Contacts of the helix formed by residues 578 - 588 (chain A) in PDB entry 3EPZ
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 THR 578 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A LEU* 4.2 22.3 - - + +
519A ASN 4.3 0.7 - - - +
520A SER* 3.2 35.4 + - - +
522A SER 3.7 16.6 - - - +
574A PRO 4.2 2.2 + - - -
575A ILE* 2.5 36.8 + - - +
577A LEU* 1.3 77.9 - - - +
579A PRO* 1.3 79.4 - - + +
580A CYS 4.4 2.0 - - - +
581A MSE 3.1 14.0 + - - +
582A ARG 3.4 6.8 + - - -
703A GOL 4.0 1.0 + - - -
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Residues in contact with PRO 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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520A SER 4.2 7.0 - - - +
521A ASP* 3.9 15.0 - - + +
522A SER 3.4 15.9 - - - +
523A THR* 5.0 8.5 - - + -
577A LEU 4.1 4.3 - - - +
578A THR* 1.3 89.6 - - + +
580A CYS* 1.3 56.1 + - - +
582A ARG* 3.0 29.5 + - + +
583A ASP* 3.5 9.4 - - - +
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Residues in contact with CYS 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A LEU* 3.6 35.7 - - - -
522A SER 3.3 7.3 + - - +
523A THR 3.2 9.6 - - - -
524A TYR* 3.2 38.2 - - - +
527A LEU* 3.8 23.7 - - + +
578A THR* 3.2 2.3 - - - -
579A PRO* 1.3 79.0 - - - +
581A MSE 1.3 60.2 + - - +
583A ASP* 3.3 10.9 + - - +
584A LEU* 3.1 24.7 + - - +
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Residues in contact with MSE 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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512A VAL* 4.4 2.5 - - - -
516A LEU* 3.7 26.0 - - + -
527A LEU* 5.6 0.2 - - - -
558A VAL* 3.8 32.8 - - + -
561A VAL* 3.8 35.2 - - + -
575A ILE 3.2 22.9 - - - +
576A PHE* 3.3 30.5 - - + +
578A THR* 3.1 7.9 + - - +
580A CYS* 1.3 78.2 - - - +
582A ARG* 1.3 59.8 + - - +
584A LEU* 3.8 18.7 - - + +
585A ILE* 2.9 38.7 + - + +
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Residues in contact with ARG 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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578A THR 3.4 0.8 + - - -
579A PRO* 3.0 16.4 + - + +
581A MSE 1.3 77.1 - - - +
583A ASP* 1.3 66.6 + - - +
585A ILE* 3.7 3.3 + - - +
586A LYS* 3.3 21.5 + - - +
703A GOL 3.1 38.7 + - - +
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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
----------------------------------------------------------
524A TYR* 3.7 31.5 + - + +
579A PRO 3.5 12.8 - - - +
580A CYS* 3.4 9.6 - - - +
581A MSE 3.2 0.2 - - - -
582A ARG* 1.3 78.4 - - - +
584A LEU* 1.3 59.1 + - - +
586A LYS* 3.2 7.5 + - - +
587A LEU* 2.9 35.9 + - + +
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Residues in contact with LEU 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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512A VAL* 5.2 0.7 - - + -
524A TYR* 4.8 4.9 - - + -
527A LEU* 4.5 8.7 - - + -
550A LEU* 3.9 34.1 - - + -
551A LEU* 4.5 11.9 - - + -
554A ALA* 3.8 22.4 - - + +
557A VAL* 3.9 28.3 - - + -
558A VAL* 3.9 13.0 - - + -
580A CYS 3.1 15.6 + - - +
581A MSE 3.2 20.6 + - - +
583A ASP* 1.3 72.9 - - - +
585A ILE* 1.3 56.4 + - - +
587A LEU* 3.2 7.9 + - + +
588A ALA* 2.8 35.0 + - - +
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Residues in contact with ILE 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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558A VAL* 4.0 23.3 - - + +
576A PHE* 3.4 44.6 - - + +
581A MSE 2.9 23.5 + - + +
582A ARG 3.8 4.3 - - - +
584A LEU* 1.3 73.9 - - - +
586A LYS* 1.3 64.8 + - - +
588A ALA* 3.3 15.8 + - - +
589A GLY* 3.7 4.0 + - - -
703A GOL 3.6 28.0 - - - +
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Residues in contact with LYS 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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582A ARG 3.3 11.4 + - - +
583A ASP* 3.2 10.2 + - - +
584A LEU 3.2 0.6 - - - -
585A ILE* 1.3 78.9 - - - +
587A LEU* 1.3 63.7 + - - +
589A GLY* 3.1 15.8 + - - -
590A VAL* 4.1 8.8 + - + +
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Residues in contact with LEU 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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524A TYR* 3.8 26.2 - - + +
551A LEU* 3.7 25.6 - - + -
554A ALA* 4.5 1.6 - - + -
583A ASP* 2.9 22.5 + - + +
584A LEU* 3.2 11.0 + - + +
586A LYS* 1.3 76.1 - - + +
588A ALA* 1.3 62.3 + - - +
589A GLY 3.1 1.2 + - - -
590A VAL* 3.3 10.7 + - + +
595A ARG* 3.1 45.9 + - + +
598A GLN* 3.9 42.6 - - + +
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Residues in contact with ALA 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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554A ALA* 3.9 19.9 - - + +
555A GLN* 3.4 42.9 + - + +
558A VAL* 4.4 7.6 - - + -
584A LEU 2.8 13.6 + - - +
585A ILE* 3.4 16.8 - - - +
586A LYS 3.2 0.4 - - - -
587A LEU* 1.3 76.5 - - - +
589A GLY* 1.3 55.2 + - - +
590A VAL 3.4 1.6 - - - -
595A ARG* 3.5 9.5 + - - +
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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