Contacts of the helix formed by residues 587 - 602 (chain A) in PDB entry 1WKB
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 587 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548A LEU* 4.9 8.1 - - + -
553A LYS* 5.8 7.0 - - + +
581A GLU* 3.8 12.8 - - - +
585A GLY 3.7 7.6 - - - +
586A ILE* 1.3 91.5 - - + +
588A ALA* 1.3 65.3 + - - +
589A GLU* 3.1 21.9 + - - +
590A ILE* 3.1 22.4 + - + +
591A ILE* 3.0 18.2 + - - +
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Residues in contact with ALA 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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574A GLU* 6.0 0.7 - - + -
577A GLU* 3.7 39.7 - - + +
578A LYS* 4.1 15.7 - - + +
581A GLU* 2.8 23.7 + - - +
586A ILE 3.3 1.7 + - - -
587A PRO* 1.3 71.7 - - - +
589A GLU* 1.3 62.3 + - + +
591A ILE* 3.4 6.0 + - - +
592A HIS* 2.9 28.2 + - - +
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Residues in contact with GLU 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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581A GLU* 3.9 4.0 - - - +
587A PRO* 3.5 17.8 - - + +
588A ALA* 1.3 88.6 + - + +
590A ILE* 1.3 56.0 + - + +
592A HIS* 3.0 10.1 + - - +
593A GLU* 2.7 47.2 + - - +
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Residues in contact with ILE 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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544A HIS* 4.2 16.6 - - + +
548A LEU* 4.0 24.7 - - + -
586A ILE* 3.9 17.5 - - + -
587A PRO* 3.1 28.7 + - + +
589A GLU* 1.3 78.4 - - + +
591A ILE* 1.3 57.7 + - - +
593A GLU* 3.2 22.4 + - - +
594A MET* 2.9 38.7 + - + +
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Residues in contact with ILE 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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563A PHE* 3.9 15.5 - - + -
566A TYR* 4.0 28.5 - - + -
567A ILE* 3.8 9.8 - - + +
577A GLU* 3.9 11.7 - - + +
580A LEU* 3.6 28.9 - - + -
581A GLU 3.8 7.4 - - - +
584A THR* 3.9 7.6 - - - +
586A ILE* 3.5 31.2 - - + +
587A PRO 3.0 12.5 + - - +
588A ALA* 3.5 7.6 - - - +
589A GLU 3.2 0.2 - - - -
590A ILE* 1.3 76.2 - - - +
592A HIS* 1.3 62.1 + - - +
594A MET* 3.5 10.5 + - - +
595A LYS* 3.2 21.5 + - - +
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Residues in contact with HIS 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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572A PHE* 3.4 33.6 - + + -
577A GLU* 2.6 34.6 + - - +
588A ALA 2.9 14.5 + - - +
589A GLU* 3.1 14.8 - - - +
591A ILE* 1.3 76.3 - - - +
593A GLU* 1.3 63.5 + - + +
595A LYS* 3.1 7.0 + - - +
596A GLU* 2.9 50.9 + - - +
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Residues in contact with GLU 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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544A HIS* 3.0 31.9 + - + +
589A GLU* 2.7 28.5 + - + +
590A ILE* 3.2 19.4 + - - +
592A HIS* 1.3 69.7 - - + +
594A MET* 1.3 68.1 + - - +
596A GLU* 2.9 31.8 + - - +
597A GLU* 2.9 17.2 + - + +
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Residues in contact with MET 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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541A ILE* 3.6 43.7 - - + +
544A HIS* 3.4 36.1 + - + -
545A ILE* 4.3 12.8 - - + -
548A LEU* 4.8 10.1 - - - -
563A PHE* 3.7 37.9 - - + -
567A ILE* 4.2 4.9 - - + -
586A ILE* 5.1 2.7 - - - -
590A ILE* 2.9 29.0 + - - +
591A ILE* 3.5 10.5 - - - +
593A GLU* 1.3 76.4 - - - +
595A LYS* 1.3 62.6 + - - +
597A GLU* 3.2 11.5 + - - +
598A PHE* 3.3 9.7 + - - +
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Residues in contact with LYS 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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566A TYR* 2.9 47.7 + - + +
567A ILE* 2.9 30.3 + - + +
570A GLU 2.6 30.5 + - - +
572A PHE* 3.6 38.1 - - + +
591A ILE 3.2 9.0 + - - +
