Contacts of the helix formed by residues 280 - 296 (chain D) in PDB entry 3HU1
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 GLY 280 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D LEU 3.3 1.6 + - - -
279D ALA* 1.3 68.1 - - - +
281D GLU* 1.3 49.4 + - - +
282D SER 3.1 4.0 - - - -
283D GLU* 2.9 34.3 + - - +
284D SER* 2.8 34.8 + - - -
287D ARG* 5.3 0.5 + - - -
320D VAL* 4.7 0.2 - - - +
323D ARG* 4.7 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D LYS* 3.3 36.1 + - - +
278D LEU* 3.7 35.0 + - + +
279D ALA 3.2 4.6 + - - +
280D GLY* 1.3 72.2 - - - +
282D SER* 1.3 56.7 + - - +
284D SER* 3.8 10.2 - - - +
285D ASN* 3.2 35.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
274D ILE* 3.5 41.1 - - - +
275D MET* 5.3 1.6 - - - -
277D LYS* 4.1 10.9 + - - +
278D LEU 3.1 15.7 + - - -
279D ALA* 4.5 1.4 - - - -
280D GLY 4.0 0.5 + - - -
281D GLU* 1.3 75.5 - - - +
283D GLU* 1.3 77.8 + - - -
285D ASN* 3.1 16.9 + - - +
286D LEU* 3.1 12.9 + - - +
320D VAL* 4.7 1.0 - - - +
324D ILE* 3.4 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C SER 4.6 1.4 - - - +
280D GLY* 2.9 33.6 + - - +
282D SER* 1.3 82.1 + - - +
284D SER* 1.3 56.8 + - - +
286D LEU* 3.3 6.8 + - - +
287D ARG* 3.1 36.9 + - - +
320D VAL* 4.0 1.4 - - - +
323D ARG* 2.8 46.7 + - - +
324D ILE* 3.4 36.9 - - + +
327D GLN* 3.5 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D GLY 2.8 14.9 + - - -
281D GLU* 3.8 12.6 - - - -
283D GLU* 1.3 75.1 - - - +
285D ASN* 1.3 62.8 + - - +
287D ARG* 3.3 29.2 + - - +
288D LYS* 2.9 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D PHE* 5.4 0.9 - - - -
269D ILE* 5.7 0.3 - - - +
274D ILE* 3.7 16.7 - - + +
277D LYS* 3.3 33.3 - - - +
281D GLU* 3.2 21.4 + - - +
282D SER 3.1 9.6 + - - +
284D SER* 1.3 80.9 + - - +
286D LEU* 1.4 56.4 + - - +
288D LYS* 3.4 11.4 + - - +
289D ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D ILE* 4.0 26.2 - - + -
274D ILE* 4.3 12.9 - - + +
282D SER 3.1 11.7 + - - +
283D GLU* 3.4 9.4 - - - +
284D SER 3.2 0.2 - - - -
285D ASN* 1.4 74.1 - - - +
287D ARG* 1.3 63.8 + - - +
289D ALA* 3.4 3.8 - - - +
290D PHE* 3.3 40.5 + - + -
303D ILE* 5.3 0.9 - - + -
309D ILE* 4.6 13.2 - - + -
324D ILE* 4.4 27.1 - - + +
327D GLN* 3.8 21.1 - - + -
328D LEU* 4.4 20.9 - - + +
331D LEU* 4.1 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D GLY 5.3 0.2 + - - -
283D GLU* 3.1 21.0 + - - +
284D SER* 3.3 27.5 + - - +
286D LEU* 1.3 75.8 - - - +
288D LYS* 1.3 53.5 + - - +
290D PHE* 2.9 6.1 + - - +
291D GLU* 2.8 59.2 + - + +
327D GLN* 3.6 32.9 - - - +
331D LEU* 4.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 288 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D PHE* 5.1 3.8 - - + -
284D SER* 2.9 28.0 + - - +
285D ASN* 3.6 14.9 - - - +
287D ARG* 1.3 73.3 - - - +
289D ALA* 1.3 61.6 + - - +
291D GLU* 4.2 19.9 + - + +
292D GLU* 3.0 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D PHE* 3.6 36.8 - - + -
269D ILE* 3.6 24.9 - - + -
285D ASN 2.9 13.9 + - - +
286D LEU 3.4 11.0 - - - +
288D LYS* 1.3 78.0 - - - +
290D PHE* 1.3 58.1 + - + +
292D GLU* 3.5 2.6 - - - +
293D ALA* 3.0 28.6 + - - +
301D ILE* 4.5 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D ILE* 4.6 2.2 - - + -
286D LEU* 3.3 26.4 + - + +
287D ARG 2.9 7.4 + - - +
289D ALA* 1.3 79.0 - - + +
291D GLU* 1.4 59.7 + - + +
293D ALA* 3.5 2.3 + - - +
294D GLU* 3.0 38.2 + - - +
301D ILE* 3.8 35.6 - - + +
303D ILE* 4.7 1.1 - - + -
328D LEU* 4.1 24.2 - - + -
331D LEU* 3.7 57.0 - - + -
332D MET* 4.2 6.1 - - - -
335D LEU* 4.2 18.5 - - + +
343D VAL* 4.2 23.1 - - + -
----------------------------------------------------------
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 ARG* 2.8 46.5 + - + +
288D LYS* 4.1 23.7 - - + +
290D PHE* 1.4 71.2 - - + +
292D GLU* 1.3 56.5 - - - +
294D GLU* 3.5 13.1 + - - +
295D LYS* 3.0 28.4 + - - +
331D LEU* 6.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D PHE* 4.1 20.9 - - + -
267D PHE* 4.1 17.2 - - + -
288D LYS* 3.0 33.6 + - + +
289D ALA 3.5 4.9 - - - +
291D GLU* 1.3 73.6 - - - +
293D ALA* 1.3 60.2 + - - +
295D LYS* 3.0 11.8 + - - +
296D ASN* 2.9 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D PHE* 3.9 15.1 - - + -
267D PHE* 5.1 2.9 - - + -
289D ALA 3.0 15.4 + - - +
290D PHE 3.8 2.0 - - - +
292D GLU* 1.3 74.8 - - - +
294D GLU* 1.4 61.6 + - - +
296D ASN 3.1 19.9 - - - +
297D ALA 3.9 1.0 - - - +
299D ALA* 3.3 19.5 - - + +
300D ILE 5.6 0.2 - - - +
301D ILE* 3.7 31.9 - - + -
341D VAL* 3.8 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D PHE* 3.0 24.7 + - - +
291D GLU* 3.6 12.3 + - - +
293D ALA* 1.4 74.5 - - - +
295D LYS* 1.3 63.3 + - - +
296D ASN 3.4 0.2 + - - -
297D ALA 4.4 7.1 + - - +
334D GLY 4.3 11.1 - - - +
335D LEU* 3.6 34.0 - - + +
336D LYS 5.1 0.9 + - - -
339D ALA* 4.3 20.8 - - + +
341D VAL* 4.1 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D GLU 3.0 15.2 + - - +
292D GLU* 3.0 18.1 + - - +
294D GLU* 1.3 77.2 - - - +
296D ASN* 1.3 73.8 + - - +
297D ALA 3.6 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D PHE* 3.8 33.0 - - + +
292D GLU* 2.9 35.5 + - - +
293D ALA 3.1 9.7 - - - +
294D GLU 3.3 0.4 - - - -
295D LYS* 1.3 92.6 + - - +
297D ALA* 1.3 74.3 + - + +
298D PRO 3.7 0.5 - - - +
299D ALA* 3.5 10.6 - - - +
----------------------------------------------------------
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