Contacts of the helix formed by residues 376 - 394 (chain C) in PDB entry 5AO4
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 HIS 376 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C VAL* 3.4 28.9 - - + +
157C PHE* 4.5 8.9 - + + -
371C ARG 5.3 0.7 - - - -
372C ARG 3.7 16.6 - - - +
373C ALA* 3.5 16.7 + - - +
374C TYR 3.3 0.8 - - - -
375C GLN* 1.3 75.7 - - - +
377C LYS* 1.3 70.0 + - + +
378C VAL* 3.3 26.8 + - + +
379C GLY* 3.2 26.3 + - - +
380C ASN* 2.5 32.5 + - - +
551C ARG* 2.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C GLN 3.8 2.0 + - - -
376C HIS* 1.3 79.4 - - + +
378C VAL* 1.3 66.8 + - + +
381C ILE* 3.2 29.5 + - + +
456C TYR* 4.6 24.0 - - + -
551C ARG* 3.4 21.2 + - - +
553C TYR* 4.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C VAL* 3.8 15.7 - - + -
376C HIS* 3.3 20.4 + - + +
377C LYS* 1.3 79.3 - - + +
379C GLY* 1.3 65.3 + - - +
381C ILE* 3.0 11.7 + - + +
382C ILE* 3.0 27.8 + - + +
451C ARG* 4.6 7.0 - - - +
453C LEU* 3.4 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C GLY* 4.6 12.1 - - - -
153C GLY* 5.4 2.9 - - - -
156C VAL* 3.8 17.3 - - - -
373C ALA 5.7 0.7 - - - -
376C HIS* 3.2 20.3 + - - -
378C VAL* 1.3 78.6 - - - +
380C ASN* 1.3 61.9 + - - +
382C ILE* 3.4 4.3 + - - +
383C ASP* 3.2 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 380 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C TYR 3.2 17.6 + - - +
375C GLN* 3.4 3.8 - - - +
376C HIS 2.5 39.4 + - - +
379C GLY* 1.3 73.9 - - - +
381C ILE* 1.3 63.5 + - - +
383C ASP* 3.6 15.4 + - - +
384C THR* 3.5 22.3 + - - +
501C ASP* 3.7 11.9 - - - +
503C ILE* 3.9 17.7 - - + +
551C ARG* 2.9 24.9 - - - +
553C TYR* 3.4 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LYS* 3.2 21.8 + - + +
378C VAL* 3.0 16.9 + - + +
380C ASN* 1.3 76.0 - - - +
382C ILE* 1.3 64.2 + - - +
384C THR* 2.6 19.2 + - - -
385C MET* 3.1 13.3 + - - +
453C LEU* 4.0 13.9 - - + -
454C PHE* 3.6 49.1 - - + +
456C TYR* 4.1 24.5 - - + +
553C TYR* 3.4 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C GLY* 4.6 10.8 - - - +
155C TYR* 3.7 43.7 - - + -
156C VAL* 4.1 9.0 - - + -
378C VAL* 3.0 32.0 + - + +
379C GLY 3.4 5.1 + - - +
381C ILE* 1.3 76.1 - - - +
383C ASP* 1.3 61.8 + - - +
385C MET* 3.4 7.5 - - - +
386C ILE* 3.0 25.7 + - + +
448C ILE* 4.9 17.3 - - + -
451C ARG* 4.1 13.9 - - - +
453C LEU* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C LEU 5.2 2.4 - - - +
152C GLY* 3.6 23.9 + - - -
216C MET* 3.4 39.8 + - + +
220C ARG* 5.8 4.5 - - + -
379C GLY 3.2 15.2 + - - +
380C ASN* 3.7 20.2 - - - +
381C ILE 3.2 0.6 - - - -
382C ILE* 1.3 78.2 - - - +
384C THR* 1.3 54.5 + - + +
386C ILE* 4.7 0.2 - - - -
387C THR* 2.6 36.6 + - - -
501C ASP* 5.4 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C ARG* 5.8 5.6 - - + +
380C ASN 3.5 11.8 + - - +
381C ILE 2.6 22.5 + - - -
383C ASP* 1.3 76.5 - - + +
385C MET* 1.3 60.3 + - - +
387C THR* 3.5 9.2 - - + +
388C ASP* 2.9 30.1 + - - +
454C PHE* 4.9 3.5 - - - -
499C ILE* 3.4 41.1 - - + +
501C ASP* 3.9 22.0 - - + +
553C TYR* 3.6 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C ILE* 3.1 21.9 + - - +
382C ILE* 3.2 9.8 + - - +
384C THR* 1.3 77.1 - - - +
386C ILE* 1.3 62.8 + - - +
