Contacts of the helix formed by residues 370 - 383 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B LEU 4.8 0.7 - - - -
229B ASP* 2.3 31.5 + - - -
230B SER* 3.8 10.8 - - - +
331B LYS* 4.1 11.6 + - - -
363B ARG* 3.2 22.9 + - - +
368B ILE 3.5 7.4 + - - -
369B ARG* 1.3 77.5 - - - +
371B VAL* 1.3 59.6 + - - +
372B PHE* 3.3 19.9 + - - +
373B LEU* 3.0 22.4 + - - +
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Residues in contact with VAL 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR 5.2 2.5 - - - +
227B GLU* 4.7 8.5 - - - +
229B ASP* 3.6 31.4 + - + +
363B ARG* 3.8 26.3 - - - +
370B SER* 1.3 70.2 + - - +
372B PHE* 1.3 63.6 + - - +
374B GLY* 2.8 18.1 + - - -
375B LYS* 3.2 29.9 + - + +
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Residues in contact with PHE 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B GLU 4.3 12.8 - - - +
328B TYR* 4.0 22.2 - + + -
331B LYS* 3.8 25.8 - - + +
332B ILE* 3.7 35.9 - - + -
335B TYR* 3.4 39.0 - + + -
370B SER* 3.3 13.5 + - - +
371B VAL* 1.3 82.1 - - - +
373B LEU* 1.3 63.3 + - + +
375B LYS* 3.2 19.7 + - + +
376B ILE* 3.3 19.9 + - + +
394B PHE* 5.1 0.4 - + - -
395B PHE* 3.5 31.2 - + - -
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Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B TYR* 3.6 34.3 - - + +
339B PHE* 5.6 0.2 - - + -
359B ALA* 3.6 35.1 - - + +
362B TRP* 3.5 47.6 - - + +
363B ARG* 3.8 7.6 - - + +
368B ILE* 3.3 29.4 - - + +
369B ARG* 4.1 1.6 - - - -
370B SER* 3.0 11.3 + - - +
372B PHE* 1.3 77.5 - - + +
374B GLY* 1.3 59.7 + - - +
376B ILE* 3.1 12.3 + - + +
377B LYS* 3.0 22.5 + - - +
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Residues in contact with GLY 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ALA 6.3 0.2 - - - -
363B ARG* 3.8 19.5 - - - +
370B SER 3.7 1.8 + - - -
371B VAL* 2.8 13.3 + - - -
373B LEU* 1.3 79.4 - - - +
375B LYS* 1.3 57.8 + - - +
377B LYS* 3.1 12.8 + - - +
378B ASP* 2.9 33.1 + - - +
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Residues in contact with LYS 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B VAL* 3.2 34.5 - - + +
372B PHE* 3.2 13.6 + - - +
374B GLY* 1.3 73.7 - - - +
376B ILE* 1.3 60.7 + - - +
378B ASP* 3.3 14.3 + - + +
379B ALA* 2.9 28.4 + - - +
382B ARG* 5.2 1.2 + - - -
394B PHE* 3.5 52.7 - - + +
395B PHE* 3.9 6.1 - - + -
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Residues in contact with ILE 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B TYR* 3.5 44.4 - - + -
339B PHE* 3.6 29.8 - - + -
359B ALA* 3.8 5.8 - - + -
372B PHE* 3.6 18.6 - - + +
373B LEU* 3.1 16.3 + - + +
375B LYS* 1.3 74.8 - - - +
377B LYS* 1.3 62.5 + - - +
379B ALA* 3.4 1.0 + - - +
380B PHE* 3.0 31.8 + - + -
389B LEU* 3.8 14.6 - - + -
395B PHE* 3.4 24.0 - - + -
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Residues in contact with LYS 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B GLU* 5.4 10.8 - - - -
356B GLY* 3.5 30.1 + - - +
357B GLY* 5.7 0.8 - - - -
359B ALA* 4.0 3.3 - - + +
360B LEU* 4.2 38.4 - - + +
363B ARG* 6.3 0.7 - - - -
373B LEU 3.0 12.6 + - - +
374B GLY* 3.1 13.9 + - - +
376B ILE* 1.3 77.3 - - - +
378B ASP* 1.3 58.5 + - - +
380B PHE* 3.3 3.3 + - - +
381B ASP* 2.9 59.8 + - - +
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Residues in contact with ASP 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B GLY 2.9 19.6 + - - +
375B LYS* 3.3 18.6 + - + +
376B ILE 3.3 0.2 - - - -
377B LYS* 1.3 79.0 - - - +
379B ALA* 1.3 57.9 + - - +
381B ASP* 2.9 29.4 + - - +
382B ARG* 3.2 36.1 + - - +
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Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B LYS 2.9 17.9 + - - +
376B ILE 3.7 3.8 - - - +
377B LYS 3.3 0.2 - - - -
378B ASP* 1.3 75.6 - - - +
380B PHE* 1.3 59.9 + - - +
381B ASP 3.2 0.7 + - - -
382B ARG* 3.4 30.8 + - - +
383B ASN* 3.9 9.0 + - - +
386B LEU* 4.4 5.3 - - + +
389B LEU* 4.3 9.4 - - + -
392B ASP* 4.0 19.9 - - + +
394B PHE* 6.0 0.2 - - + -
395B PHE* 3.5 24.7 - - + -
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Residues in contact with PHE 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B PHE* 3.5 31.6 - + + -
355B TYR* 3.5 41.3 - + + -
356B GLY* 3.6 20.4 + - - +
376B ILE* 3.0 30.0 + - + +
377B LYS 3.4 3.4 - - - +
379B ALA* 1.3 75.8 - - - +
381B ASP* 1.3 61.2 + - - +
382B ARG 3.5 0.2 - - - -
384B PRO* 3.1 36.9 - - + +
385B GLU 5.2 0.9 - - - -
386B LEU* 3.7 37.9 - - + -
389B LEU* 3.6 26.9 - - + -
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Residues in contact with ASP 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B GLY* 4.7 4.2 - - - -
377B LYS* 2.9 49.4 + - - +
378B ASP* 2.9 21.9 + - - +
380B PHE* 1.3 81.0 - - - +
382B ARG* 1.3 60.3 + - + +
384B PRO* 3.6 8.8 - - - +
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Residues in contact with ARG 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LYS 5.2 0.8 + - - -
378B ASP* 3.2 34.9 + - - +
379B ALA* 3.4 21.3 + - - +
381B ASP* 1.3 81.3 - - + +
383B ASN* 1.3 60.3 + - + +
384B PRO* 3.5 2.6 - - - +
392B ASP* 2.7 36.1 + - - +
393B ASP* 4.8 5.5 - - - +
394B PHE* 4.6 23.9 - - - +
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Residues in contact with ASN 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ALA 3.9 5.7 + - - +
382B ARG* 1.3 79.6 - - + +
384B PRO* 1.4 58.6 - - - +
385B GLU* 2.5 37.7 + - - +
386B LEU* 3.8 32.0 - - + +
392B ASP* 4.8 7.1 + - - +
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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