Contacts of the helix formed by residues 571 - 583 (chain A) in PDB entry 4K71
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 GLU 571 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554A PHE* 3.6 25.4 - - + -
557A LYS* 4.2 26.5 + - + +
558A CYS* 4.1 1.3 - - - -
567A CYS* 2.7 41.6 + - - +
570A GLU* 1.3 81.3 - - + +
572A GLY* 1.3 62.1 + - - +
573A LYS 3.5 0.7 - - - -
574A LYS* 3.6 24.9 + - - +
575A LEU* 3.3 18.5 + - - +
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Residues in contact with GLY 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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504A ALA 6.0 0.4 - - - -
507A PHE* 4.1 18.8 - - - -
554A PHE* 4.2 7.4 - - - -
568A PHE 3.3 17.7 + - - -
569A ALA 3.6 4.4 + - - -
570A GLU 3.2 3.4 - - - -
571A GLU* 1.3 75.3 - - - +
573A LYS* 1.3 64.9 + - - +
575A LEU* 3.7 2.3 + - - +
576A VAL* 3.2 30.3 + - - +
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Residues in contact with LYS 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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504A ALA* 4.3 23.8 - - + +
569A ALA 4.7 2.2 + - - +
570A GLU 4.2 8.1 + - - +
571A GLU 3.5 0.4 - - - -
572A GLY* 1.3 74.4 - - - +
574A LYS* 1.3 61.6 + - + +
576A VAL* 3.7 3.8 + - - +
577A ALA* 3.1 25.3 + - - +
20C SER* 3.1 23.5 + - - +
21C ASN* 3.3 23.2 + - - +
22C PHE* 3.8 17.8 - - + -
69C GLU* 3.0 40.8 + - - -
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Residues in contact with LYS 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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570A GLU 5.0 6.0 + - - +
571A GLU* 3.6 26.4 + - - +
572A GLY 3.3 0.6 - - - -
573A LYS* 1.3 81.7 - - + +
575A LEU* 1.3 53.8 - - - +
577A ALA* 3.1 8.2 + - + +
578A ALA* 2.6 39.0 + - - +
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Residues in contact with LEU 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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507A PHE* 3.8 24.0 - - + -
550A ASP* 3.5 42.6 - - + +
551A PHE* 3.7 18.8 - - + +
554A PHE* 3.4 38.8 - - + -
571A GLU 3.3 16.7 + - - +
572A GLY 3.8 2.9 - - - +
574A LYS* 1.3 75.9 - - - +
576A VAL* 1.3 51.8 + - + +
578A ALA* 3.6 5.6 - - - +
579A SER* 2.7 49.5 + - - +
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Residues in contact with VAL 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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502A PHE* 4.2 24.6 - - + -
503A ASN 4.3 3.1 - - - +
504A ALA* 3.8 30.3 - - + +
507A PHE* 3.7 40.6 - - + -
572A GLY 3.2 18.7 + - - +
573A LYS 3.7 4.7 - - - +
574A LYS 3.2 0.6 - - - -
575A LEU* 1.3 75.4 - - + +
577A ALA* 1.3 57.9 + - - +
579A SER* 3.8 5.1 - - - -
580A GLN* 3.0 31.5 + - - +
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Residues in contact with ALA 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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573A LYS 3.1 14.9 + - - +
574A LYS* 3.1 11.5 + - + +
576A VAL* 1.3 78.5 - - - +
578A ALA* 1.3 55.9 + - - +
580A GLN* 3.7 9.2 - - - +
581A ALA* 3.0 29.0 + - - +
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Residues in contact with ALA 578 (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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550A ASP* 3.8 23.5 - - + +
574A LYS 2.6 21.3 + - - +
575A LEU* 3.6 7.0 - - - +
577A ALA* 1.3 70.0 - - - +
579A SER* 1.3 59.8 + - - +
581A ALA* 3.2 7.4 + - - +
582A ALA* 2.8 29.6 + - - +
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Residues in contact with SER 579 (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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502A PHE* 4.2 16.2 - - - -
532A LEU* 4.3 14.7 - - - +
547A ALA* 4.4 11.9 + - - +
550A ASP* 4.4 3.8 - - - +
575A LEU* 2.7 42.4 + - - +
576A VAL* 3.8 5.2 - - - -
578A ALA* 1.3 71.6 - - - +
580A GLN* 1.3 61.7 + - - +
582A ALA* 3.1 17.3 + - - +
583A LEU* 3.1 18.0 + - - +
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Residues in contact with GLN 580 (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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501A GLU* 4.3 13.7 + - - -
502A PHE* 3.5 43.5 - - + +
576A VAL* 3.0 20.3 + - - +
577A ALA* 3.7 8.7 - - - +
578A ALA 3.3 0.2 - - - -
579A SER* 1.3 75.9 - - - +
581A ALA* 1.3 59.1 + - - +
583A LEU* 3.3 6.1 + - - -
585A LEU* 2.8 65.0 + - + +
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Residues in contact with ALA 581 (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 ALA 3.0 15.7 + - - +
578A ALA* 3.5 10.1 - - - +
580A GLN* 1.3 73.6 - - - +
582A ALA* 1.3 64.3 + - - +
584A GLY* 3.1 13.3 + - - -
585A LEU* 3.7 14.8 - - + +
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Residues in contact with ALA 582 (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 GLN* 3.2 40.8 + - - +
546A ALA* 3.9 13.0 - - + +
547A ALA* 3.8 19.5 - - + +
550A ASP* 4.3 3.1 - - - +
578A ALA 2.8 16.7 + - - +
579A SER 3.1 8.5 + - - +
581A ALA* 1.3 73.5 - - - +
583A LEU* 1.3 59.8 + - - +
584A GLY 3.3 3.3 + - - -
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Residues in contact with LEU 583 (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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502A PHE* 3.8 23.3 - - + -
532A LEU* 3.6 33.0 - - + +
536A LYS* 2.7 54.4 + - + +
539A ALA* 4.4 5.2 - - + -
543A GLN* 3.7 39.7 - - + +
544A LEU* 4.2 13.7 - - + -
547A ALA* 4.2 9.9 - - + -
579A SER 3.1 13.6 + - - +
580A GLN* 3.9 4.9 - - - +
581A ALA 3.2 0.6 - - - -
582A ALA* 1.3 75.2 - - - +
584A GLY* 1.3 54.4 + - - +
585A LEU* 3.2 5.6 + - - +
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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