Contacts of the helix formed by residues 370 - 383 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228C LEU 5.8 0.2 - - - -
229C ASP 3.2 17.0 - - - -
230C SER* 3.5 14.6 - - - +
331C LYS* 3.9 11.9 + - - -
363C ARG* 3.6 15.5 + - - +
368C ILE 3.6 9.1 + - - -
369C ARG* 1.3 77.0 - - - +
371C VAL* 1.3 60.3 + - - +
372C PHE* 3.7 12.2 - - - +
373C LEU* 3.0 40.1 + - - +
374C GLY 3.6 2.6 + - - -
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Residues in contact with VAL 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C THR 4.7 4.3 - - - +
227C GLU* 4.7 5.6 - - - +
229C ASP* 3.1 41.0 + - + +
363C ARG* 3.4 28.5 - - - +
370C SER* 1.3 69.2 - - - +
372C PHE* 1.3 67.8 + - - +
374C GLY* 3.1 10.7 + - - -
375C LYS* 3.3 39.1 + - + +
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Residues in contact with PHE 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C GLU 4.0 13.7 - - - +
228C LEU* 5.8 1.6 - - + -
229C ASP 4.3 0.2 + - - -
328C TYR* 3.6 27.6 - + - -
331C LYS* 4.2 23.8 - - + +
332C ILE* 3.6 34.5 - - + -
335C TYR* 3.9 26.5 - + + -
370C SER* 3.0 12.0 - - - +
371C VAL* 1.3 84.5 - - - +
373C LEU* 1.3 61.5 + - - +
375C LYS* 3.1 18.9 + - - +
376C ILE* 3.2 28.6 + - + +
394C PHE* 5.2 3.1 - + - -
395C PHE* 3.4 33.2 - + - -
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Residues in contact with LEU 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C TYR* 3.5 32.3 - - + +
339C PHE* 5.2 0.7 - - + -
359C ALA* 3.8 23.4 - - + +
362C TRP* 3.3 42.0 - - + +
363C ARG* 3.6 13.7 - - + -
368C ILE* 3.2 32.1 - - + +
369C ARG* 4.1 1.3 - - - -
370C SER* 3.0 15.8 + - - +
372C PHE* 1.3 77.7 - - + +
374C GLY* 1.3 60.0 + - - +
376C ILE* 3.0 32.2 + - + +
377C LYS* 3.3 6.1 + - - +
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Residues in contact with GLY 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C ARG* 4.3 21.9 - - - +
370C SER 3.6 2.2 + - - -
371C VAL* 3.1 13.2 + - - +
373C LEU* 1.3 78.6 - - - +
375C LYS* 1.3 53.6 + - - +
377C LYS* 3.4 13.8 + - - +
378C ASP* 2.6 25.0 + - - +
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Residues in contact with LYS 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C VAL* 3.3 40.1 - - + +
372C PHE* 3.1 13.2 + - - +
374C GLY* 1.3 74.7 - - - +
376C ILE* 1.3 62.8 + - - +
378C ASP* 2.9 21.6 - - - +
379C ALA* 3.4 16.3 + - - +
394C PHE* 3.5 39.0 - - + -
395C PHE* 3.5 8.5 - - + -
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Residues in contact with ILE 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C TYR* 4.4 5.6 - - + -
339C PHE* 3.9 13.9 - - + -
359C ALA* 3.9 14.6 - - + -
372C PHE* 3.3 34.3 - - + +
373C LEU* 3.0 24.1 + - + +
375C LYS* 1.3 77.2 - - - +
377C LYS* 1.3 63.0 + - - +
379C ALA* 3.3 3.8 + - - +
380C PHE* 3.1 50.0 + - + -
389C LEU* 3.7 20.4 - - + -
395C PHE* 3.4 24.7 - - + -
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Residues in contact with LYS 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C GLU* 5.9 3.8 - - - -
356C GLY* 3.3 32.9 - - - +
357C GLY* 5.2 1.6 - - - +
359C ALA* 4.0 11.4 - - + +
360C LEU* 4.1 35.7 - - + +
373C LEU 3.3 5.3 + - - +
374C GLY* 3.7 10.5 - - - +
375C LYS 3.4 0.6 - - - -
376C ILE* 1.3 79.4 - - - +
378C ASP* 1.3 59.4 + - - +
380C PHE* 2.9 21.1 + - - +
381C ASP* 3.0 36.4 + - - +
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Residues in contact with ASP 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C GLY 2.6 26.9 + - - +
375C LYS* 2.9 22.6 - - - +
377C LYS* 1.3 75.8 - - - +
379C ALA* 1.3 63.7 + - - +
380C PHE 3.3 0.2 - - - -
381C ASP* 3.4 20.9 + - + +
382C ARG* 3.4 17.5 + - - +
394C PHE* 6.1 0.7 - - - +
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Residues in contact with ALA 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C LYS 3.4 16.7 + - - +
376C ILE 3.3 7.2 + - - +
377C LYS 3.1 1.0 - - - -
378C ASP* 1.3 85.3 - - - +
380C PHE* 1.3 60.2 + - - +
381C ASP 3.6 0.2 + - - -
382C ARG* 3.7 8.5 + - - +
383C ASN* 3.7 8.0 + - - +
386C LEU* 4.2 9.1 - - + +
389C LEU* 4.6 6.7 - - + -
392C ASP* 3.5 40.7 - - + +
395C PHE* 3.6 13.5 - - + -
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Residues in contact with PHE 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C PHE* 3.7 36.6 - + + -
343C ARG* 4.7 2.5 - - - -
355C TYR* 3.7 36.8 - + + -
356C GLY* 4.0 13.5 - - - +
376C ILE* 3.1 43.0 + - + -
377C LYS 2.9 7.1 + - - +
379C ALA* 1.3 76.4 - - - +
381C ASP* 1.3 61.0 + - - +
383C ASN 3.0 28.4 - - - -
384C PRO* 3.0 14.7 - - + +
386C LEU* 4.2 31.9 - - + -
388C ASN 6.4 0.2 - - - -
389C LEU* 4.1 16.8 - - + -
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Residues in contact with ASP 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C GLY* 5.4 3.8 - - - -
377C LYS* 3.0 45.5 + - - +
378C ASP* 3.4 18.1 - - + +
379C ALA 3.3 0.6 - - - -
380C PHE* 1.3 79.3 - - - +
382C ARG* 1.3 61.2 + - - +
383C ASN 3.4 0.5 + - - -
384C PRO* 4.0 10.6 - - - +
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Residues in contact with ARG 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378C ASP* 3.4 12.1 + - - +
379C ALA 4.0 8.1 - - - +
380C PHE 3.3 0.8 - - - -
381C ASP* 1.3 79.4 - - - +
383C ASN* 1.3 61.4 + - + +
384C PRO* 4.1 2.1 - - - +
392C ASP* 5.1 4.7 + - - +
393C ASP* 2.8 45.1 + - - +
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Residues in contact with ASN 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379C ALA 3.7 5.0 + - - +
380C PHE* 3.0 11.2 + - - +
381C ASP 3.2 0.8 - - - -
382C ARG* 1.3 83.5 - - + +
384C PRO* 1.3 69.8 - - - +
385C GLU* 3.2 29.6 + - - +
386C LEU* 3.1 52.6 + - + +
387C GLN 4.9 0.4 - - - +
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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