Contacts of the helix formed by residues 370 - 383 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A ASP 3.2 15.7 - - - -
230A SER* 3.5 15.3 - - - +
331A LYS* 3.9 11.2 + - - -
335A TYR* 4.7 0.3 + - - -
362A TRP 4.6 0.4 + - - -
363A ARG* 3.2 22.6 + - - +
368A ILE 3.4 11.4 + - - -
369A ARG* 1.3 76.4 - - - +
371A VAL* 1.3 65.0 + - - +
372A PHE* 3.7 10.8 + - - +
373A LEU* 3.1 28.8 + - - +
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Residues in contact with VAL 371 (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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226A THR 4.7 4.0 - - - +
227A GLU* 4.3 11.7 - - - +
229A ASP* 3.0 46.4 + - + +
363A ARG* 3.4 21.3 - - - +
370A SER* 1.3 72.0 - - - +
372A PHE* 1.3 65.2 + - - +
374A GLY* 3.1 11.9 + - - -
375A LYS* 3.5 21.9 + - - +
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Residues in contact with PHE 372 (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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227A GLU 4.2 13.7 - - - +
228A LEU* 5.8 1.6 - - + -
229A ASP 4.3 0.6 + - - +
328A TYR* 3.9 24.5 - + + -
331A LYS* 3.8 35.2 - - + +
332A ILE* 3.8 27.6 - - + -
335A TYR* 3.7 35.2 - + + -
370A SER* 3.0 12.0 - - - +
371A VAL* 1.3 83.7 - - - +
373A LEU* 1.3 61.8 + - - +
375A LYS* 3.3 18.6 + - + +
376A ILE* 3.4 21.0 + - + +
389A LEU* 5.2 0.7 - - + -
395A PHE* 3.4 31.9 - + - -
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Residues in contact with LEU 373 (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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335A TYR* 3.9 26.0 - - + +
339A PHE* 5.4 0.9 - - + -
359A ALA* 3.9 33.7 - - + +
362A TRP* 3.2 42.2 - - + +
363A ARG* 3.6 13.3 - - + +
368A ILE* 3.2 35.0 - - + +
369A ARG* 4.3 0.9 - - - -
370A SER* 3.1 15.7 + - - +
372A PHE* 1.3 75.8 - - - +
374A GLY* 1.3 63.6 + - - +
376A ILE* 3.3 16.5 + - + +
377A LYS* 3.3 15.9 + - - +
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Residues in contact with GLY 374 (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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363A ARG* 3.4 25.3 - - - +
371A VAL 3.1 10.5 + - - -
373A LEU* 1.3 76.2 - - - +
375A LYS* 1.3 63.7 + - - +
377A LYS* 3.1 14.6 + - - +
378A ASP* 2.9 23.6 + - - +
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Residues in contact with LYS 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A TYR* 5.4 0.7 - - - +
371A VAL* 3.5 19.7 + - - +
372A PHE* 3.3 13.2 + - + +
374A GLY* 1.3 76.8 - - - +
376A ILE* 1.3 61.5 + - - +
378A ASP* 3.3 19.7 + - - +
379A ALA* 3.1 19.9 + - - +
382A ARG* 4.6 2.6 + - - -
394A PHE* 3.6 50.2 - - + -
395A PHE* 3.9 7.7 - - + -
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Residues in contact with ILE 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A TYR* 3.6 38.6 - - + -
339A PHE* 4.1 9.2 - - + -
359A ALA* 3.8 15.3 - - + -
372A PHE* 3.4 22.8 + - + +
373A LEU* 3.3 15.9 + - + +
374A GLY 3.2 0.8 - - - -
375A LYS* 1.3 75.4 - - - +
377A LYS* 1.3 64.7 + - - +
379A ALA* 3.1 10.4 + - - +
380A PHE* 3.2 38.1 + - + -
389A LEU* 4.0 11.0 - - + -
395A PHE* 3.5 22.9 - - + -
