Contacts of the strand formed by residues 365 - 369 (chain F) in PDB entry 1MK9
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 365 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361F ALA* 3.4 3.3 - - - +
362F SER* 2.8 42.0 + - - +
364F LYS* 1.3 90.1 + - - +
366F PHE* 1.3 65.0 + - - +
367F THR* 4.8 6.1 - - - -
379F SER* 4.9 4.0 - - - -
380F VAL 3.3 13.2 - - - -
381F GLN* 5.0 2.3 - - - +
382F THR* 3.5 6.7 + - - -
385F GLY* 4.0 3.3 - - - -
737G HIS* 5.8 3.6 - - - -
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Residues in contact with PHE 366 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330F LEU* 4.4 14.1 - - + -
359F TRP* 3.9 21.5 - + + -
360F ALA 3.1 25.8 - - - -
361F ALA* 4.2 0.9 - - + +
365F SER* 1.3 77.3 - - - +
367F THR* 1.3 66.0 + - - +
368F LEU* 3.3 44.4 - - + -
378F TYR* 4.1 2.8 - + - +
379F SER* 3.4 0.5 + - - -
380F VAL* 3.0 35.7 + - + -
382F THR* 3.7 18.2 - - + -
385F GLY* 4.0 16.6 - - - -
388F ILE* 3.5 35.9 - - + -
389F ALA* 4.2 5.6 - - - -
392F ILE* 3.5 11.0 - - + -
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Residues in contact with THR 367 (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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359F TRP* 3.0 9.2 - - - +
360F ALA 2.9 38.3 + - - -
365F SER* 4.8 1.7 - - - -
366F PHE* 1.3 77.3 + - - +
368F LEU* 1.3 64.9 - - - +
377F TYR* 3.9 19.3 - - + -
378F TYR 3.4 11.2 - - - +
379F SER* 2.7 29.0 + - - +
737G HIS* 2.8 39.0 - - - +
739G TRP* 3.8 11.7 - - + -
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Residues in contact with LEU 368 (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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330F LEU* 5.2 2.2 - - + -
337F VAL* 4.1 27.8 - - + -
356F ILE* 3.9 22.2 - - + -
358F ARG 3.8 7.0 - - - +
359F TRP* 3.7 21.3 - - + -
366F PHE* 3.3 32.3 - - + -
367F THR* 1.3 73.1 - - - +
369F ASP* 1.3 59.2 + - - +
370F PHE* 4.0 23.3 + - + -
377F TYR* 3.4 8.9 - - - +
378F TYR* 2.8 50.0 + - + +
392F ILE* 4.0 13.2 - - + -
739G TRP* 4.8 0.4 - - - -
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Residues in contact with ASP 369 (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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356F ILE* 3.8 4.5 - - - +
357F LYS* 2.9 42.0 + - - +
358F ARG* 3.2 44.3 + - + +
368F LEU* 1.3 72.7 - - - +
370F PHE* 1.3 62.5 + - - +
371F GLY* 2.4 39.2 + - - -
377F TYR* 3.0 35.1 + - + +
739G TRP* 4.2 4.9 - - + -
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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