Contacts of the helix formed by residues 563 - 577 (chain A) in PDB entry 1HS6
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 ARG 563 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A PRO 3.9 0.8 + - - +
265A PHE 3.5 14.8 + - - +
266A PRO 3.7 1.1 - - - +
267A TYR* 3.9 17.5 - - - +
268A GLY* 3.4 26.3 - - - +
279A THR* 3.6 15.3 - - - +
281A THR* 3.0 26.1 + - - +
282A LEU* 3.8 10.1 - - - +
289A LEU* 5.2 1.4 - - - +
292A VAL* 4.3 16.8 - - - +
532A SER* 4.3 3.0 + - - -
533A GLU* 3.5 15.8 + - - -
561A GLN* 2.8 16.5 - - - +
562A GLY* 1.3 72.8 - - - +
564A MET* 1.3 68.7 + - - +
565A LYS* 3.1 29.5 - - + +
566A PHE* 2.8 43.7 + - + +
567A THR* 2.9 10.9 + - - -
901A BES 4.4 7.7 + - - +
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Residues in contact with MET 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PRO* 2.9 26.9 + - + +
267A TYR* 3.4 42.2 - - + +
375A ASP* 5.7 0.2 - - - +
378A TYR* 5.6 5.8 - - + -
562A GLY 3.0 6.0 + - - +
563A ARG* 1.3 71.5 - - - +
565A LYS* 1.3 62.6 + - - +
567A THR* 4.3 5.6 - - - +
568A ARG* 3.0 42.0 + - - +
569A PRO* 3.4 1.0 - - - +
598A VAL* 4.3 10.8 - - + -
599A THR* 3.5 36.3 - - + +
602A LEU* 3.6 28.3 - - + -
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Residues in contact with LYS 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PRO 4.7 0.6 + - - -
348A GLU* 5.9 1.3 - - - -
533A GLU* 2.8 35.6 + - - +
536A PHE* 3.4 11.4 - - + -
537A ARG* 4.3 14.0 - - - +
563A ARG* 3.9 28.9 - - + +
564A MET* 1.3 77.2 - - - +
566A PHE* 1.3 75.7 + - + +
569A PRO* 3.2 21.9 - - - +
901A BES 4.7 13.6 + - - +
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Residues in contact with PHE 566 (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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281A THR* 3.6 3.8 - - - -
532A SER* 3.5 31.0 - - - -
533A GLU* 3.6 18.4 - - - -
536A PHE* 3.4 44.4 - + + -
557A MET* 3.9 14.8 - - + -
561A GLN* 3.7 28.7 - - - +
563A ARG* 2.8 43.0 + - - +
565A LYS* 1.3 101.1 - - + +
567A THR* 1.3 65.8 + - - +
568A ARG 3.4 0.7 - - - -
569A PRO* 3.5 1.4 - - - +
570A LEU* 3.1 31.8 + - + +
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Residues in contact with THR 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A ALA* 3.0 29.8 + - - +
561A GLN* 3.0 20.5 + - - +
562A GLY* 3.4 11.7 - - - -
563A ARG 2.9 11.5 + - - -
564A MET* 4.5 2.5 - - - -
566A PHE* 1.3 78.5 - - - +
568A ARG* 1.3 63.7 + - - +
570A LEU* 3.9 3.6 - - - +
571A PHE* 3.0 42.6 + - + -
595A MET* 6.0 2.0 - - - -
599A THR* 4.4 10.1 - - + -
603A VAL* 4.1 13.0 - - + -
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Residues in contact with ARG 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ASP 4.3 6.9 + - - -
376A VAL* 5.5 4.4 + - - +
378A TYR* 5.2 11.7 + - - -
564A MET* 3.0 33.5 + - + +
567A THR* 1.3 77.5 - - + +
569A PRO* 1.3 65.9 - - + +
571A PHE* 3.4 2.6 + - - +
572A LYS* 2.8 45.5 + - - +
599A THR* 5.3 0.2 - - + -
602A LEU* 3.7 45.5 + - + +
603A VAL* 4.0 19.1 - - + -
605A LYS* 6.1 0.2 - - - +
606A ASP* 2.8 42.7 + - - +
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Residues in contact with PRO 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A PHE* 3.8 9.6 - - + -
540A ARG* 3.5 33.2 - - - +
564A MET 3.4 1.8 - - - +
565A LYS* 3.2 27.8 - - - +
566A PHE 3.5 5.2 - - - +
568A ARG* 1.3 96.9 - - + +
570A LEU* 1.3 58.8 + - - +
572A LYS* 4.1 13.9 - - + +
573A ASP* 2.8 36.2 + - - +
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Residues in contact with LEU 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A PHE* 4.0 9.9 - - + +
539A LEU* 4.3 20.9 - - + -
540A ARG* 4.1 22.9 - - + +
543A ILE* 5.8 1.1 - - + -
554A ALA* 4.1 15.3 - - + +
