Contacts of the helix formed by residues 291 - 302 (chain D) in PDB entry 6VSU
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 291 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D LEU* 3.5 6.6 - - - +
278D PHE* 3.4 29.7 - - - -
289D GLY 4.0 0.8 + - - -
290D LEU* 1.3 74.9 - - - +
292D PHE* 1.3 63.6 + - - +
293D ARG* 3.5 8.4 + - - +
294D ASP* 2.8 55.6 + - - +
295D VAL* 3.2 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D LEU* 3.6 18.0 - - + +
278D PHE* 4.2 17.8 - - + -
291D SER* 1.3 73.0 - - - +
293D ARG* 1.3 62.3 + - - +
295D VAL* 3.1 5.7 + - - +
296D LEU* 3.0 55.2 + - + +
328D VAL* 3.5 44.2 - - + -
331D LYS* 3.6 39.9 - - + -
332D LEU* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D GLU* 2.7 43.6 + - - -
291D SER* 3.2 7.5 + - - +
292D PHE* 1.3 78.0 - - - +
294D ASP* 1.3 67.2 + - - +
296D LEU* 3.2 23.6 + - - +
297D ASN* 2.8 48.2 + - - +
300D HIS* 4.3 5.1 + - - -
331D LYS* 4.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D MET* 5.8 0.2 - - - +
246D PHE* 4.1 7.7 - - + -
250D ARG* 2.8 41.5 + - - +
254D GLU* 4.6 0.9 - - - +
289D GLY 4.9 0.5 - - - +
290D LEU* 3.7 22.0 - - + +
291D SER* 2.8 47.8 + - - +
293D ARG* 1.3 77.1 - - - +
295D VAL* 1.3 63.0 + - - +
297D ASN* 3.2 10.7 + - - +
298D ILE* 3.2 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D LEU* 4.2 17.5 - - + -
269D ILE* 4.6 1.3 - - + -
273D CYS* 3.9 18.4 - - - -
274D LEU* 3.7 19.1 - - + -
290D LEU* 3.9 16.6 - - + -
291D SER 3.2 11.6 + - - +
292D PHE* 3.1 9.6 + - - +
294D ASP* 1.3 73.0 - - - +
296D LEU* 1.3 57.4 + - - +
298D ILE* 3.1 10.3 + - - +
299D LEU* 2.8 38.4 + - + +
332D LEU* 3.8 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D GLU* 3.4 34.8 - - - +
292D PHE* 3.0 48.4 + - + +
293D ARG* 3.8 22.2 - - - +
295D VAL* 1.3 74.6 - - - +
297D ASN* 1.3 62.4 + - - +
299D LEU* 4.3 13.7 - - + +
300D HIS* 2.8 47.2 + - + +
331D LYS* 4.2 4.3 - - - -
332D LEU* 4.8 4.9 - - + -
335D GLU* 3.9 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ARG* 4.2 7.7 - - - +
254D GLU* 3.2 38.1 + - - +
293D ARG* 2.8 42.6 + - - +
294D ASP* 3.5 5.3 + - - +
296D LEU* 1.3 76.4 - - - +
298D ILE* 1.3 61.3 + - - +
300D HIS* 4.9 2.5 + - - -
301D ASN* 2.7 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D LEU* 4.2 26.9 - - + -
184D LEU* 4.5 13.2 - - + -
220D VAL* 4.2 24.0 - - + -
246D PHE* 4.9 6.3 - - + -
253D LEU* 3.5 39.5 - - + +
254D GLU* 4.5 6.5 - - + +
256D LEU* 4.3 8.5 - - + -
290D LEU* 4.7 11.9 - - + -
294D ASP 3.2 16.7 + - - +
295D VAL* 3.1 9.3 + - - +
297D ASN* 1.3 74.9 - - - +
299D LEU* 1.3 67.0 - - + +
301D ASN* 3.5 1.2 + - - +
302D LEU* 3.1 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D LEU* 4.4 7.6 - - + -
184D LEU* 4.3 12.6 - - + -
267D ILE* 4.1 33.7 - - + -
269D ILE* 3.8 21.5 - - + -
295D VAL* 2.8 33.2 + - + +
296D LEU* 4.2 16.4 - - + +
298D ILE* 1.3 74.9 - - + +
300D HIS* 1.3 63.4 + - + +
301D ASN 3.4 0.2 + - - -
302D LEU* 3.4 3.9 + - + -
332D LEU* 4.6 6.1 - - + +
335D GLU* 5.2 7.0 - - + +
336D LEU* 4.2 20.4 - - + +
339D LYS* 2.8 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D GLU* 3.4 31.1 - - + +
104D GLU* 3.9 39.3 + - + +
293D ARG* 4.3 3.8 + - - -
296D LEU* 2.8 42.0 + - + +
297D ASN* 4.5 3.7 + - - +
299D LEU* 1.3 76.7 - - + +
301D ASN* 1.3 63.8 + - - +
302D LEU 4.5 0.3 - - - +
335D GLU* 2.8 36.8 + - + +
339D LYS* 3.8 9.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D GLU* 2.9 35.0 + - - +
255D ASN* 4.6 4.8 - - - +
256D LEU 3.8 8.4 + - - +
297D ASN* 2.7 34.2 + - - +
298D ILE 4.4 0.4 - - - +
299D LEU 3.3 0.4 - - - -
300D HIS* 1.3 80.6 - - - +
302D LEU* 1.3 64.6 + - - +
303D GLN* 3.4 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D LEU* 4.2 15.3 - - + -
256D LEU* 3.5 35.4 - - + +
258D LEU* 4.1 17.7 - - + -
265D VAL* 4.8 2.7 - - + -
267D ILE* 3.7 31.9 - - + -
298D ILE* 3.1 16.8 + - + +
299D LEU* 3.6 9.0 - - + +
300D HIS 3.4 1.1 - - - +
301D ASN* 1.3 76.9 - - - +
303D GLN* 1.3 70.9 + - - +
304D ALA* 3.7 20.9 + - + -
339D LYS* 2.8 30.5 + - + -
----------------------------------------------------------
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