Contacts of the helix formed by residues 382 - 397 (chain C) in PDB entry 3ELP
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 ASP 382 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C GLU* 1.3 74.3 - - - +
383C GLU* 1.3 66.9 + - - +
384C GLU* 4.4 6.0 - - + +
385C ASP* 3.0 28.3 + - - +
386C LEU* 3.1 13.1 + - - +
15D PHE 4.7 4.5 - - - +
16D GLN* 5.2 0.9 - - - -
17D HIS* 2.8 41.8 + - - +
18D PHE* 4.1 1.7 + - - +
19D ALA* 3.0 19.4 + - - +
20D THR* 3.1 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C LYS* 6.1 1.1 - - - +
271C LYS* 4.9 15.6 + - - +
272C ASN* 3.6 20.3 + - - +
275C ALA* 3.2 34.6 - - + +
381C GLU 3.3 5.1 + - - -
382C ASP* 1.3 69.4 + - - +
384C GLU* 1.3 65.8 + - - +
386C LEU* 3.1 8.9 + - - +
387C LEU* 2.9 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C ASP* 4.7 5.2 - - + +
383C GLU* 1.3 81.6 - - - +
385C ASP* 1.3 75.8 + - - +
387C LEU* 3.2 8.9 + - - +
388C GLU* 3.0 50.5 + - + +
16D GLN* 2.9 41.6 + - - +
17D HIS* 4.0 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C LEU* 4.5 9.9 - - + +
382C ASP* 3.0 12.1 + - - +
384C GLU* 1.3 85.6 - - - +
386C LEU* 1.3 59.3 + - + +
388C GLU* 3.5 11.4 + - - +
389C ASP* 3.0 29.1 + - - +
17D HIS* 3.0 46.6 + - - -
20D THR* 2.8 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ASN* 4.1 19.7 - - + +
276C VAL* 4.5 9.6 - - + -
334C LEU* 3.3 32.3 - - + -
335C PHE* 3.9 18.6 - - + -
346C SER* 3.7 24.2 - - - +
378C VAL* 3.8 21.8 - - + -
381C GLU* 3.9 14.8 - - + +
382C ASP 3.1 11.4 + - - +
383C GLU* 3.1 8.0 + - - +
385C ASP* 1.3 74.2 - - - +
387C LEU* 1.3 67.6 + - - +
389C ASP* 3.2 4.1 + - - +
390C LEU* 3.1 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ALA* 4.1 6.5 - - + +
276C VAL* 4.0 29.2 - - + +
279C PHE* 3.7 50.5 - - + -
383C GLU* 2.9 38.1 + - + +
384C GLU* 3.5 10.5 - - - +
386C LEU* 1.3 77.4 - - - +
388C GLU* 1.3 59.4 + - + +
390C LEU* 3.7 2.0 - - + +
391C ASP* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C GLU* 3.0 39.6 + - + +
385C ASP* 3.9 13.4 - - - +
387C LEU* 1.3 74.6 - - + +
389C ASP* 1.3 60.5 + - - +
391C ASP* 3.9 7.4 - - - +
392C GLN* 3.0 30.1 + - - +
17D HIS* 5.4 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C LEU* 3.3 9.0 - - - +
333C LYS* 2.8 26.0 + - - +
334C LEU* 3.0 23.1 + - + -
335C PHE* 3.0 36.4 + - + -
385C ASP 3.0 17.9 + - - +
386C LEU 3.2 5.3 + - - +
388C GLU* 1.3 76.8 - - - +
390C LEU* 1.3 62.4 + - - +
392C GLN* 3.0 21.4 + - - +
393C ALA* 3.0 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C VAL* 3.8 33.4 - - + -
279C PHE* 4.2 13.5 - - + -
280C LEU* 4.2 18.2 - - + -
328C PHE* 3.4 30.7 - - + -
332C LEU* 3.9 5.8 - - + -
335C PHE* 3.6 28.9 - - + -
376C LEU* 4.0 11.0 - - + -
386C LEU 3.1 19.4 + - - +
387C LEU* 3.7 4.7 - - - +
389C ASP* 1.3 77.6 - - - +
391C ASP* 1.3 52.4 + - - +
393C ALA* 3.1 3.3 + - - +
394C LEU* 2.8 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C PHE* 3.4 20.5 - - + -
283C ASN* 3.6 17.3 + - - -
387C LEU 3.0 18.6 + - - +
388C GLU* 3.9 7.2 - - - +
390C LEU* 1.3 75.5 - - - +
392C GLN* 1.3 57.9 + - - +
394C LEU* 3.8 4.5 - - - +
395C LYS* 2.9 67.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ASN* 3.0 46.2 + - - +
333C LYS* 3.4 30.2 - - - +
388C GLU 3.0 19.4 + - - +
389C ASP* 3.0 26.1 - - - +
391C ASP* 1.3 79.2 + - - +
393C ALA* 1.3 56.0 + - - +
395C LYS* 3.5 8.2 + - - +
396C ALA* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C PHE* 3.3 47.4 - - + +
331C ASN* 3.8 3.6 - - - -
332C LEU* 3.8 17.3 - - + +
389C ASP 3.0 13.7 + - - +
390C LEU 3.5 2.2 - - - +
392C GLN* 1.3 83.6 - - - +
394C LEU* 1.3 63.8 + - - +
396C ALA* 3.4 2.9 + - - +
397C ALA* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C PHE* 4.4 2.2 - - + -
280C LEU* 3.8 24.0 - - + -
283C ASN* 3.5 30.5 - - - +
285C TRP* 3.9 29.8 - - + +
286C VAL* 4.4 5.2 - - + -
316C PHE* 4.7 5.8 - - + -
318C ILE* 3.9 28.9 - - + -
328C PHE* 3.9 13.2 - - + -
390C LEU* 2.8 26.2 + - + +
391C ASP* 3.8 3.8 - - - +
393C ALA* 1.3 70.2 - - - +
395C LYS* 1.3 66.6 + - - +
397C ALA* 3.0 12.4 + - - -
398C HIS* 3.2 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C TRP* 4.3 16.8 - - + +
391C ASP* 2.9 51.7 + - - +
392C GLN* 3.7 7.6 - - - +
394C LEU* 1.3 76.4 - - - +
396C ALA* 1.3 60.3 + - - +
398C HIS 2.7 27.9 - - - +
399C PRO* 4.5 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C ILE* 3.6 9.8 - - - +
331C ASN* 3.0 36.6 - - - +
392C GLN* 3.0 20.5 + - - +
393C ALA 3.5 2.2 - - - +
395C LYS* 1.3 72.9 - - - +
397C ALA* 1.3 57.7 + - - +
398C HIS 3.0 8.8 + - - -
399C PRO* 4.2 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C ILE* 4.4 3.1 - - + -
324C HIS* 3.3 40.0 - - - +
327C ILE* 3.3 20.7 - - + +
328C PHE* 3.7 8.3 - - + +
393C ALA 3.1 14.2 + - - +
394C LEU 3.0 7.8 + - - +
396C ALA* 1.3 75.5 - - - +
398C HIS* 1.3 77.3 + - + +
399C PRO* 4.0 4.9 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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