Contacts of the helix formed by residues 269 - 284 (chain D) in PDB entry 3P9K
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 269 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLU* 6.1 1.6 - - - -
268D TRP* 1.3 77.6 - - - +
270D ASP* 1.3 65.3 + - - +
271D GLN* 3.1 22.8 + - - +
272D HIS* 3.1 24.0 + - - -
273D CYS* 3.0 19.8 + - - -
322D PRO 3.1 7.8 + - - -
323D GLY* 3.4 24.0 - - - -
325D ARG* 5.6 0.7 - - - +
327D ARG* 3.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D SER* 1.3 73.0 - - - +
271D GLN* 1.3 77.0 + - - +
273D CYS* 3.3 5.8 + - - +
274D ALA* 3.0 24.4 + - - +
325D ARG* 4.5 12.1 + - - +
327D ARG* 3.1 31.4 + - - +
331D GLU* 5.8 2.3 - - - +
335D LEU* 4.1 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLU* 5.8 0.2 - - - +
269D SER* 3.1 25.8 + - - +
270D ASP* 1.3 89.2 + - - +
272D HIS* 1.3 65.9 + - + +
274D ALA* 3.3 15.6 + - - +
275D THR* 3.3 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D PHE* 3.2 34.3 - + + -
268D TRP* 3.2 43.3 - + + -
269D SER* 3.1 17.2 + - - +
271D GLN* 1.3 82.0 - - + +
273D CYS* 1.3 57.6 + - - +
275D THR* 3.2 7.5 + - - -
276D LEU 2.9 24.1 + - - -
322D PRO* 3.6 16.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D PHE* 5.3 0.2 - - - -
265D LEU* 3.7 42.0 - - + -
268D TRP* 3.8 6.7 - - - -
269D SER 3.0 16.2 + - - +
270D ASP 3.5 9.6 - - - +
272D HIS* 1.3 78.7 - - - +
274D ALA* 1.3 53.1 + - - +
276D LEU* 3.6 6.0 - - - +
277D LEU* 2.7 41.8 + - + +
327D ARG* 3.6 23.1 - - - -
335D LEU* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ASP 3.0 13.3 + - - +
271D GLN* 3.6 10.8 - - - +
272D HIS 3.2 0.2 - - - -
273D CYS* 1.3 72.5 - - - +
275D THR* 1.3 67.8 + - - +
277D LEU* 4.1 4.8 - - - +
278D LYS* 2.9 27.1 + - - +
335D LEU* 4.7 10.2 - - + +
338D GLY 6.3 3.4 - - - -
339D ALA* 5.0 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D PHE* 3.4 34.8 - - + +
271D GLN 3.3 10.5 + - - -
272D HIS* 3.2 12.9 + - - -
274D ALA* 1.3 80.0 - - - +
276D LEU* 1.3 62.5 + - - +
278D LYS* 3.4 5.4 + - - +
279D ASN* 3.1 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D VAL* 4.2 5.6 - - + -
249D MET* 3.7 46.9 - - + +
250D PHE* 3.9 11.0 - - + -
253D VAL* 4.2 8.5 - - + -
261D MET* 3.8 24.5 - - + -
264D ILE* 3.8 20.6 - - + -
265D LEU* 3.9 13.0 - - + -
268D TRP* 5.2 2.9 - - + -
272D HIS 2.9 17.2 + - - +
273D CYS* 3.6 5.8 - - - +
275D THR* 1.3 78.0 - - - +
277D LEU* 1.3 57.3 + - - +
279D ASN* 3.2 8.3 + - - +
280D CYS* 3.0 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D MET* 3.6 28.9 - - + -
265D LEU* 4.3 17.5 - - + -
273D CYS 2.7 26.0 + - - +
274D ALA* 4.1 2.5 - - - +
276D LEU* 1.3 71.4 - - - +
278D LYS* 1.3 60.0 + - - +
280D CYS* 3.3 5.4 + - - +
281D TYR* 2.9 29.5 + - - +
290D VAL* 4.6 4.3 - - + -
335D LEU* 3.8 38.1 - - + +
339D ALA* 3.6 15.7 - - + -
341D PHE* 3.8 8.1 - - + -
358D PHE* 4.0 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D ALA 2.9 19.3 + - - +
275D THR* 3.6 7.0 - - - +
277D LEU* 1.3 76.4 - - - +
279D ASN* 1.3 60.4 + - - +
281D TYR* 3.3 19.3 + - + +
282D ASP* 2.9 63.5 + - - +
339D ALA* 4.1 20.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D MET 3.0 26.2 + - - +
250D PHE* 3.1 24.5 + - - +
251D LYS 3.7 14.8 - - - +
252D GLU* 4.6 1.1 - - - -
253D VAL* 3.4 16.5 + - + +
275D THR* 3.1 21.7 + - - +
276D LEU* 3.5 5.8 - - - +
278D LYS* 1.3 75.4 - - - +
280D CYS* 1.3 66.1 + - - +
282D ASP* 3.2 11.9 + - - +
283D ALA* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D VAL* 4.8 0.7 - - - -
253D VAL* 3.8 8.3 - - - -
259D ILE* 3.6 32.3 - - + -
261D MET* 3.8 33.0 - - - -
276D LEU* 3.0 25.2 + - - -
277D LEU* 3.4 9.2 - - - +
279D ASN* 1.3 77.2 - - - +
281D TYR* 1.3 55.4 + - - +
283D ALA* 2.7 24.1 + - - +
284D LEU* 3.0 16.4 + - - +
290D VAL* 3.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D LEU 2.9 14.3 + - - +
278D LYS* 3.3 18.8 - - - +
280D CYS* 1.3 76.6 - - - +
282D ASP* 1.3 71.4 + - - +
283D ALA 3.5 0.2 + - - -
284D LEU* 3.5 1.4 + - - -
339D ALA 3.4 21.8 - - - +
340D GLY* 3.5 29.0 + - - -
341D PHE* 3.7 28.2 - + + -
360D LYS* 2.8 68.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D LYS* 2.9 56.4 + - - +
279D ASN* 3.6 11.6 - - - +
280D CYS 3.0 0.2 - - - -
281D TYR* 1.3 81.4 - - - +
283D ALA* 1.3 59.2 + - - +
284D LEU 3.4 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D VAL* 3.4 35.7 - - + +
254D PRO 3.5 15.0 - - - +
255D SER* 3.5 14.7 + - - +
256D GLY 3.3 22.1 + - - +
259D ILE* 4.3 4.7 - - + -
279D ASN 3.0 2.9 + - - +
280D CYS 2.7 13.4 + - - +
282D ASP* 1.3 73.2 - - - +
284D LEU* 1.3 61.0 + - - +
285D PRO* 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D GLY 3.7 8.3 - - - +
257D ASP 3.5 26.0 - - - +
259D ILE* 3.7 21.5 - - + -
280D CYS 3.0 15.7 + - - +
281D TYR 3.5 1.2 + - - +
282D ASP 3.4 3.9 - - - +
283D ALA* 1.3 80.3 - - - +
285D PRO* 1.3 65.8 - - + +
288D GLY* 4.0 3.4 - - - +
289D LYS* 3.6 37.7 - - - +
290D VAL* 3.7 16.8 - - + -
341D PHE* 3.9 17.0 - - + -
360D LYS* 2.8 29.5 + - - -
----------------------------------------------------------
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