Contacts of the helix formed by residues 580 - 589 (chain A) in PDB entry 6EJ9
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 LYS 580 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578A ASP 4.0 8.7 - - - +
579A PHE* 1.3 79.8 - - - +
581A PRO* 1.3 75.5 - - + +
582A GLN* 3.2 26.7 - - - +
583A ASP* 2.9 27.0 + - - +
604A VAL* 4.0 28.2 - - - +
605A ASN* 3.9 20.4 - - + +
608A ILE* 3.8 12.3 - - - +
750A GLU* 4.5 16.1 + - - -
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Residues in contact with PRO 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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580A LYS* 1.3 89.6 - - + +
582A GLN* 1.3 61.0 + - - +
583A ASP 3.0 5.2 + - - -
584A PHE* 3.2 19.8 + - - +
605A ASN* 3.4 29.8 - - - +
607A GLU* 3.6 28.9 - - + +
608A ILE* 3.9 6.0 - - + +
611A GLN* 3.4 24.7 + - - +
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Residues in contact with GLN 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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580A LYS* 3.6 26.0 - - - +
581A PRO* 1.3 80.7 - - - +
583A ASP* 1.3 70.7 + - - +
584A PHE 3.4 0.4 - - - -
585A HIS* 3.3 24.4 + - - -
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Residues in contact with ASP 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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554A ASN* 4.3 4.2 + - - -
578A ASP 4.7 0.3 - - - +
579A PHE* 3.7 29.8 - - + -
580A LYS* 2.9 35.7 + - - +
582A GLN* 1.3 89.6 + - - +
584A PHE* 1.3 64.0 + - - +
585A HIS* 3.1 4.9 - - - -
586A ARG* 2.9 48.0 + - - +
587A PHE* 4.1 7.1 + - + -
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Residues in contact with PHE 584 (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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580A LYS 4.2 1.2 + - - -
581A PRO 3.2 15.2 + - - +
582A GLN 3.4 1.0 - - - -
583A ASP* 1.3 76.5 - - - +
585A HIS* 1.3 62.8 + - - +
587A PHE* 3.1 36.4 + + + +
588A GLN* 3.8 29.9 + - + -
608A ILE* 3.9 14.6 - - + +
611A GLN* 3.7 48.2 - - + +
612A LEU* 4.2 6.3 - - + -
615A TYR* 3.7 37.5 - + + -
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Residues in contact with HIS 585 (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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582A GLN 3.3 27.5 + - - -
583A ASP* 3.1 1.7 + - - -
584A PHE* 1.3 79.9 - - - +
586A ARG* 1.3 84.7 + - + +
588A GLN* 3.3 29.6 + - - +
589A GLN* 4.1 4.2 + - - +
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Residues in contact with ARG 586 (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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552A ILE* 3.6 31.7 - - + +
553A THR 4.2 9.3 + - - -
554A ASN* 2.8 32.7 + - - +
555A TRP 5.3 1.6 + - - +
579A PHE* 4.0 8.9 - - + -
583A ASP* 2.9 40.5 + - - +
585A HIS* 1.3 98.4 - - + +
587A PHE* 1.3 67.8 + - + +
589A GLN* 3.4 23.8 - - - +
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Residues in contact with PHE 587 (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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429A ILE* 4.0 39.8 - - + +
430A ARG* 5.9 2.3 + - - +
552A ILE* 4.4 13.4 - - + +
579A PHE* 3.8 42.6 - + + -
583A ASP 4.4 6.3 - - - -
584A PHE* 3.1 31.7 + + + +
586A ARG* 1.3 79.4 - - + +
588A GLN* 1.3 62.4 + - + +
589A GLN* 3.4 5.1 + - - +
594A THR* 5.2 1.4 + - - -
597A ALA* 4.2 7.9 - - + -
600A PHE* 3.8 19.3 - + - -
608A ILE* 3.9 26.0 - - + -
612A LEU* 4.2 24.0 - - + -
615A TYR* 6.1 3.7 - - + -
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Residues in contact with GLN 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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430A ARG* 6.1 0.9 - - - -
584A PHE* 3.8 31.9 - - + +
585A HIS* 3.3 20.7 + - - +
586A ARG 3.2 1.4 - - - -
587A PHE* 1.3 79.5 - - + +
589A GLN* 1.3 64.7 + - - +
590A THR* 3.7 9.5 + - - +
615A TYR* 3.4 41.0 + - + +
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Residues in contact with GLN 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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430A ARG* 4.5 7.3 + - - -
552A ILE* 4.3 7.7 - - + +
585A HIS 4.1 3.7 + - - +
586A ARG* 3.4 20.3 + - - +
587A PHE 3.4 3.6 + - - +
588A GLN* 1.3 80.1 - - - +
590A THR* 1.3 61.7 + - - +
591A ALA* 2.9 34.4 + - + +
592A ARG* 3.2 21.7 + - - +
594A THR* 3.0 36.3 + - - +
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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