388C ASP* 3.3 4.1 + - - +
389C ALA* 3.1 22.3 + - - +
444C ILE* 4.2 10.2 - - + +
447C GLN* 3.2 40.8 - - + +
448C ILE* 3.4 37.2 - - + +
452C ASN 4.0 6.3 - - - +
453C LEU* 3.6 31.4 - - + -
454C PHE* 3.2 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C PHE* 5.4 5.4 - - + -
216C MET* 3.6 24.2 - - + -
382C ILE* 3.0 18.3 + - + +
383C ASP* 4.7 0.4 - - - -
385C MET* 1.3 76.0 - - - +
387C THR* 1.3 63.0 + - - +
389C ALA* 3.3 5.4 + - - +
390C PHE* 3.0 38.8 + - + -
427C PHE* 5.2 13.2 - - + -
445C LEU* 5.1 7.0 - - - -
448C ILE* 4.7 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C MET* 3.3 20.3 + - - +
220C ARG* 3.1 29.8 + - - +
221C PHE* 3.7 19.5 - - + +
224C LEU* 5.3 0.9 - - + -
383C ASP 2.6 23.8 + - - -
384C THR* 3.5 11.1 - - + -
385C MET 3.2 0.2 - - - -
386C ILE* 1.3 77.4 - - - +
388C ASP* 1.3 58.1 + - - +
390C PHE* 3.3 8.7 + - - +
391C LEU* 3.0 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C THR 2.9 19.0 + - - +
385C MET* 3.3 6.3 + - - +
387C THR* 1.3 76.5 - - - +
389C ALA* 1.3 57.3 + - - +
391C LEU* 3.3 16.0 + - - +
392C LYS* 2.9 29.7 + - - +
444C ILE* 4.4 18.0 - - + +
454C PHE* 4.4 17.2 - - + -
499C ILE* 5.0 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C MET 3.1 10.7 + - - +
386C ILE 3.7 6.7 - - - +
388C ASP* 1.3 76.3 - - - +
390C PHE* 1.3 66.3 + - + +
392C LYS* 3.1 21.8 + - - +
393C ALA* 3.2 10.0 + - - +
430C ILE* 5.0 3.2 - - + +
441C ALA* 4.0 20.1 - - + +
444C ILE* 4.5 10.7 - - + +
445C LEU* 3.5 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C PRO* 4.1 11.7 - - + -
213C PHE* 4.1 17.9 - + - -
216C MET* 3.8 25.8 - - + -
217C PHE* 5.0 4.7 - + - -
221C PHE* 3.6 23.8 - + + -
386C ILE* 3.0 20.8 + - + +
387C THR* 3.4 9.4 - - - +
389C ALA* 1.3 78.9 - - + +
391C LEU* 1.3 63.6 + - - +
393C ALA* 3.4 2.6 + - - -
394C ASP* 3.2 23.2 + - - +
409C ILE* 4.2 24.0 - - + +
426C ILE* 3.4 39.3 - - + -
427C PHE* 4.3 20.6 - + + -
430C ILE* 4.7 9.2 - - + -
445C LEU* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C PHE* 3.4 21.3 - - + -
224C LEU* 3.9 20.2 - - + +
225C ALA* 3.6 33.0 - - + +
387C THR* 3.0 25.5 + - + +
388C ASP* 3.3 19.0 + - + +
390C PHE* 1.3 75.7 - - - +
392C LYS* 1.3 60.6 + - - +
394C ASP* 3.5 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C ASP* 2.9 17.1 + - - +
389C ALA* 3.1 13.9 - - - +
391C LEU* 1.3 79.2 - - - +
393C ALA* 1.3 55.4 + - - +
394C ASP 5.5 0.2 - - - -
437C LYS 5.0 6.8 - - - +
438C LEU* 5.1 0.8 - - - +
440C ASP* 3.5 22.1 - - + +
441C ALA* 3.3 33.8 - - + +
444C ILE* 3.5 24.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
389C ALA 3.2 9.4 + - - +
390C PHE 3.4 3.3 + - - +
392C LYS* 1.3 77.3 - - - +
394C ASP* 1.3 68.9 + - - +
409C ILE* 4.9 7.3 - - + +
430C ILE* 3.5 32.3 - - + -
438C LEU* 3.5 27.5 - - + +
441C ALA* 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C PHE* 4.9 2.2 - - + -
225C ALA* 4.3 9.2 - - - +
390C PHE 3.2 17.4 + - - +
391C LEU* 3.5 15.9 + - + +
392C LYS 3.4 2.2 - - - -
393C ALA* 1.3 87.4 - - - +
408C ARG* 3.3 27.3 - - - +
409C ILE* 3.6 9.9 + - + -
410C SER* 2.6 43.9 + - - -
----------------------------------------------------------
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