Contacts of the helix formed by residues 370 - 383 (chain F) in PDB entry 5UQ9
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 370 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228F LEU 4.2 1.1 - - - -
229F ASP 3.3 17.7 - - - -
230F SER* 3.5 17.9 - - - -
331F LYS* 4.2 6.7 + - - -
335F TYR* 4.9 0.9 + - - -
363F ARG* 3.2 23.8 - - - +
368F ILE 3.3 10.9 + - - -
369F ARG* 1.3 76.7 - - - +
371F VAL* 1.3 64.3 + - - +
372F PHE* 3.8 11.8 + - - +
373F LEU* 3.1 26.4 + - - +
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Residues in contact with VAL 371 (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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227F GLU 5.4 1.8 - - - +
228F LEU 4.7 0.7 - - - +
229F ASP* 3.3 38.7 + - + +
363F ARG* 4.4 13.0 - - - +
370F SER* 1.3 71.2 - - - +
372F PHE* 1.3 59.8 + - - +
374F GLY* 2.8 20.0 + - - -
375F LYS* 3.2 29.1 - - + +
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Residues in contact with PHE 372 (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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227F GLU 4.3 12.9 + - - +
228F LEU* 4.1 5.6 + - - +
328F TYR* 4.3 17.9 - + + -
331F LYS* 3.9 41.1 - - + +
332F ILE* 3.8 22.7 - - + -
335F TYR* 3.5 40.4 - + + -
370F SER* 3.1 10.8 - - - +
371F VAL* 1.3 77.7 - - - +
373F LEU* 1.3 62.9 + - - +
375F LYS* 3.2 24.3 + - + +
376F ILE* 3.4 25.9 + - + +
389F LEU* 5.5 0.7 - - + -
394F PHE* 5.9 0.2 - + - -
395F PHE* 3.4 28.3 - + - -
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Residues in contact with LEU 373 (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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335F TYR* 3.5 32.3 - - + +
359F ALA* 3.6 29.7 - - + +
362F TRP* 3.6 50.0 - - + -
363F ARG* 3.9 8.1 - - + +
368F ILE* 3.2 28.3 - - + +
370F SER* 3.1 16.1 + - - +
371F VAL 3.1 1.0 - - - -
372F PHE* 1.3 78.1 - - + +
374F GLY* 1.3 62.1 + - - +
376F ILE* 3.1 19.0 + - + +
377F LYS* 3.2 11.4 + - - +
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Residues in contact with GLY 374 (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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360F LEU* 6.5 0.2 - - - -
363F ARG* 3.5 30.1 - - - +
370F SER 4.0 1.8 + - - -
371F VAL* 2.8 11.9 + - - -
373F LEU* 1.3 79.3 - - - +
375F LYS* 1.3 60.8 + - - +
377F LYS* 3.2 7.5 + - - +
378F ASP* 3.1 30.7 + - - +
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Residues in contact with LYS 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227F GLU* 4.4 27.9 + - - +
328F TYR* 5.1 1.4 + - - -
371F VAL* 3.2 37.3 - - + +
372F PHE* 3.2 12.8 + - + +
374F GLY* 1.3 76.3 - - - +
376F ILE* 1.3 56.3 + - - +
378F ASP* 4.0 8.4 - - - +
379F ALA* 3.2 24.6 + - - +
382F ARG* 5.3 2.1 + - - -
394F PHE* 3.5 46.2 - - + +
395F PHE* 3.6 10.9 - - + -
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Residues in contact with ILE 376 (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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335F TYR* 3.6 20.2 - - + -
339F PHE* 3.6 30.5 - - + -
359F ALA* 3.7 7.4 - - + -
372F PHE* 3.6 36.1 - - + +
373F LEU* 3.1 16.7 + - + +
375F LYS* 1.3 76.3 - - - +
377F LYS* 1.3 65.1 + - - +
379F ALA* 3.2 4.7 + - - +
380F PHE* 3.1 33.7 + - + -
389F LEU* 3.8 20.2 - - + -
395F PHE* 3.8 18.4 - - + -
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Residues in contact with LYS 377 (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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168F GLU* 2.8 41.4 + - - -
356F GLY* 3.3 32.3 - - - +
357F GLY* 5.0 2.5 - - - +
359F ALA* 4.2 2.2 - - + +
360F LEU* 3.8 28.2 - - + +
363F ARG* 5.1 5.2 - - - +
373F LEU 3.2 11.0 + - - +
374F GLY* 3.2 9.6 + - - +
376F ILE* 1.3 77.5 - - - +
378F ASP* 1.3 53.7 + - - +
380F PHE* 2.9 4.3 + - - +
381F ASP* 2.6 62.5 + - - +
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Residues in contact with ASP 378 (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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374F GLY 3.1 18.6 + - - +
375F LYS* 4.2 7.3 - - - +
377F LYS* 1.3 78.0 - - - +
379F ALA* 1.3 57.3 + - - +
381F ASP* 3.8 15.6 - - - +
382F ARG* 2.9 50.0 + - - +
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Residues in contact with ALA 379 (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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375F LYS 3.2 16.1 + - - +
376F ILE 3.2 10.3 + - - +
377F LYS 3.1 0.6 - - - -
378F ASP* 1.3 78.3 - - - +
380F PHE* 1.3 57.0 + - - +
382F ARG* 3.7 7.4 - - - +
383F ASN* 3.4 21.7 + - - +
386F LEU* 4.1 8.3 - - + +
389F LEU* 4.1 10.5 - - + -
392F ASP* 3.8 27.3 - - - +
395F PHE* 3.8 20.2 - - + -
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Residues in contact with PHE 380 (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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339F PHE* 3.7 28.3 - + + -
355F TYR* 3.7 38.4 - + + -
356F GLY* 3.8 19.7 - - - +
376F ILE* 3.1 41.3 + - + -
377F LYS 2.9 6.1 + - - +
379F ALA* 1.3 75.3 - - - +
381F ASP* 1.3 62.1 + - - +
382F ARG 3.2 1.1 - - - -
383F ASN 3.8 4.5 - - - -
384F PRO* 3.0 41.3 - - + +
386F LEU* 4.0 36.1 - - + -
388F ASN 6.2 0.2 - - - -
389F LEU* 4.2 17.5 - - + -
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Residues in contact with ASP 381 (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 GLY* 4.8 5.2 - - - -
377F LYS* 2.6 58.1 + - - +
378F ASP* 3.8 14.7 - - - +
380F PHE* 1.3 72.9 - - - +
382F ARG* 1.3 63.8 + - - +
383F ASN 3.5 0.2 + - - -
384F PRO* 4.1 9.2 - - - +
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Residues in contact with ARG 382 (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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375F LYS 5.3 1.8 + - - -
378F ASP* 2.9 40.1 + - - +
379F ALA* 3.7 7.2 - - - +
380F PHE 3.2 0.2 - - - -
381F ASP* 1.3 78.1 - - - +
383F ASN* 1.3 61.8 + - + +
384F PRO* 4.2 1.9 - - - +
392F ASP* 3.4 30.5 + - - +
393F ASP* 5.2 4.9 - - - +
394F PHE* 4.1 20.6 - - - +
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Residues in contact with ASN 383 (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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379F ALA 3.4 10.0 + - - +
380F PHE* 3.1 6.0 - - - +
382F ARG* 1.3 83.6 - - + +
384F PRO* 1.3 68.2 - - - +
385F GLU* 3.0 34.6 + - - +
386F LEU* 3.1 31.6 + - + +
387F GLN* 4.9 5.1 + - - +
392F ASP* 5.8 2.0 - - - +
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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