Contacts of the helix formed by residues 374 - 388 (chain B) in PDB entry 5J3V
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 ASN 374 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B LEU* 3.4 14.7 - - - +
314B ASP* 3.8 24.5 + - - +
370B ILE* 4.5 6.9 - - - +
371B SER* 3.3 21.4 + - - +
373B TRP* 1.3 76.4 + - - +
375B LEU* 1.3 64.0 + - - +
376B ARG* 3.2 11.8 + - - +
377B LYS* 2.9 49.3 + - - +
378B CYS* 3.1 25.5 + - - +
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B THR* 4.7 9.2 - - - +
270B GLU* 4.4 35.0 - - + +
273B ALA* 3.7 44.2 - - + +
274B LEU* 3.7 10.5 - - + +
277B CYS* 3.9 16.8 - - + -
307B GLY* 4.3 17.7 - - - +
374B ASN* 1.3 76.7 - - - +
376B ARG* 1.3 57.6 + - - +
378B CYS* 3.7 0.6 + - - -
379B SER* 2.7 38.2 + - - +
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Residues in contact with ARG 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLY 3.5 12.5 + - - +
308B MET* 3.3 28.7 + - - +
309B LYS 4.6 3.6 - - - +
310B TYR* 3.4 52.9 + - - +
311B SER 5.7 0.7 - - - +
314B ASP* 5.3 5.2 - - - +
370B ILE* 5.8 2.8 - - - +
374B ASN* 3.2 13.5 + - - +
375B LEU* 1.3 80.0 - - - +
377B LYS* 1.3 74.7 + - + +
379B SER* 3.4 4.0 + - - -
380B ALA* 3.2 21.5 + - + +
415B GLU* 2.7 35.6 + - - -
419B LEU* 3.5 25.0 - - + +
457B ILE* 4.4 6.5 - - - +
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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
----------------------------------------------------------
370B ILE* 3.9 24.5 - - - +
371B SER 2.9 26.3 + - - -
372B ASP* 3.9 22.3 + - - +
373B TRP* 4.4 17.3 - - + -
374B ASN* 2.9 27.8 + - - +
376B ARG* 1.3 86.8 - - + +
378B CYS* 1.3 60.3 + - - +
380B ALA* 3.4 6.6 + - - +
381B ALA* 3.1 28.2 + - - +
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Residues in contact with CYS 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 4.0 7.9 - - + -
277B CYS* 3.6 28.5 - - - -
278B GLU* 3.6 33.2 - - - -
281B LEU* 3.8 9.0 - - - +
373B TRP* 3.5 25.5 - - + -
374B ASN 3.1 18.0 + - - +
375B LEU 4.1 3.4 - - - +
376B ARG 3.3 0.2 - - - -
377B LYS* 1.3 77.9 - - - +
379B SER* 1.3 59.8 - - - +
382B ALA* 3.4 21.1 + - - +
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Residues in contact with SER 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B CYS* 3.4 18.9 - - - -
304B LEU* 3.6 31.4 - - - +
307B GLY* 3.8 11.1 - - - -
308B MET* 3.7 11.7 - - - +
375B LEU* 2.7 26.2 + - - +
376B ARG 3.7 4.7 - - - -
377B LYS 3.2 0.2 - - - -
378B CYS* 1.3 78.0 - - - +
380B ALA* 1.3 62.3 + - - +
382B ALA* 3.5 2.9 + - - +
383B LEU* 3.2 22.5 + - - +
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B MET* 3.5 23.3 - - + +
376B ARG 3.2 16.0 + - - +
377B LYS* 3.4 7.6 + - - +
379B SER* 1.3 76.6 - - - +
381B ALA* 1.3 59.5 - - - +
383B LEU* 3.4 2.4 + - - +
384B ASP* 3.0 27.9 + - - +
419B LEU* 4.4 19.5 - - + -
423B ALA* 4.1 8.2 - - + +
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Residues in contact with ALA 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 3.8 29.4 - - + -
373B TRP* 4.6 6.3 - - + -
377B LYS 3.1 16.4 + - - +
378B CYS* 4.0 0.7 - - - +
380B ALA* 1.3 77.4 - - - +
382B ALA* 1.3 61.1 + - - +
384B ASP* 3.2 7.6 + - - +
385B VAL* 3.0 29.9 + - + +
