Contacts of the helix formed by residues 369 - 385 (chain A) in PDB entry 4J15
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 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367A ASP 3.4 5.6 + - - -
368A LEU* 1.3 76.6 - - - +
370A THR* 1.3 59.2 + - - +
371A PRO* 3.5 12.6 - - - +
372A ASN* 3.1 34.4 + - - +
373A GLU* 2.8 27.2 + - - +
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Residues in contact with THR 370 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A LEU 4.0 0.4 + - - -
369A SER* 1.3 70.7 - - - +
371A PRO* 1.4 73.3 - - + +
373A GLU* 3.1 21.5 + - - +
374A LYS* 3.0 24.5 + - + +
422A GLY 5.1 0.2 - - - +
423A GLU* 6.0 3.6 - - + +
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Residues in contact with PRO 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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369A SER* 3.5 13.7 - - - +
370A THR* 1.4 95.0 - - + +
372A ASN* 1.3 60.1 + - - +
374A LYS* 3.3 8.3 + - + +
375A LEU* 3.0 27.0 + - - +
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Residues in contact with ASN 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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355A LEU* 3.7 13.4 - - + +
360A VAL* 3.7 41.2 - - - +
362A MET* 4.6 9.7 - - - +
368A LEU* 4.1 18.2 - - + -
369A SER* 3.1 29.9 + - - +
371A PRO* 1.3 78.4 + - - +
373A GLU* 1.3 58.3 + - - +
375A LEU* 4.4 5.3 - - - +
376A LEU* 2.9 32.1 + - - +
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Residues in contact with GLU 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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368A LEU* 3.8 38.5 - - + +
369A SER 2.8 20.7 + - - +
370A THR* 3.5 25.6 + - - +
372A ASN* 1.3 70.2 - - - +
374A LYS* 1.3 61.0 + - - +
376A LEU* 3.4 2.2 + - - +
377A GLY* 2.8 26.3 + - - -
389A TYR* 4.5 3.2 + - - -
394A TYR* 5.3 0.5 + - - -
417A ASP* 4.7 4.5 - - - +
419A PHE* 3.9 19.4 - - + -
422A GLY* 3.4 16.0 - - - +
423A GLU* 5.3 0.7 - - - -
424A GLU* 4.0 25.5 + - - +
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Residues in contact with LYS 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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370A THR* 3.0 14.7 + - + +
371A PRO* 3.5 12.1 - - + +
372A ASN 3.3 0.2 - - - -
373A GLU* 1.3 78.2 - - - +
375A LEU* 1.3 57.0 + - - +
377A GLY* 3.3 0.9 + - - -
378A HIS* 2.8 31.8 + - - +
421A ARG 3.9 17.7 - - - +
422A GLY* 3.4 15.4 + - - +
423A GLU* 4.8 12.8 - - + -
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Residues in contact with LEU 375 (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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355A LEU* 3.6 22.2 - - + -
358A ALA* 4.2 15.0 - - + +
360A VAL* 3.7 23.6 - - + -
371A PRO 3.0 16.5 + - - +
372A ASN* 3.8 6.7 - - - +
374A LYS* 1.3 72.2 - - - +
376A LEU* 1.3 61.2 + - - +
378A HIS* 3.1 14.1 + - + +
379A LEU* 2.8 52.5 + - + +
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Residues in contact with LEU 376 (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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346A LEU* 4.8 2.2 - - + -
351A ALA* 3.6 43.5 - - + +
354A MET* 4.1 26.7 - - + -
355A LEU* 4.1 14.4 - - + -
368A LEU* 3.9 22.9 - - + -
372A ASN 2.9 17.3 + - - +
373A GLU 3.9 2.9 - - - +
375A LEU* 1.3 76.1 - - - +
377A GLY* 1.3 57.8 + - - +
379A LEU* 3.0 5.9 + - + +
380A VAL* 2.9 36.3 + - + +
389A TYR* 3.4 23.1 - - + +
391A LEU* 4.2 5.6 - - + -
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Residues in contact with GLY 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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373A GLU 2.8 17.2 + - - -
