Contacts of the helix formed by residues 365 - 378 (chain C) in PDB entry 5G04
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 LEU 365 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP 4.4 12.0 + - - +
53A GLY* 5.5 4.9 - - - -
362C PRO 5.2 4.0 - - - +
363C ARG 3.6 6.9 + - - +
364C TYR* 1.3 73.4 - - - +
366C GLY* 1.3 67.6 + - - +
367C ALA 2.9 1.2 + - - -
368C TRP* 3.2 33.7 + - + +
369C THR* 3.9 7.4 + - - +
391C ALA* 3.7 11.7 - - - +
394C VAL* 3.6 30.5 - - + -
395C ASN* 3.4 42.4 - - + +
398C ASP* 3.8 22.2 - - + +
400C ARG* 4.3 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 366 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP 5.1 3.2 + - - -
364C TYR* 3.1 14.3 + - - -
365C LEU* 1.3 75.4 - - - +
367C ALA* 1.3 56.0 + - - +
369C THR* 3.0 8.7 - - - +
370C LEU* 2.9 34.0 + - - +
400C ARG* 3.4 21.8 - - - +
79R TYR* 3.9 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 367 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C CYS* 5.2 0.4 - - - -
354C PHE* 4.0 23.9 - - + +
357C ALA* 5.0 2.7 - - + -
358C LEU* 3.4 31.1 - - + +
364C TYR* 3.3 19.0 + - + +
365C LEU 2.9 1.6 + - - -
366C GLY* 1.3 73.1 - - - +
368C TRP* 1.3 55.7 + - - +
370C LEU* 3.7 9.8 - - - +
371C MET* 2.7 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 368 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 3.4 28.2 - - + +
355C GLN* 6.2 2.5 - - + -
358C LEU* 3.0 36.8 - - + +
362C PRO 4.6 2.0 + - - -
365C LEU* 3.2 29.8 + - + +
367C ALA* 1.3 76.6 - - - +
369C THR* 1.3 62.8 + - - +
371C MET* 3.3 30.3 - - + +
372C GLY 3.2 16.5 + - - -
387C ALA* 3.8 22.9 - - - +
390C HIS* 3.2 49.4 + + + -
391C ALA* 3.6 24.5 - - + +
394C VAL* 4.2 8.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 369 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C LEU 3.9 1.5 + - - +
366C GLY 3.0 22.7 - - - +
368C TRP* 1.3 74.3 - - - +
370C LEU* 1.3 69.0 + - - +
372C GLY* 3.0 10.9 + - - -
373C HIS* 3.3 30.5 + - - -
388C TYR* 3.7 9.8 - - - -
391C ALA* 4.2 3.2 - - - +
398C ASP* 4.2 13.2 - - - +
400C ARG* 3.5 33.6 - - - +
401C ALA* 3.9 24.4 + - - -
79R TYR* 3.5 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 370 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ASP* 5.3 0.9 - - - +
305C ASN* 4.4 9.2 - - - +
335C CYS* 4.2 9.9 - - - -
339C ASN* 5.0 1.1 - - - +
354C PHE* 3.6 35.7 - - + -
364C TYR* 5.6 0.4 - - + -
366C GLY* 2.9 19.3 + - - +
367C ALA 3.7 3.8 - - - +
369C THR* 1.3 72.8 - - - +
371C MET* 1.3 55.4 + - - +
373C HIS* 2.9 31.7 + - - +
374C GLU* 3.2 14.6 + - - +
78R ARG* 3.4 36.1 - - - +
79R TYR* 3.0 50.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 371 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C ALA* 4.1 16.8 - - + +
354C PHE* 4.6 7.1 - - + +
355C GLN* 3.4 46.2 - - + +
358C LEU* 4.8 2.7 - - - -
367C ALA 2.7 22.8 + - - +
368C TRP* 3.3 35.9 - - + +
370C LEU* 1.3 69.9 - - - +
372C GLY* 1.3 60.1 + - - +
