* 1.3 76.1 - - - +
598A CYS* 1.3 57.6 + - - +
599A MET 3.1 0.2 - - - -
600A GLY* 3.0 19.6 + - - -
601A GLN 3.8 9.8 + - - -
602A THR* 4.3 8.1 - - + +
661A ALA* 3.4 35.9 - - + +
662A VAL* 4.3 2.5 - - + -
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Residues in contact with CYS 598 (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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538A MET* 4.3 10.5 - - - -
539A GLN* 4.1 35.4 - - + -
542A LYS* 3.1 40.0 + - + +
594A GLU 3.0 16.4 + - - +
595A ALA* 3.5 19.5 + - - -
596A PHE 3.4 0.2 - - - -
597A ALA* 1.3 75.9 - - - +
599A MET* 1.3 66.7 + - - +
600A GLY 3.3 1.2 + - - -
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Residues in contact with MET 599 (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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538A MET* 3.5 18.8 - - + -
542A LYS* 4.6 12.3 - - - +
560A LEU* 3.6 49.6 - - + +
561A THR* 4.1 10.5 - - - +
564A LEU* 4.0 27.7 - - + +
595A ALA 3.3 18.1 + - - +
596A PHE 3.2 4.6 + - - +
597A ALA 3.1 1.0 - - - -
598A CYS* 1.3 86.8 - - - +
600A GLY* 1.3 58.3 + - - +
601A GLN* 3.4 11.3 + - + +
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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