Contacts of the helix formed by residues 348 - 365 (chain D) in PDB entry 6S6A
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 ARG 348 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D GLU 5.1 3.6 - - - +
345D SER* 3.2 15.3 + - - +
346D PHE 3.1 3.6 - - - -
347D GLU* 1.3 73.7 - - + +
349D LYS* 1.3 56.8 + - - +
350D GLY 3.6 2.2 - - - +
351D LEU* 3.3 35.1 - - + +
352D ILE* 3.1 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 349 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D MET* 4.4 13.5 - - - +
317D ILE* 4.7 6.7 - - - -
327D TYR* 2.8 25.8 + - - +
329D LYS* 5.1 1.0 - - - +
346D PHE* 3.4 48.9 - - + +
347D GLU 2.9 10.5 + - - +
348D ARG* 1.3 69.3 - - - +
350D GLY* 1.3 69.1 + - - +
351D LEU 3.1 1.1 - - - -
352D ILE* 4.0 12.1 - - + +
353D ASP* 2.7 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D ARG 3.6 0.2 - - - -
349D LYS* 1.3 77.9 - - - +
351D LEU* 1.3 61.6 + - - +
353D ASP* 4.7 1.2 - - - +
354D TYR* 3.4 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 351 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D ASN 3.6 24.0 - - - +
254D SER* 4.3 11.0 - - - -
255D GLY 5.3 1.6 - - - +
348D ARG* 3.3 43.4 + - + +
350D GLY* 1.3 72.2 - - - +
352D ILE* 1.3 55.9 - - + +
354D TYR* 2.7 31.0 + - + +
355D ASN* 2.5 37.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 352 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D PHE* 3.3 23.1 - - + -
254D SER* 4.1 20.6 - - - -
255D GLY 5.2 2.2 - - - +
256D ILE* 4.6 8.7 - - + -
327D TYR* 3.9 27.8 - - + +
341D LEU* 4.1 13.2 - - + -
345D SER 3.5 20.9 - - - +
346D PHE* 3.9 20.0 - - + +
348D ARG* 3.1 24.7 + - + +
349D LYS* 3.3 9.3 + - + -
351D LEU* 1.3 80.8 - - + +
353D ASP* 1.3 57.3 + - - +
355D ASN* 3.8 5.5 + - - +
356D PHE* 3.2 21.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 353 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D TYR* 3.6 4.4 + - - -
329D LYS* 2.6 40.4 + - - +
349D LYS* 2.7 46.7 + - - +
350D GLY 4.7 0.9 - - - +
352D ILE* 1.3 73.4 - - - +
354D TYR* 1.3 68.1 + - - +
356D PHE* 3.6 7.1 - - - +
357D HIS* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D GLY 3.4 16.8 + - - +
351D LEU* 2.7 22.6 + - + +
353D ASP* 1.3 78.9 - - - +
355D ASN* 1.3 63.6 - - - +
357D HIS* 3.1 17.1 + - - +
358D CYS* 3.5 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 355 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ILE* 6.5 0.4 - - + -
250D PHE* 3.7 20.4 - - + -
253D ASN* 3.2 38.0 + - + +
254D SER* 3.2 20.1 + - - +
351D LEU* 2.5 33.5 + - - +
352D ILE 4.3 0.4 - - - -
354D TYR* 1.3 73.1 - - - +
356D PHE* 1.3 51.5 + - - +
358D CYS* 3.0 14.1 + - - +
359D PHE* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 356 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D PHE* 3.2 27.6 - + + -
329D LYS* 3.5 52.0 - - + -
330D GLU 3.4 23.3 - - - -
331D VAL* 4.7 10.1 - - + -
337D LEU* 4.3 16.4 - - + -
352D ILE* 3.2 16.1 + - + +
353D ASP* 3.6 10.5 - - - +
354D TYR 3.2 0.4 - - - -
355D ASN* 1.3 75.0 - - - +
357D HIS* 1.3 59.9 + - - +
359D PHE* 3.0 10.6 + + + +
