Contacts of the helix formed by residues 558 - 573 (chain A) in PDB entry 4BSN
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 HIS 558 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514A LYS* 3.3 38.7 - - + +
554A PHE* 3.5 38.6 + + - +
555A LEU 2.8 19.2 - - - +
556A ARG 4.9 0.4 - - - -
557A ALA* 1.3 96.5 + - + +
559A TRP* 1.3 64.4 + - - +
560A LYS 5.1 0.2 - - - +
561A PHE* 3.7 22.5 - + + +
562A LEU* 3.3 11.3 + - - +
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Residues in contact with TRP 559 (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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555A LEU 4.7 1.1 - - - -
557A ALA 4.2 1.2 + - - -
558A HIS* 1.3 68.3 - - - +
560A LYS* 1.3 68.7 + - + +
561A PHE 3.1 1.6 - - - -
562A LEU* 2.9 25.9 + - + +
563A LYS* 2.8 36.6 + - + +
598A HIS* 3.4 38.5 - - + +
599A PHE* 4.7 4.5 - + - -
601A GLN 5.6 0.9 - - - -
603A GLN* 3.4 46.1 - - + +
604A VAL* 6.0 3.4 - - + -
605A GLY* 4.5 9.2 - - - -
606A GLU* 3.8 34.6 - - + +
608A MET 5.3 0.7 - - - -
609A PRO* 6.1 0.2 - - + -
610A PHE* 3.4 50.3 - + + -
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Residues in contact with LYS 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A HIS 3.7 0.2 - - - -
559A TRP* 1.3 87.0 - - + +
561A PHE* 1.3 58.3 + - - +
563A LYS* 3.5 13.0 - - + +
564A THR* 3.0 29.5 + - - -
605A GLY* 6.1 3.4 - - - -
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Residues in contact with PHE 561 (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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518A VAL* 3.7 29.6 - - + -
521A ILE* 3.5 42.0 - - + -
522A LYS* 5.3 1.1 - - + -
554A PHE* 3.6 33.0 - + + -
555A LEU* 4.6 5.4 - - + -
558A HIS* 3.7 26.8 - + + +
559A TRP 3.1 0.6 - - - -
560A LYS* 1.3 78.9 - - - +
562A LEU* 1.3 63.0 + - - +
564A THR* 3.3 7.9 + - - -
565A VAL* 3.1 35.7 + - + +
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Residues in contact with LEU 562 (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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555A LEU* 3.7 45.9 - - + +
558A HIS 3.3 11.3 + - - +
559A TRP* 2.9 23.8 + - + +
561A PHE* 1.3 75.7 - - - +
563A LYS* 1.3 59.7 + - - +
565A VAL* 3.3 6.4 + - + -
566A VAL* 2.9 53.9 + - + +
591A ILE* 4.0 10.5 - - + -
595A CYS* 4.3 13.7 - - + -
598A HIS* 4.2 24.0 - - + +
599A PHE* 4.4 9.4 - - + -
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Residues in contact with LYS 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A TRP* 2.8 28.2 + - + +
560A LYS* 3.5 15.9 - - + +
562A LEU* 1.3 77.5 - - - +
564A THR* 1.3 63.0 + - - +
566A VAL* 5.0 0.2 - - - -
567A ASN* 2.9 49.0 + - - +
606A GLU* 3.1 38.7 + - + +
610A PHE* 3.6 20.6 - - + -
613A GLU* 3.6 14.8 + - - -
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Residues in contact with THR 564 (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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525A LEU* 5.0 16.4 - - + -
560A LYS 3.0 13.4 + - - -
561A PHE* 3.3 9.5 + - - -
563A LYS* 1.3 79.4 - - - +
565A VAL* 1.3 57.7 + - + +
567A ASN* 3.8 7.8 - - - +
568A LYS* 3.1 32.0 + - + +
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Residues in contact with VAL 565 (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 ILE* 5.5 6.3 - - + -
544A ILE* 6.2 1.6 - - + -
545A MET* 5.9 0.4 - - - -
548A VAL* 3.6 40.8 - - + -
555A LEU* 4.5 11.9 - - + -
561A PHE* 3.1 32.4 + - + +
562A LEU* 3.6 9.6 - - + +
564A THR* 1.3 75.7 - - + +
566A VAL* 1.3 61.8 + - + +
568A LYS* 2.8 24.6 + - + +
569A LEU* 2.9 26.8 + - + +
591A ILE* 4.4 5.2 - - + -
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Residues in contact with VAL 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A LEU* 2.9 43.5 + - + +
