Contacts of the helix formed by residues 278 - 296 (chain D) in PDB entry 6AH0
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 278 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D TYR 3.2 4.7 - - - +
277D ASP* 1.3 77.6 - - - +
279D ALA* 1.3 65.6 + - - +
280D ILE 3.4 2.2 - - - -
281D VAL* 3.5 4.4 + - - +
282D SER* 2.9 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D ASP 3.3 5.6 + - - -
278D ASP* 1.3 71.4 - - - +
280D ILE* 1.3 62.1 + - - +
282D SER* 4.1 0.4 - - - +
283D GLN* 3.2 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D ASP 3.4 0.2 - - - -
279D ALA* 1.3 75.3 - - - +
281D VAL* 1.3 57.4 + - - +
283D GLN* 3.2 2.3 + - - -
284D LYS* 2.9 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D TYR* 6.2 0.7 - - - -
278D ASP* 3.5 6.6 + - - +
279D ALA 3.4 0.4 - - - -
280D ILE* 1.3 73.7 - - - +
282D SER* 1.3 52.6 + - - +
284D LYS* 4.5 1.1 - - - +
285D LYS* 2.3 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D GLN* 5.1 8.0 - - - +
272D LEU* 5.5 4.3 - - - +
273D SER* 5.5 7.6 - - - +
276D TYR* 4.2 15.5 + - - +
278D ASP 2.9 17.5 + - - -
279D ALA 4.2 0.4 - - - -
281D VAL* 1.3 75.3 - - - +
283D GLN* 1.3 52.5 - - - +
285D LYS* 4.4 1.1 - - - +
286D ALA* 2.2 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D GLN* 6.5 0.2 - - - +
279D ALA 3.2 14.8 + - - -
280D ILE* 3.7 2.5 - - - +
281D VAL 3.2 0.6 - - - -
282D SER* 1.3 74.4 - - - +
284D LYS* 1.3 56.8 + - - +
286D ALA* 3.3 1.1 - - - +
287D ASP* 2.3 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D ILE 2.9 13.4 + - - -
281D VAL* 3.7 1.6 - - - +
283D GLN* 1.3 75.7 - - - +
285D LYS* 1.3 58.8 + - - +
287D ASP* 3.9 1.3 - - - +
288D GLU* 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D VAL 2.3 28.3 + - - -
282D SER* 3.6 2.2 - - - +
284D LYS* 1.3 69.5 - - - +
286D ALA* 1.3 55.7 + - - +
288D GLU* 3.2 2.3 + - - +
289D VAL* 2.9 24.8 + - - -
309D LEU 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 286 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D LEU 5.6 2.2 - - - -
269D GLN* 5.0 14.6 - - - +
272D LEU* 6.2 2.9 - - - +
282D SER 2.2 28.7 + - - -
283D GLN* 3.5 1.6 - - - +
285D LYS* 1.3 67.4 - - - +
287D ASP* 1.3 57.8 + - - +
289D VAL* 3.2 3.5 + - - +
290D LEU* 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D GLN 2.3 27.5 + - - -
284D LYS* 3.9 1.6 - - - +
286D ALA* 1.3 69.9 - - - +
288D GLU* 1.3 56.1 + - - +
290D LEU* 3.2 2.8 + - - +
291D GLU* 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 288 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D LYS 2.9 18.5 + - - -
285D LYS* 3.6 2.5 - - - +
287D ASP* 1.3 77.2 - - - +
289D VAL* 1.3 55.3 + - - +
291D GLU* 3.2 2.6 + - - +
292D ILE* 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D LYS 2.9 14.1 + - - -
286D ALA* 3.2 4.4 + - - +
288D GLU* 1.3 76.8 - - - +
290D LEU* 1.3 56.0 + - - +
292D ILE* 3.2 3.0 + - - +
293D LEU* 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D ALA 2.9 14.2 + - - -
287D ASP* 3.2 4.9 + - - +
289D VAL* 1.3 74.6 - - - +
291D GLU* 1.3 56.3 + - - +
293D LEU* 3.2 3.2 + - - +
294D LYS* 2.9 25.1 + - - -
329D LEU* 5.8 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D ASP 2.9 14.5 + - - -
288D GLU* 3.2 4.9 + - - +
290D LEU* 1.3 76.6 - - - +
292D ILE* 1.3 55.9 + - - +
294D LYS* 3.2 3.3 + - - +
295D THR* 2.8 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D GLU 2.9 14.1 + - - -
289D VAL* 3.2 4.4 + - - +
291D GLU* 1.3 72.7 - - - +
293D LEU* 1.3 64.6 + - - +
295D THR* 3.2 11.0 + - - +
296D ALA* 3.3 10.0 + - - +
302D CYS* 5.6 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D VAL 2.9 13.6 + - - -
290D LEU* 3.2 5.5 + - - +
292D ILE* 1.3 79.2 - - - +
294D LYS* 1.3 60.2 + - - +
296D ALA* 3.5 8.8 + - - -
325D ARG* 5.2 15.2 - - - +
329D LEU* 5.5 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D LEU 2.9 13.6 + - - -
291D GLU* 3.6 4.3 - - - +
293D LEU* 1.3 73.7 - - - +
295D THR* 1.3 63.6 + - - +
296D ALA* 3.4 1.6 + - - -
329D LEU* 5.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D GLU 2.8 14.2 + - - -
292D ILE* 3.2 6.1 + - - +
294D LYS* 1.3 77.7 - - - +
296D ALA* 1.3 67.7 + - - +
297D SER* 3.0 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D ILE 3.3 12.1 + - - +
293D LEU 3.5 7.4 + - - -
294D LYS 3.3 3.7 - - - -
295D THR* 1.3 76.1 - - - +
297D SER* 1.3 66.2 + - - +
298D ASP 3.3 8.8 + - - +
299D ASP* 5.4 0.6 - - - -
301D GLU* 5.6 0.3 - - - -
302D CYS* 4.8 8.5 + - - -
----------------------------------------------------------
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