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B CYS 4.8 1.8 - - - +
280B TRP* 4.0 29.6 - - + +
281B LEU* 3.9 14.1 - - + +
304B LEU* 4.2 14.6 - - + -
378B CYS 3.4 15.8 + - - +
379B SER 3.8 5.2 - - - +
380B ALA 3.3 0.4 - - - -
381B ALA* 1.3 79.2 - - - +
383B LEU* 1.3 57.2 + - - +
385B VAL* 3.6 3.8 + - - +
386B LEU* 3.1 36.7 + - + +
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ILE* 4.6 16.4 - - + -
304B LEU* 4.6 15.4 - - + +
305B VAL* 5.1 2.0 - - + -
308B MET* 3.6 28.5 - - + -
379B SER 3.2 17.7 + - - +
380B ALA 3.8 4.5 - - - +
381B ALA 3.3 0.2 - - - -
382B ALA* 1.3 74.4 - - - +
384B ASP* 1.3 59.7 + - - +
386B LEU* 3.6 6.3 + - + +
387B ALA* 3.0 27.7 + - - +
394B LEU* 4.7 5.5 - - + +
398B ILE* 4.2 20.6 - - + -
420B VAL* 3.9 15.0 - - + -
423B ALA* 3.8 15.9 - - + +
424B ILE* 3.6 23.1 - - + -
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Residues in contact with ASP 384 (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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380B ALA 3.0 17.3 + - - +
381B ALA* 3.2 9.1 + - - +
383B LEU* 1.3 79.7 - - - +
385B VAL* 1.3 64.7 + - + +
387B ALA* 3.4 13.7 - - - +
388B ASN* 3.4 17.2 + - - -
423B ALA* 3.1 25.6 - - + +
426B GLU* 4.2 9.9 - - - +
460B TRP* 6.4 0.4 - - - -
464B ARG* 3.3 21.9 + - - -
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Residues in contact with VAL 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 4.2 15.5 - - + -
284B ALA* 3.5 35.4 - - + +
381B ALA* 3.0 16.2 + - + +
382B ALA* 4.0 3.8 - - - +
383B LEU 3.4 0.2 - - - -
384B ASP* 1.3 76.6 - - + +
386B LEU* 1.3 62.1 + - + +
387B ALA 3.0 1.3 - - - -
388B ASN* 2.8 28.4 + - + +
389B VAL* 3.3 16.6 + - + +
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Residues in contact with LEU 386 (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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280B TRP* 5.4 11.0 - - + +
284B ALA* 5.9 2.5 - - + -
289B CYS* 4.3 11.7 - - - -
293B LEU* 4.0 21.3 - - + -
300B LEU* 4.1 18.2 - - + -
301B ILE* 5.8 4.3 - - + -
304B LEU* 4.0 23.3 - - + -
382B ALA* 3.1 23.8 + - + +
383B LEU* 4.0 8.1 - - + +
385B VAL* 1.3 78.2 - - + +
387B ALA* 1.3 60.6 + - - +
388B ASN 3.2 0.2 - - - -
389B VAL* 3.7 8.2 - - + +
390B TYR* 3.3 41.3 + - + +
394B LEU* 3.6 22.8 - - + +
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Residues in contact with ALA 387 (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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383B LEU 3.0 18.7 + - - +
384B ASP 3.4 8.7 - - - +
385B VAL 3.0 0.6 - - - -
386B LEU* 1.3 76.7 - - - +
388B ASN* 1.3 58.4 + - - +
389B VAL 3.3 0.9 - - - -
391B ARG* 3.3 18.4 - - - -
394B LEU* 3.7 12.3 - - + +
423B ALA 4.0 1.3 - - - +
424B ILE* 3.8 22.2 - - + -
426B GLU 3.6 14.1 - - - +
427B GLY* 3.2 16.6 - - - -
428B CYS* 3.9 9.1 + - - -
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Residues in contact with ASN 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ASP* 3.4 19.1 + - - -
385B VAL* 2.8 17.2 + - + +
387B ALA* 1.3 76.4 - - - +
389B VAL* 1.3 64.0 + - + +
391B ARG* 3.9 11.3 - - - +
426B GLU* 2.8 52.2 + - - +
427B GLY* 3.6 5.8 - - - -
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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