374C GLU* 3.2 9.6 + - - +
375C TYR* 2.8 69.7 + - + +
387C ALA* 4.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 372 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C TRP 3.2 5.2 + - - -
369C THR 3.0 9.3 + - - -
371C MET* 1.3 77.0 - - - +
373C HIS* 1.3 51.6 + - - +
375C TYR* 2.9 6.6 + - - +
376C MET* 2.7 32.7 + - - +
384C ALA* 3.8 3.8 - - - +
387C ALA* 3.7 19.0 - - - +
388C TYR* 3.5 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C THR* 3.3 27.8 + - - -
370C LEU* 2.9 21.1 + - - +
372C GLY* 1.3 71.6 - - - -
374C GLU* 1.3 66.7 + - - +
376C MET* 3.0 6.9 - - - +
377C GLU* 2.8 40.9 + - - +
388C TYR* 3.0 39.2 - + - -
404C GLY* 4.7 6.0 - - - -
78R ARG* 4.6 5.7 + - - +
79R TYR* 3.3 46.0 + + + -
81R PRO* 5.6 1.5 - - + +
131R LEU* 3.5 18.6 - - + -
133R LEU* 4.8 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 374 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C TYR* 5.3 1.6 + - - -
342C SER* 3.0 33.9 + - - -
347C HIS* 3.8 12.5 + - + +
350C ALA* 4.5 0.9 - - + -
351C ALA* 3.8 23.8 - - + +
354C PHE* 3.2 32.8 - - + -
370C LEU 3.2 12.5 + - - +
371C MET 3.7 4.0 - - - +
372C GLY 3.1 1.2 - - - -
373C HIS* 1.3 89.0 - - - +
375C TYR* 1.3 62.8 - - - +
377C GLU* 3.1 23.3 + - - +
378C MET* 3.3 15.8 + - - +
78R ARG* 3.4 17.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 375 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C ALA* 4.6 10.7 - - + +
355C GLN* 4.2 6.8 + - - -
371C MET* 2.8 56.8 + - + +
372C GLY 3.4 5.8 - - - +
374C GLU* 1.3 72.1 - - - +
376C MET* 1.3 64.8 + - - +
378C MET* 3.5 27.9 - - + +
379C LYS 3.3 3.6 + - - -
380C ASN* 3.2 38.7 + - - +
383C ALA* 3.5 29.6 - - + -
384C ALA 3.8 6.5 - - - +
387C ALA* 3.8 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 376 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C GLY 2.7 14.4 + - - +
373C HIS* 3.0 19.3 - - - +
375C TYR* 1.3 74.0 - - - +
377C GLU* 1.3 53.8 + - - +
379C LYS* 3.0 20.8 + - - +
380C ASN 4.9 1.3 - - - -
381C THR* 3.9 11.4 - - - +
384C ALA* 4.0 12.5 - - - +
388C TYR* 4.0 4.3 - - - +
408C THR* 3.5 38.6 - - - +
411C ILE* 3.8 36.8 - - + -
95R LEU* 4.2 8.1 - - + -
130R ILE* 2.9 29.2 - - + +
131R LEU* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C TYR* 5.3 5.4 + - - -
347C HIS* 3.4 43.1 - - + +
373C HIS* 2.8 36.8 + - - +
374C GLU* 3.1 7.6 + - - +
376C MET* 1.3 72.5 - - - +
378C MET* 1.3 57.5 + - - +
379C LYS* 3.0 24.6 + - - +
129R LYS* 3.4 33.4 + - - +
130R ILE* 3.7 3.4 - - - -
131R LEU* 2.9 46.4 + - - +
133R LEU* 5.5 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C HIS* 4.3 10.9 - - + +
348C GLU* 3.5 58.6 - - + +
351C ALA* 5.7 1.3 - - + -
374C GLU 3.3 16.4 + - - +
375C TYR* 3.5 35.0 - - + +
377C GLU* 1.3 75.3 - - - +
379C LYS* 1.3 62.4 + - - +
380C ASN* 3.2 27.2 + - - +
----------------------------------------------------------
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