Contacts of the helix formed by residues 549 - 561 (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 ASP 549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A LYS* 4.5 5.2 + - - -
547A TRP* 2.7 40.2 + - + +
548A GLU* 1.3 78.2 - - - +
550A ALA* 1.3 61.4 + - - +
551A ILE 3.2 0.2 - - - -
552A PRO* 3.3 18.6 - - - +
553A LEU* 4.0 9.3 - - - +
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Residues in contact with ALA 550 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A LEU* 4.8 9.3 - - + +
542A CYS* 3.5 32.8 - - + -
543A ILE* 3.9 9.0 - - + -
547A TRP* 3.1 19.0 + - + +
548A GLU 3.0 1.0 - - - -
549A ASP* 1.3 80.8 - - - +
551A ILE* 1.3 54.0 - - - +
552A PRO 3.4 0.7 - - - -
553A LEU* 3.1 13.8 + - + +
554A ALA* 2.8 34.8 + - - +
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Residues in contact with ILE 551 (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* 3.8 9.8 - - + +
548A GLU* 3.3 20.4 - - + +
550A ALA* 1.3 77.7 - - - +
552A PRO* 1.3 67.9 - - + +
554A ALA* 3.3 2.1 + - - +
555A LEU* 2.8 46.5 + - + +
574A LEU* 4.0 2.0 - - + +
577A PHE* 3.6 32.3 - - + -
579A LYS* 4.1 9.9 - - + +
580A SER* 3.7 38.1 - - - +
583A GLN* 3.9 11.7 - - - +
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Residues in contact with PRO 552 (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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548A GLU 3.8 3.8 - - - +
549A ASP* 3.3 18.4 - - - +
551A ILE* 1.3 100.6 - - + +
553A LEU* 1.3 66.9 + - + +
555A LEU* 3.8 9.6 - - + +
556A LYS* 3.0 26.6 + - - +
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Residues in contact with LEU 553 (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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527A ASN* 3.6 33.9 - - - +
535A ARG* 4.0 23.1 + - - +
539A LEU* 3.6 27.4 - - + +
549A ASP 4.0 11.0 - - - +
550A ALA* 3.1 17.0 + - + +
552A PRO* 1.3 84.3 - - + +
554A ALA* 1.3 62.4 + - - +
556A LYS* 3.3 10.3 + - + +
557A MET* 3.0 19.9 + - - +
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Residues in contact with ALA 554 (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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539A LEU* 3.9 14.1 - - + +
543A ILE* 3.9 14.6 - - + -
550A ALA 2.8 15.1 + - - +
553A LEU* 1.3 80.2 - - - +
555A LEU* 1.3 61.8 + - - +
557A MET* 3.4 1.7 + - - +
558A ALA* 3.0 25.5 + - - +
570A LEU* 4.1 16.1 - - + +
574A LEU* 3.7 29.9 - - + +
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Residues in contact with LEU 555 (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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551A ILE* 2.8 29.0 + - + +
552A PRO* 3.8 9.0 - - + +
554A ALA* 1.3 79.3 - - - +
556A LYS* 1.3 59.4 + - - +
558A ALA* 3.5 2.1 + - - +
559A THR* 2.9 32.6 + - - +
571A PHE* 5.0 4.5 - - + -
574A LEU* 3.8 21.7 - - + +
580A SER* 6.2 0.2 - - - -
583A GLN* 3.5 39.5 - - + +
584A ALA* 4.1 14.8 - - - +
587A THR* 3.7 33.0 - - + +
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Residues in contact with LYS 556 (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 ARG* 6.0 4.0 - - - +
552A PRO 3.0 18.7 + - - +
553A LEU* 3.6 11.2 - - + +
554A ALA 3.2 0.2 - - - -
555A LEU* 1.3 74.7 - - - +
557A MET* 1.3 57.9 + - - +
559A THR* 4.0 4.3 - - - -
560A GLU* 2.7 82.6 + - + +
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Residues in contact with MET 557 (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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532A SER* 3.6 35.0 - - - +
535A ARG* 3.8 31.9 - - + +
536A PHE* 4.0 13.2 - - + +
539A LEU* 4.2 7.2 - - + -
553A LEU 3.0 16.2 + - - +
554A ALA 4.0 0.2 - - - +
556A LYS* 1.3 78.5 - - - +
558A ALA* 1.3 62.4 + - - +
559A THR 3.4 0.3 + - - -
560A GLU* 4.8 3.8 - - - -
561A GLN* 2.8 40.2 + - + +
566A PHE* 3.9 25.8 - - + -
570A LEU* 3.6 22.2 - - + -
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Residues in contact with ALA 558 (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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554A ALA 3.0 19.1 + - - +
555A LEU* 3.8 7.6 - - - +
557A MET* 1.3 79.5 - - - +
559A THR* 1.3 59.3 + - + +
561A GLN* 2.8 17.4 - - - +
567A THR* 3.0 20.1 + - - +
570A LEU* 3.9 24.7 - - + +
571A PHE* 4.0 26.0 - - + +
574A LEU* 5.0 1.6 - - + -
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Residues in contact with THR 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* 2.9 20.0 + - - +
556A LYS* 3.4 5.0 + - - -
558A ALA* 1.3 77.9 - - + +
560A GLU* 1.3 72.4 + - - +
561A GLN* 3.1 5.5 + - - +
571A PHE* 3.8 17.7 - - + -
587A THR* 3.6 29.3 - - + +
591A HIS* 3.8 33.7 + - + +
595A MET* 5.5 1.3 - - + -
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Residues in contact with GLU 560 (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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263A PRO* 3.6 17.0 - - - +
556A LYS* 2.7 73.5 + - + +
557A MET* 4.6 3.9 - - - +
559A THR* 1.3 78.5 - - - +
561A GLN* 1.3 59.4 + - + +
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Residues in contact with GLN 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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263A PRO* 3.8 17.9 - - + +
264A SER* 4.9 0.7 - - - -
281A THR* 3.9 21.8 - - + +
557A MET* 2.8 33.0 - - + +
558A ALA* 2.8 22.5 - - - +
559A THR 3.7 4.0 - - - +
560A GLU* 1.3 78.9 - - + +
562A GLY* 1.3 58.2 + - - +
563A ARG* 2.8 40.8 + - - +
566A PHE* 3.7 26.5 - - + +
567A THR* 3.0 18.4 + - - -
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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