Contacts of the helix formed by residues 302 - 316 (chain D) in PDB entry 3H2U
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 PRO 302 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D CYS* 3.9 3.4 - - - -
268D GLU* 3.1 26.7 - - - +
300D GLY 4.1 3.4 - - - +
301D PRO* 1.3 89.0 - - + +
303D GLY* 1.3 66.1 + - - +
304D ARG* 2.9 8.0 + - + +
305D SER* 3.0 28.4 + - - +
306D MET* 3.1 8.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D CYS* 3.5 8.4 - - - -
250D PHE* 3.4 34.0 - - - -
266D VAL* 3.9 12.8 - - - +
268D GLU* 2.7 15.2 + - - -
302D PRO* 1.3 69.0 - - - +
304D ARG* 1.3 63.1 + - - +
306D MET* 4.6 0.2 - - - -
307D LEU* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D PHE* 3.5 26.7 - - + -
252D GLN* 6.2 0.9 - - - +
302D PRO* 2.9 5.7 + - + +
303D GLY* 1.3 77.5 - - - +
305D SER* 1.3 65.8 + - - +
307D LEU* 3.4 13.6 - - - +
308D ALA* 3.7 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D PRO* 3.9 11.4 - - - -
302D PRO* 3.0 31.5 + - - +
304D ARG* 1.3 75.3 - - - +
306D MET* 1.3 64.9 + - - +
307D LEU 3.1 1.8 - - - -
308D ALA* 3.1 8.6 + - - +
309D ALA* 2.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D TYR* 3.2 42.2 - - + +
206D HIS* 5.6 0.2 - - - -
222D CYS* 5.0 3.8 - - + -
266D VAL* 4.1 8.5 - - + -
297D CYS* 3.8 35.4 - - + -
298D ALA* 4.4 15.5 - - - +
301D PRO* 4.2 24.1 - - + +
302D PRO 3.1 15.3 + - - +
303D GLY 4.0 2.9 - - - +
305D SER* 1.3 78.0 - - - +
307D LEU* 1.3 64.3 + - - +
309D ALA* 3.2 5.1 + - + +
310D LEU* 2.8 57.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D PHE* 3.9 9.9 - - + -
252D GLN* 3.7 31.9 - - + +
253D LEU 3.5 26.0 - - - +
254D ALA* 4.1 2.2 - - - -
264D PHE* 4.0 18.8 - - + -
266D VAL* 4.0 19.7 - - + +
303D GLY 3.0 16.1 + - - +
304D ARG 3.4 7.9 - - - +
305D SER 3.1 0.2 - - - -
306D MET* 1.3 77.7 - - - +
308D ALA* 1.3 58.1 + - - +
310D LEU* 3.7 1.2 - - - +
311D ILE* 2.8 62.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D ARG 3.7 7.0 + - - +
305D SER* 3.1 9.2 + - - +
307D LEU* 1.3 75.5 - - - +
309D ALA* 1.3 58.3 + - - +
311D ILE* 3.5 11.1 - - - +
312D ALA* 2.7 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D TYR* 3.3 28.7 - - + +
301D PRO* 6.5 0.4 - - + -
305D SER 2.9 14.1 + - - +
306D MET* 3.5 14.1 - - + +
308D ALA* 1.3 77.1 - - - +
310D LEU* 1.3 52.8 + - - +
312D ALA* 3.6 3.9 - - - +
313D ALA* 2.7 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D TYR* 3.8 26.7 - - + -
224D CYS* 4.4 10.5 - - - -
264D PHE* 3.5 22.2 - - + -
266D VAL* 3.6 28.9 - - + -
297D CYS* 4.3 9.4 - - - -
306D MET* 2.8 44.8 + - + +
307D LEU 3.7 1.1 - - - +
309D ALA* 1.3 73.8 - - - +
311D ILE* 1.3 66.9 + - - +
313D ALA* 4.2 2.9 - - + -
314D GLN* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D ALA* 4.2 15.3 - - + -
255D CYS 4.5 13.0 - - - +
256D GLY* 5.2 12.6 - - - -
257D GLN* 5.7 2.5 - - + +
262D LYS* 4.6 10.0 - - + -
264D PHE* 3.9 8.7 - - + -
307D LEU* 2.8 59.0 + - + +
308D ALA* 3.5 9.6 - - - +
310D LEU* 1.3 73.5 - - - +
312D ALA* 1.3 55.7 + - + +
314D GLN* 3.4 13.6 + - - +
315D ALA* 2.8 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D ALA* 2.7 22.4 + - + +
309D ALA* 3.8 3.4 - - - +
311D ILE* 1.3 74.5 - - + +
313D ALA* 1.3 62.0 + - - +
315D ALA* 2.8 25.0 - - + +
316D THR* 3.0 16.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D LEU* 3.8 21.1 - - + +
195D GLY* 5.7 5.6 - - - +
203D LEU 5.7 0.9 - - - +
204D TYR* 3.8 28.0 - - + -
309D ALA 2.7 22.1 + - - +
310D LEU* 3.2 4.9 + - + +
312D ALA* 1.3 70.6 - - - +
314D GLN* 1.3 64.8 + - - +
316D THR* 2.8 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D THR* 6.1 5.4 - - + -
262D LYS* 3.4 47.0 - - - +
263D GLY 4.8 2.3 + - - -
264D PHE* 3.8 19.2 - - + -
310D LEU 2.9 10.5 + - - +
311D ILE* 3.4 15.6 + - - +
313D ALA* 1.3 74.3 - - - +
315D ALA* 1.3 68.0 + - - +
316D THR 4.3 0.2 - - - -
317D ALA* 3.2 20.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 315 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D ILE* 2.8 20.6 + - + +
312D ALA* 2.8 23.8 - - + +
314D GLN* 1.3 75.5 - - - +
316D THR* 1.3 50.8 + - + +
317D ALA* 2.3 26.6 + - - +
318D LEU 4.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D LEU* 4.4 14.7 + - + +
195D GLY* 6.1 1.4 - - - -
312D ALA* 3.3 13.9 - - + +
313D ALA* 2.8 20.7 + - - +
315D ALA* 1.3 70.6 - - + +
317D ALA* 1.3 60.6 + - - +
318D LEU* 3.6 16.3 - - - +
----------------------------------------------------------
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