374A LYS 3.6 2.2 - - - -
376A LEU* 1.3 76.4 - - - +
378A HIS* 1.3 61.1 + - - +
380A VAL* 3.5 2.1 + - - +
381A LYS* 3.0 24.3 + - - +
386A THR 4.9 0.5 - - - +
389A TYR* 4.0 16.1 + - - -
421A ARG 5.8 0.7 - - - -
422A GLY* 3.9 20.2 - - - -
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Residues in contact with HIS 378 (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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374A LYS* 2.8 19.9 + - - +
375A LEU* 3.6 14.4 - - + +
377A GLY* 1.3 75.6 - - - +
379A LEU* 1.3 73.1 + - + +
381A LYS* 3.2 10.8 + - + +
382A GLU* 3.0 51.7 + - + +
422A GLY* 5.2 0.2 - - - -
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Residues in contact with LEU 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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354A MET* 3.8 51.6 - - + +
355A LEU* 4.5 2.7 - - + +
358A ALA* 4.6 9.6 - - + -
375A LEU* 2.8 45.6 + - + +
376A LEU* 3.5 11.0 - - - +
378A HIS* 1.3 80.1 - - + +
380A VAL* 1.3 51.6 + - - +
382A GLU* 3.4 6.4 + - + +
383A LYS* 2.8 36.4 + - - +
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Residues in contact with VAL 380 (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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344A LEU* 4.1 6.5 - - + -
346A LEU* 3.9 27.8 - - + -
354A MET* 4.3 9.0 - - + -
376A LEU* 2.9 19.7 + - + +
377A GLY 3.7 3.6 - - - +
379A LEU* 1.3 72.6 - - - +
381A LYS* 1.3 62.5 + - - +
384A TYR* 2.7 39.0 + - + +
385A ASP 3.6 0.3 + - - -
386A THR* 3.8 25.4 + - + +
389A TYR* 3.7 37.7 - - + -
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Residues in contact with LYS 381 (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 GLU* 4.2 10.1 + - - +
338A LYS* 3.0 43.8 - - - +
377A GLY 3.0 18.6 + - - +
378A HIS* 3.6 12.8 - - + +
380A VAL* 1.3 77.3 - - - +
382A GLU* 1.3 63.9 + - - +
385A ASP* 3.0 32.3 + - - +
386A THR 3.5 23.8 - - - +
387A ASP* 3.2 32.0 + - - +
421A ARG* 5.9 0.4 - - - +
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Residues in contact with GLU 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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378A HIS* 3.0 41.1 + - + +
379A LEU* 3.5 10.8 - - + +
381A LYS* 1.3 81.9 - - - +
383A LYS* 1.3 62.5 + - - +
385A ASP* 4.4 2.4 + - - +
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Residues in contact with LYS 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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354A MET* 4.6 16.6 - - + +
379A LEU 2.8 21.6 + - - +
382A GLU* 1.3 75.8 - - - +
384A TYR* 1.3 97.6 + - + +
385A ASP 3.7 0.2 - - - -
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Residues in contact with TYR 384 (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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340A LEU* 3.8 22.0 - - + +
344A LEU* 3.5 42.2 - - + -
346A LEU* 4.0 22.2 - - + +
354A MET* 4.8 7.0 - - + -
380A VAL* 2.7 30.1 + - + +
383A LYS* 1.3 115.7 + - + +
385A ASP* 1.3 69.9 + - - +
386A THR* 3.3 5.7 + - + -
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Residues in contact with ASP 385 (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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338A LYS* 3.3 43.1 - - - +
339A PHE 4.9 0.7 + - - -
340A LEU* 4.1 8.3 - - + +
381A LYS* 3.0 23.5 + - - +
382A GLU 4.4 1.7 + - - +
383A LYS 3.7 1.6 - - - -
384A TYR* 1.3 79.9 - - - +
386A THR* 1.3 59.3 + - - +
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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