563A LYS* 5.2 0.2 - - - -
565A VAL* 1.3 70.6 - - - +
567A ASN* 1.3 56.5 + - - +
569A LEU* 3.1 10.7 + - + +
570A PHE* 3.0 44.8 + - + -
588A PHE* 4.1 16.2 - - + -
591A ILE* 4.5 11.7 - - + -
599A PHE* 3.9 20.0 - - + -
610A PHE* 3.6 30.1 - - + -
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Residues in contact with ASN 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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563A LYS* 2.9 54.4 + - - +
564A THR* 3.8 7.8 - - - +
566A VAL* 1.3 76.1 - - - +
568A LYS* 1.3 57.0 + - - +
570A PHE* 3.5 13.6 + - - +
571A GLU* 3.0 27.7 + - - +
610A PHE* 3.2 18.2 - - - -
613A GLU* 5.5 0.7 - - - +
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Residues in contact with LYS 568 (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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525A LEU* 4.7 23.1 - - + +
528A CYS* 5.7 5.1 - - - -
544A ILE* 5.2 4.5 - - + -
545A MET* 4.2 5.4 - - + -
564A THR* 3.1 18.9 + - + +
565A VAL* 2.8 15.9 + - + +
567A ASN* 1.3 73.9 - - - +
569A LEU* 1.3 58.9 + - - +
571A GLU* 3.7 17.0 + - + +
572A PHE* 2.9 64.5 + - + +
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Residues in contact with LEU 569 (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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545A MET* 3.6 32.8 - - + -
548A VAL* 5.0 0.4 - - + -
565A VAL* 2.9 45.9 + - + +
566A VAL* 3.2 12.3 - - + +
568A LYS* 1.3 74.5 - - - +
570A PHE* 1.3 66.8 + - + +
572A PHE* 3.1 3.5 + - - +
573A MET* 3.0 34.0 + - + +
584A ALA* 3.8 11.8 - - + +
587A THR* 4.0 4.7 - - + -
588A PHE* 3.6 44.2 - - + +
591A ILE* 3.9 16.8 - - + -
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Residues in contact with PHE 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 VAL* 3.0 33.6 + - + +
567A ASN* 3.8 17.5 - - - +
568A LYS 3.4 0.2 - - - -
569A LEU* 1.3 76.9 - - + +
571A GLU* 1.3 61.0 + - - +
573A MET* 3.4 29.1 + - + +
574A HIS* 3.9 6.1 + - - +
588A PHE* 3.4 33.7 - + - -
610A PHE* 3.7 4.9 - + - -
614A ILE* 3.6 33.2 - - + -
621A ILE* 3.9 30.4 - - + +
633A PHE* 3.5 30.7 - + - -
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Residues in contact with GLU 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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567A ASN 3.0 18.0 + - - +
568A LYS* 3.7 20.6 + - + +
570A PHE* 1.3 77.3 - - - +
572A PHE* 1.3 88.8 + - - +
573A MET 3.2 0.7 - - - -
574A HIS* 3.3 24.2 + - + +
575A GLU* 4.3 1.4 + - - +
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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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528A CYS* 3.9 27.4 - - - -
537A LYS* 5.3 5.2 - - + -
541A ALA* 3.7 33.9 - - + -
544A ILE* 4.3 6.7 - - + -
545A MET* 3.4 28.5 - - + -
568A LYS* 2.9 38.4 + - + +
569A LEU 3.1 5.3 + - - +
571A GLU* 1.3 96.2 - - - +
573A MET* 1.3 55.9 + - - +
574A HIS 3.1 4.9 - - - -
575A GLU* 3.4 30.9 - - + +
580A VAL* 4.2 13.6 - - + +
581A GLN* 4.4 5.0 - - - -
584A ALA* 4.7 6.4 - - + +
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Residues in contact with MET 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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569A LEU* 3.0 30.1 + - + +
570A PHE* 3.5 39.5 - - + +
571A GLU 3.2 0.6 - - - -
572A PHE* 1.3 75.7 - - - +
574A HIS* 1.3 58.1 + - - +
575A GLU 3.2 4.4 + - - -
581A GLN* 3.8 16.3 - - - +
584A ALA* 3.9 24.9 - - + +
585A CYS* 4.0 13.9 - - - -
588A PHE* 4.8 4.5 - - + -
621A ILE* 4.4 10.4 - - + +
624A ASP* 4.1 6.9 - - - +
625A LEU* 3.5 53.1 - - + +
633A PHE* 4.0 15.3 - - + -
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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