360D ARG* 2.7 63.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 357 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D ASP 3.1 14.0 + - - +
354D TYR* 3.3 12.1 - - - +
356D PHE* 1.3 77.6 - - + +
358D CYS* 1.3 60.5 + - - +
360D ARG* 3.8 11.8 + - - +
361D LYS* 3.3 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 358 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ILE* 6.5 1.3 - - + -
354D TYR 3.5 4.2 + - - +
355D ASN* 3.0 17.4 + - - +
357D HIS* 1.3 74.5 - - - +
359D PHE* 1.3 63.1 + - - +
360D ARG 3.0 1.0 + - - -
361D LYS* 3.1 8.3 + - - +
362D ALA* 2.9 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 359 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D LEU 5.2 0.4 - - - -
246D LEU* 3.1 38.7 - - + +
247D LEU* 3.4 35.2 - - + -
249D ILE* 5.2 4.8 - - + +
250D PHE* 3.1 33.7 - + + -
261D LEU* 4.9 5.4 - - + -
331D VAL* 5.2 5.4 - - + -
337D LEU* 4.2 13.5 - - + -
355D ASN 2.9 15.0 + - - +
356D PHE* 3.3 24.0 - + - +
358D CYS* 1.3 71.5 - - - +
360D ARG* 1.3 57.6 + - - +
362D ALA* 3.3 14.8 - - - +
363D ILE* 3.0 46.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 360 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D LYS* 5.2 8.7 + - - +
330D GLU* 3.8 18.0 + - - -
331D VAL* 3.2 41.2 + - + +
356D PHE* 2.7 46.7 + - + +
357D HIS* 4.0 12.0 + - - +
359D PHE* 1.3 75.2 - - - +
361D LYS* 1.3 64.0 - - - +
362D ALA 3.1 1.3 - - - -
363D ILE* 3.1 18.3 + - - +
364D HIS* 3.2 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 361 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357D HIS* 3.3 30.9 + - + +
358D CYS* 3.1 6.1 + - - +
360D ARG* 1.3 81.3 - - - +
362D ALA* 1.3 56.3 + - - +
364D HIS* 3.7 8.5 + - + +
365D GLU* 3.1 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 362 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D LEU* 3.4 28.7 - - + +
358D CYS* 2.9 15.3 + - - +
359D PHE* 3.3 14.1 - - - +
360D ARG 3.1 0.4 - - - -
361D LYS* 1.3 76.4 - - - +
363D ILE* 1.3 56.3 + - - +
365D GLU* 3.9 14.0 - - - +
366D VAL* 3.2 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 363 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D LEU* 4.7 20.9 - - + -
246D LEU* 4.9 8.5 - - + -
261D LEU* 4.5 13.0 - - + -
331D VAL* 4.1 20.6 - - + -
332D THR* 5.2 5.9 - - + +
335D LEU* 4.8 15.7 - - + -
359D PHE* 3.0 50.3 - - + +
360D ARG 3.1 5.9 + - - +
362D ALA* 1.3 78.6 - - + +
364D HIS* 1.3 62.7 + - - +
365D GLU 3.1 1.3 - - - -
366D VAL* 3.3 15.2 + - + +
367D PHE* 3.3 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 364 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D VAL 3.7 1.5 + - - -
332D THR* 3.7 31.8 - - + +
360D ARG* 3.2 47.5 + - - +
361D LYS* 3.7 9.8 + - + +
363D ILE* 1.3 74.6 - - - +
365D GLU* 1.3 56.4 + - - +
367D PHE* 3.2 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 365 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361D LYS* 3.1 38.6 + - + +
362D ALA* 3.9 13.0 - - - +
364D HIS* 1.3 71.4 - - - +
366D VAL* 1.3 55.7 + - + +
367D PHE* 2.8 23.1 + - - +
----------------------------------------------------------
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