592A HIS* 3.1 9.9 + - - +
593A GLU 3.1 0.6 - - - -
594A MET* 1.3 76.2 - - - +
596A GLU* 1.3 60.1 - - - +
598A PHE* 3.3 2.0 + - - +
599A GLU* 2.9 58.5 + - + +
630A ARG* 4.1 1.8 - - - +
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Residues in contact with GLU 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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27A ILE* 4.0 20.5 - - + +
572A PHE* 4.0 22.0 - - + -
592A HIS* 2.9 36.1 + - - +
593A GLU* 2.9 28.2 + - - +
595A LYS* 1.3 78.0 - - - +
597A GLU* 1.3 56.7 + - - +
599A GLU* 3.8 1.8 - - - +
600A TYR* 2.8 33.4 + - - +
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Residues in contact with GLU 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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25A PRO 5.3 0.9 - - - +
27A ILE* 3.4 25.9 + - - +
148A ARG* 2.8 26.5 + - - +
540A THR* 3.1 24.0 - - - +
543A ARG* 4.9 11.4 + - - -
544A HIS* 3.7 27.5 + - + +
593A GLU* 2.9 16.8 + - - +
594A MET 3.4 6.1 - - - +
596A GLU* 1.3 75.8 - - - +
598A PHE* 1.3 57.3 + - - +
600A TYR* 3.7 2.8 - - - +
601A TRP* 2.9 51.6 + - - +
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Residues in contact with PHE 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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537A ALA* 4.1 5.4 - - + -
540A THR* 3.5 21.2 + - - +
541A ILE* 4.7 0.2 - - + -
567A ILE* 3.7 18.6 - - + -
568A PHE* 3.4 52.5 - + + -
594A MET 3.3 9.0 + - - +
595A LYS 3.7 5.4 - - - +
596A GLU 3.3 0.2 - - - -
597A GLU* 1.3 78.5 - - - +
599A GLU* 1.3 69.1 + - - +
602A TYR* 3.0 67.6 + + + +
629A PHE* 3.8 9.9 - + - -
630A ARG* 4.4 0.7 - - - -
633A HIS* 3.4 38.1 - + - -
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Residues in contact with GLU 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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32A LYS* 3.0 27.6 + - - +
567A ILE 4.0 2.3 - - - +
570A GLU 4.2 0.5 - - - +
572A PHE* 3.5 30.2 - - + -
595A LYS* 2.9 40.3 + - + +
596A GLU* 3.9 3.1 - - - +
598A PHE* 1.3 79.6 - - + +
600A TYR* 1.3 58.4 + - - +
602A TYR 3.5 2.8 - - - +
630A ARG* 2.9 31.5 + - - -
632A GLU* 4.7 4.5 - - - +
633A HIS* 3.7 21.5 + - - -
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Residues in contact with TYR 600 (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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27A ILE* 3.4 44.9 - - + -
30A LYS 2.7 29.9 + - - -
31A PRO* 3.8 3.9 + - + -
32A LYS* 2.8 51.9 + - + +
35A LYS* 3.5 31.3 - - + +
73A ASN* 3.0 22.7 + - - +
596A GLU 2.8 18.7 + - - +
597A GLU 3.7 2.2 - - - +
599A GLU* 1.3 79.1 - - - +
601A TRP* 1.3 87.5 + + - +
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Residues in contact with TRP 601 (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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25A PRO* 3.6 29.1 + - + -
27A ILE* 3.5 10.0 - - + +
35A LYS* 2.8 36.5 + - + +
36A PHE 3.8 3.4 - - - -
37A TYR* 3.5 31.8 - - + +
73A ASN* 3.3 33.0 - - - -
74A VAL 3.8 7.6 - - - -
75A LEU* 3.5 36.3 - - + +
148A ARG* 3.6 15.2 - - - +
540A THR* 4.0 10.5 - - + -
597A GLU* 2.9 51.1 + - - +
600A TYR* 1.3 98.8 - + - +
602A TYR* 1.3 60.0 + - - +
603A PRO 3.1 2.6 - - - +
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Residues in contact with TYR 602 (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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32A LYS* 2.6 31.6 + - - -
35A LYS* 3.9 0.2 - - - -
37A TYR* 3.8 19.3 - + - -
534A ILE 4.1 0.9 + - - -
536A MET* 3.5 31.2 - - + +
537A ALA* 3.2 27.9 + - + +
540A THR* 4.2 3.1 - - + -
598A PHE* 3.0 49.8 + + + +
599A GLU 3.5 4.7 - - - +
601A TRP* 1.3 75.7 - - - +
603A PRO* 1.3 59.0 - - + +
604A LEU* 4.0 11.7 - - + -
625A HIS* 2.9 34.5 + + - -
629A PHE* 4.6 5.4 - + - -
633A HIS* 3.6 34.1 + - + +
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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