Contacts of the helix formed by residues 580 - 586 (chain A) in PDB entry 4MS0
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 HIS 580 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568A ARG* 4.1 15.5 + - - -
574A TYR* 6.1 3.4 - + + -
575A LEU* 2.9 45.0 + - + +
578A PHE* 3.2 5.6 + - + -
579A ASP* 1.3 76.0 - - - +
581A PRO* 1.4 88.7 - - + +
582A LEU* 3.2 48.2 + - + +
583A ALA* 3.0 15.9 + - - +
584A ALA* 3.6 4.0 + - - +
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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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579A ASP 3.7 3.3 - - - +
580A HIS* 1.4 106.4 - - + +
582A LEU* 1.3 59.8 + - + +
584A ALA* 3.1 18.9 + - + +
585A LEU* 3.1 13.2 + - - +
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Residues in contact with LEU 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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568A ARG* 4.1 19.5 - - - +
575A LEU* 4.4 6.7 - - + -
580A HIS* 3.1 30.9 + - + +
581A PRO* 1.3 77.2 - - + +
583A ALA* 1.3 56.4 + - - +
585A LEU* 3.3 8.9 + - + +
586A TYR* 2.9 42.9 + - + +
590A THR* 3.3 19.3 - - + +
591A MET* 4.1 25.1 - - - -
594A HIS* 3.7 31.2 - - + +
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Residues in contact with ALA 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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575A LEU* 3.5 28.2 - - - +
576A GLN* 4.0 18.1 - - + +
579A ASP* 4.6 5.2 - - + +
580A HIS* 3.0 13.5 + - - +
582A LEU* 1.3 76.6 - - - +
584A ALA* 1.3 60.7 + - - +
586A TYR 3.1 23.2 - - - +
587A SER* 3.6 8.7 - - - -
590A THR* 3.6 7.7 - - + +
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Residues in contact with ALA 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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579A ASP* 6.3 0.4 - - + +
580A HIS 3.6 2.9 + - - +
581A PRO* 3.1 15.0 + - + +
583A ALA* 1.3 79.1 - - - +
585A LEU* 1.3 65.2 + - - +
586A TYR 3.5 0.3 + - - -
587A SER* 4.7 3.1 + - - -
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Residues in contact with LEU 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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581A PRO 3.1 12.0 + - - +
582A LEU* 3.7 12.6 - - + +
584A ALA* 1.3 78.1 - - - +
586A TYR* 1.3 103.1 + - + +
587A SER 4.0 1.1 + - - -
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Residues in contact with TYR 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 LEU* 2.9 32.6 + - + +
583A ALA* 3.1 8.8 - - - +
585A LEU* 1.3 114.0 - - + +
587A SER* 1.3 60.2 + - - +
588A THR 3.4 2.0 - - - -
590A THR* 3.0 47.5 + - + -
593A GLN* 3.5 43.1 - - + +
594A HIS* 3.8 21.3 + - + -
597A SER* 3.7 24.1 + - - -
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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