Contacts of the helix formed by residues 536 - 543 (chain F) in PDB entry 4MNE
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 SER 536 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102E GLU* 4.5 3.8 + - - -
535F SER* 1.3 78.3 - - - +
537F LEU* 1.3 65.3 + - - +
538F TYR* 3.4 8.1 + - - +
539F HIS* 3.1 28.2 + - - +
540F HIS* 3.2 12.6 + - - -
579F SER 3.9 1.3 - - - -
580F ASN* 3.4 26.1 + - - -
582F ILE 3.4 5.8 - - - -
583F PHE* 3.6 18.8 - - - -
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Residues in contact with LEU 537 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535F SER 3.9 0.4 + - - -
536F SER* 1.3 72.7 - - - +
538F TYR* 1.3 62.1 + - - +
540F HIS* 3.5 11.2 + - + -
541F LEU* 3.1 43.8 + - + +
548F PHE* 4.7 1.8 - - + -
556F ILE* 4.1 28.5 - - + -
579F SER* 3.2 13.0 + - - +
582F ILE* 2.5 35.1 + - + +
584F LEU* 4.7 8.7 - - + +
645F VAL* 3.9 23.3 - - + -
648F GLU* 6.0 0.2 - - + -
649F LEU* 3.7 27.6 - - + -
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Residues in contact with TYR 538 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E GLU* 3.4 55.4 + - + +
103E ILE* 5.8 0.5 - - - +
221E ASN* 3.5 28.4 + - - -
536F SER* 3.1 8.7 - - - +
537F LEU* 1.3 77.0 - - - +
539F HIS* 1.3 65.6 - - - +
542F HIS* 3.0 52.1 + + + +
543F ILE* 3.9 10.4 - - + +
579F SER* 2.9 24.0 + - - -
580F ASN* 3.3 39.5 - - - +
619F TRP* 4.9 1.6 - + - -
654F LEU* 4.2 14.0 - - + +
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Residues in contact with HIS 539 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E GLU* 4.1 9.8 + - - +
535F SER* 3.4 30.2 + - - -
536F SER* 3.1 17.9 + - - +
538F TYR* 1.3 80.2 - - - +
540F HIS* 1.3 57.0 + - - +
543F ILE* 3.0 53.0 + - + +
544F ILE* 3.2 47.4 + - + +
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Residues in contact with HIS 540 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535F SER* 3.9 24.6 + - - -
536F SER 3.2 19.0 + - - -
537F LEU* 3.8 8.5 - - + +
538F TYR 3.3 0.2 - - - -
539F HIS* 1.3 77.7 - - - +
541F LEU* 1.3 62.2 + - - +
544F ILE* 3.8 13.9 - - + +
545F GLU 3.1 6.6 + - - -
546F THR* 2.8 55.3 + - + +
548F PHE* 3.9 23.8 - + + -
584F LEU* 4.0 22.3 - - + +
587F ASP* 3.6 27.3 + - - -
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Residues in contact with LEU 541 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537F LEU* 3.1 28.8 + - + +
540F HIS* 1.3 80.1 - - - +
542F HIS* 1.3 76.6 + - + +
545F GLU* 4.1 14.6 - - - +
546F THR 5.2 2.9 - - - +
548F PHE* 4.1 26.0 - - + -
553F LEU* 4.7 3.8 - - + -
648F GLU* 3.8 22.4 - - + +
649F LEU* 3.7 48.9 - - + +
652F GLY* 4.0 11.8 - - - +
682F ARG* 4.9 13.4 + - - +
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Residues in contact with HIS 542 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E LYS* 3.4 21.7 - - - +
538F TYR* 3.0 45.6 + + + +
541F LEU* 1.3 96.8 + - + +
543F ILE* 1.3 65.3 + - + +
545F GLU* 4.6 5.0 - - - +
648F GLU* 3.0 31.7 + - + +
652F GLY 3.5 26.0 + - - -
653F GLN* 3.6 20.6 - - - -
654F LEU* 3.4 19.3 - - + +
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Residues in contact with ILE 543 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E GLU* 3.6 36.3 - - + +
103E ILE* 4.0 24.2 - - - +
104E LYS* 3.6 23.2 - - - +
105E PRO* 4.8 9.0 - - + +
538F TYR* 3.9 12.3 - - + -
539F HIS* 3.0 50.5 + - + +
542F HIS* 1.3 87.6 - - + +
544F ILE* 1.3 65.2 + - + +
545F GLU* 3.4 2.5 + - - +
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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