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Residues in contact with LYS 377 (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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168A GLU* 4.2 15.1 + - - +
356A GLY* 3.7 21.7 - - - +
357A GLY* 6.0 0.2 - - - -
359A ALA* 4.1 8.9 - - + +
360A LEU* 4.1 44.4 - - + +
363A ARG* 5.8 1.1 - - + -
373A LEU 3.3 8.7 + - - +
374A GLY* 3.1 14.4 + - - +
376A ILE* 1.3 79.4 - - - +
378A ASP* 1.3 53.1 + - - +
380A PHE* 3.2 2.6 + - - +
381A ASP* 2.6 74.0 + - - +
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Residues in contact with ASP 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLY 2.9 18.2 - - - +
375A LYS* 3.6 24.1 + - - +
376A ILE 3.3 0.2 - - - -
377A LYS* 1.3 81.5 - - - +
379A ALA* 1.3 63.6 + - - +
381A ASP* 4.1 3.1 - - - +
382A ARG* 3.0 47.8 + - - +
76H LYS* 3.0 30.3 + - - +
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Residues in contact with ALA 379 (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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375A LYS 3.1 5.2 + - - +
376A ILE 3.1 11.3 + - - +
378A ASP* 1.3 77.7 - - - +
380A PHE* 1.3 57.8 + - + +
382A ARG* 3.6 5.8 + - - +
383A ASN* 3.4 21.0 + - - +
386A LEU* 4.0 10.2 - - + +
389A LEU* 3.9 13.7 - - + -
392A ASP* 2.9 33.9 - - + +
395A PHE* 3.5 19.7 - - + -
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Residues in contact with PHE 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PHE* 3.5 33.2 - + + -
343A ARG* 5.3 0.9 - - - -
355A TYR* 3.6 28.5 - + + -
356A GLY* 3.5 31.6 - - - +
376A ILE* 3.2 44.9 + - + +
377A LYS 4.1 0.2 - - - +
379A ALA* 1.3 75.1 - - + +
381A ASP* 1.3 62.8 + - - +
382A ARG 3.3 0.4 - - - -
383A ASN 3.5 14.4 - - - -
384A PRO* 2.9 37.5 - - + +
386A LEU* 4.0 24.9 - - + -
389A LEU* 4.0 22.2 - - + -
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Residues in contact with ASP 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLY* 4.9 6.2 - - - -
377A LYS* 2.6 66.9 + - - +
378A ASP* 3.9 6.8 + - - +
380A PHE* 1.3 76.0 - - - +
382A ARG* 1.3 61.3 + - - +
383A ASN 3.5 0.2 + - - -
384A PRO* 4.2 8.1 - - - +
75H VAL* 6.0 0.9 - - - +
76H LYS* 3.9 31.3 + - + +
80H ALA* 4.6 6.9 - - - +
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Residues in contact with ARG 382 (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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375A LYS 4.6 1.8 + - - -
378A ASP* 3.0 38.7 + - - +
379A ALA* 3.6 13.0 - - - +
381A ASP* 1.3 78.0 - - - +
383A ASN* 1.3 59.2 + - + +
384A PRO* 4.1 1.9 - - - +
392A ASP* 2.7 39.6 + - - -
393A ASP* 6.2 0.2 - - - -
394A PHE* 3.9 17.4 - - - +
34H ARG* 3.3 15.8 + - - -
76H LYS* 4.6 15.1 - - + +
79H GLN* 3.5 45.6 + - + +
80H ALA* 4.3 22.4 - - + +
83H ASP* 3.8 12.2 - - - +
84H PHE* 6.1 0.7 - - - -
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Residues in contact with ASN 383 (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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379A ALA 3.4 8.7 + - - +
380A PHE* 3.2 11.0 - - - +
382A ARG* 1.3 82.2 - - + +
384A PRO* 1.3 66.2 - - - +
385A GLU* 3.2 19.5 + - - +
386A LEU* 3.3 49.7 + - + +
387A GLN 4.9 0.2 - - - +
34H ARG* 3.1 33.6 + - - +
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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