557A MET* 3.6 42.0 - - + -
558A ALA* 3.9 20.0 - - + +
566A PHE* 3.1 29.2 + - + +
567A THR 3.9 2.9 - - - +
569A PRO* 1.3 77.6 - - - +
571A PHE* 1.3 64.9 + - - +
573A ASP* 3.1 4.5 + - + +
574A LEU* 2.9 31.7 + - + +
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Residues in contact with PHE 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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555A LEU* 5.0 4.9 - - + -
558A ALA* 4.0 17.3 - - + -
559A THR* 3.8 22.7 - - + -
567A THR* 3.0 45.8 + - + +
568A ARG* 3.7 4.0 - - - +
570A LEU* 1.3 77.7 - - - +
572A LYS* 1.3 64.8 + - - +
574A LEU* 3.8 7.9 - - + +
575A ALA* 3.0 24.4 + - - +
584A ALA* 3.5 29.7 - - + +
587A THR* 4.5 5.4 - - + -
588A TYR* 4.0 21.8 - - + -
595A MET* 4.7 9.6 - - + -
603A VAL* 3.9 22.4 - - + -
606A ASP* 6.0 0.7 - - + -
607A LEU* 3.8 22.4 - - + +
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Residues in contact with LYS 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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540A ARG* 6.0 0.7 - - - +
568A ARG* 2.8 39.4 + - - +
569A PRO* 3.8 13.0 - - + +
570A LEU 3.2 0.2 - - - -
571A PHE* 1.3 81.1 - - - +
573A ASP* 1.3 66.5 + - - +
575A ALA* 3.2 4.1 + - + +
576A ALA* 3.0 22.5 + - - +
606A ASP* 2.9 57.3 + - + +
607A LEU* 4.5 4.0 - - + -
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Residues in contact with ASP 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A ARG* 2.9 57.2 + - - +
543A ILE* 3.6 24.4 - - + +
544A GLN* 3.0 23.2 - - + +
569A PRO 2.8 20.2 + - - +
570A LEU* 3.7 5.4 - - + +
572A LYS* 1.3 80.7 - - - +
574A LEU* 1.3 64.3 + - - +
576A ALA* 3.0 16.0 + - - +
577A PHE* 3.1 10.0 + - - +
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Residues in contact with LEU 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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543A ILE* 3.7 22.0 - - + -
551A ILE* 4.0 12.1 - - + +
554A ALA* 3.7 35.4 - - + +
555A LEU* 3.8 27.4 - - + +
558A ALA* 5.0 2.9 - - + -
570A LEU* 2.9 27.8 + - + +
571A PHE* 3.8 8.3 - - + +
573A ASP* 1.3 78.9 - - - +
575A ALA* 1.3 62.4 + - - +
577A PHE 3.2 7.3 - - - +
580A SER* 2.7 38.2 + - - +
581A HIS 3.3 5.5 + - - -
584A ALA* 3.9 13.5 - - + -
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Residues in contact with ALA 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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571A PHE 3.0 17.3 + - - +
572A LYS* 3.7 4.7 - - - +
573A ASP 3.1 0.2 - - - -
574A LEU* 1.3 79.1 - - - +
576A ALA* 1.3 60.2 + - - +
577A PHE 3.5 0.3 + - - -
578A ASP* 5.5 0.2 - - - -
581A HIS* 2.9 43.9 - - + +
584A ALA* 4.1 6.7 - - + +
585A VAL* 5.3 1.6 - - + -
607A LEU* 3.8 23.8 - - + -
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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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546A LYS* 4.2 10.1 + - - -
572A LYS 3.0 15.8 + - - +
573A ASP* 3.0 7.8 + - - +
575A ALA* 1.3 77.5 - - - +
577A PHE* 1.3 59.7 + - - +
578A ASP 3.5 3.7 + - - -
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Residues in contact with PHE 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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543A ILE* 4.0 22.4 - - + +
546A LYS* 3.4 60.3 - - + +
547A TRP 4.0 2.9 - - - -
548A GLU* 3.8 14.1 - - + -
551A ILE* 3.6 29.8 - - + -
573A ASP 3.1 12.8 + - - +
574A LEU 3.2 0.7 + - - +
575A ALA 3.2 1.3 - - - -
576A ALA* 1.3 78.0 - - - +
578A ASP* 1.3 75.1 + - - +
579A LYS* 3.1 26.9 - - + -
580A SER* 2.9 23.6 + - - +
581A HIS* 2.9 23.0 + - - +
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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