Contacts of the helix formed by residues 584 - 597 (chain A) in PDB entry 4MXP
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 584 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582A ALA 3.8 0.2 - - - -
583A THR* 1.3 82.8 - - - +
585A GLU* 1.3 65.0 + - - +
586A GLN* 4.0 11.6 - - - +
587A SER* 2.8 39.7 + - - -
588A LEU* 3.0 10.6 + - - +
636A ILE* 3.8 11.7 - - - +
640A GLU* 3.8 19.1 - - - +
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Residues in contact with GLU 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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584A ASP* 1.3 75.1 - - - +
586A GLN* 1.3 62.8 + - - +
588A LEU* 3.3 7.8 + - - +
589A LYS* 3.0 50.5 + - - +
633A ARG* 2.8 56.4 + - - +
636A ILE* 3.9 13.4 - - + +
637A LYS* 5.0 9.1 - - + +
640A GLU* 4.6 3.5 + - - +
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Residues in contact with GLN 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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584A ASP* 3.3 12.3 + - - +
585A GLU* 1.3 79.7 - - - +
587A SER* 1.3 62.1 + - - +
589A LYS* 3.4 23.3 + - - +
590A GLN* 3.1 40.4 + - - +
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Residues in contact with SER 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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581A GLU 5.3 0.9 - - - -
582A ALA* 4.4 3.4 - - - -
583A THR* 2.8 31.0 + - - -
584A ASP* 2.8 33.8 + - - -
586A GLN* 1.3 73.2 - - - +
588A LEU* 1.3 58.2 + - - +
590A GLN* 3.3 9.4 + - - +
591A ILE* 3.0 39.4 + - - +
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Residues in contact with LEU 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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579A LEU* 4.0 15.5 - - + -
582A ALA* 4.0 14.3 - - + +
584A ASP 3.0 13.1 + - - +
585A GLU* 3.5 10.1 - - - +
587A SER* 1.3 73.3 + - - +
589A LYS* 1.3 65.2 + - - +
591A ILE* 3.2 3.6 + - + -
592A VAL* 2.9 45.4 + - + +
629A VAL* 4.0 7.2 - - + +
632A THR* 3.9 19.5 - - + -
633A ARG* 3.6 59.2 - - + +
636A ILE* 4.2 7.9 - - + -
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Residues in contact with LYS 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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585A GLU* 3.0 50.3 + - - +
586A GLN* 3.5 27.8 + - - +
588A LEU* 1.3 76.4 - - - +
590A GLN* 1.3 61.6 + - - +
592A VAL* 3.9 5.5 - - - +
593A ALA* 3.1 25.0 + - - +
633A ARG* 4.1 9.9 - - - +
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Residues in contact with GLN 590 (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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586A GLN* 3.1 31.4 + - - +
587A SER* 3.6 12.9 - - - +
588A LEU 3.2 0.2 - - - -
589A LYS* 1.3 77.5 - - - +
591A ILE* 1.3 67.7 + - + +
593A ALA* 3.4 5.5 + - - +
594A GLU* 3.0 23.6 + - - +
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Residues in contact with ILE 591 (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 LYS* 3.7 48.0 - - + +
579A LEU* 4.1 12.1 - - + -
581A GLU* 4.1 9.6 - - + +
582A ALA* 3.7 33.2 - - + +
587A SER* 3.0 24.1 + - - +
588A LEU* 3.2 4.2 + - - +
590A GLN* 1.3 76.6 - - + +
592A VAL* 1.3 56.5 + - - +
594A GLU* 3.2 7.4 + - - +
595A LEU* 2.9 38.9 + - + +
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Residues in contact with VAL 592 (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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579A LEU* 4.0 6.1 - - + -
588A LEU* 2.9 36.1 + - + +
589A LYS* 3.9 5.4 - - - +
591A ILE* 1.3 75.3 - - - +
593A ALA* 1.3 59.0 + - - +
595A LEU* 3.3 5.1 + - - +
596A LYS* 2.9 49.2 + - + +
625A PHE* 4.2 12.1 - - + -
629A VAL* 3.8 32.5 - - + -
633A ARG* 5.6 1.8 - - - +
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Residues in contact with ALA 593 (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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589A LYS 3.1 17.8 + - - +
590A GLN* 3.8 6.3 - - - +
591A ILE 3.3 0.2 - - - -
592A VAL* 1.3 78.4 - - - +
594A GLU* 1.3 61.0 + - - +
596A LYS* 3.4 6.7 + - - +
597A SER* 3.2 22.9 + - - -
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Residues in contact with GLU 594 (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 LYS* 5.4 10.3 - - - -
590A GLN 3.0 13.3 + - - +
591A ILE* 3.5 11.4 - - - +
593A ALA* 1.3 77.0 - - - +
595A LEU* 1.3 64.1 + - + +
597A SER* 2.6 29.4 + - - -
598A LYS* 3.4 28.0 + - - +
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Residues in contact with LEU 595 (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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575A PHE* 3.8 42.5 - - + +
578A LYS* 3.9 21.5 - - + -
579A LEU* 4.0 9.2 - - + -
591A ILE* 2.9 37.3 + - + +
592A VAL 3.3 4.2 + - - +
594A GLU* 1.3 77.9 - - + +
596A LYS* 1.3 57.7 + - - +
598A LYS* 3.0 43.1 + - - +
601A TYR* 3.4 11.2 - - - +
625A PHE* 3.8 31.9 - - + -
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Residues in contact with LYS 596 (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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592A VAL* 2.9 37.7 + - + +
593A ALA* 3.9 6.1 - - - +
595A LEU* 1.3 75.6 - - - +
597A SER* 1.3 59.8 + - - +
598A LYS 3.2 2.3 + - - +
601A TYR* 3.7 57.0 + - + +
602A ARG* 5.2 4.3 + - - +
625A PHE* 4.0 12.8 - - + -
626A GLU* 5.3 5.9 + - - +
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Residues in contact with SER 597 (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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593A ALA 3.2 12.3 + - - -
594A GLU* 2.6 30.5 + - - -
595A LEU 3.1 0.2 - - - -
596A LYS* 1.3 75.8 - - - +
598A LYS* 1.3 59.9 + - - +
602A ARG* 3.0 27.1 + - - +
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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