Contacts of the helix formed by residues 302 - 314 (chain B) in PDB entry 2XH7
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 302 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PHE* 3.8 18.9 - - + -
256B GLY 5.5 0.3 - - - +
258B TYR* 2.6 33.0 + - - +
275B GLY* 5.3 1.6 - - - -
299B ALA* 3.1 21.5 + - + +
301B ASP* 1.3 73.8 - - - +
303B TRP* 1.3 63.8 + - - +
304B GLU* 3.3 3.6 + - - +
305B ALA* 3.1 31.3 + - + +
306B TRP* 3.2 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ASP* 3.0 44.9 + - + +
302B ASP* 1.3 74.5 - - - +
304B GLU* 1.3 62.8 + - - +
306B TRP* 3.2 10.6 + - - +
307B SER* 3.1 25.6 + - - -
322B LEU* 3.6 34.3 - - + -
329B ARG* 3.4 47.3 - - + +
332B THR* 3.9 16.6 - - + -
333B ALA* 3.6 28.7 - - + -
336B LYS* 3.6 34.5 - - + +
338B ALA* 4.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ASP* 3.3 3.9 - - - +
303B TRP* 1.3 78.2 - - - +
305B ALA* 1.3 62.1 + - - +
307B SER* 3.4 6.4 + - - +
308B HIS* 3.0 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLY* 5.0 8.7 - - - -
298B PHE* 3.7 28.9 - - + -
302B ASP* 3.1 34.8 + - - +
304B GLU* 1.3 78.0 - - - +
306B TRP* 1.3 62.6 + - - +
308B HIS* 3.9 6.2 - - - +
309B PHE* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ASP* 3.4 33.0 - - - -
297B PRO* 3.6 14.4 - - + -
298B PHE* 3.1 36.7 + - + -
299B ALA 2.9 20.9 + - - -
300B GLU* 5.6 0.2 - - - -
302B ASP 3.2 25.6 - - - -
303B TRP* 3.2 8.2 + - - +
305B ALA* 1.3 76.7 - - - +
307B SER* 1.3 58.1 + - - +
309B PHE* 3.2 2.8 + - - +
310B PHE* 2.9 31.7 + - - +
317B ILE* 3.8 14.0 - - + +
318B VAL 3.5 20.2 - - - -
319B ALA* 3.8 10.5 - - - -
322B LEU* 3.7 36.8 - - + +
338B ALA* 3.2 37.5 - - + +
339B ALA* 4.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TRP 3.1 14.1 + - - -
304B GLU* 3.9 7.1 - - - -
306B TRP* 1.3 77.1 - - - +
308B HIS* 1.3 61.8 + - - +
310B PHE* 3.5 1.6 + - - +
311B LYS* 3.2 34.3 + - - +
336B LYS* 2.7 36.7 + - - +
337B LYS 3.6 13.1 + - - +
338B ALA* 4.1 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLY 6.3 0.4 - - - -
276B PRO* 5.5 16.0 - - + +
279B ALA* 5.2 12.0 - - + +
304B GLU 3.0 17.6 + - - +
305B ALA* 3.9 6.7 - - - +
307B SER* 1.3 79.7 - - - +
309B PHE* 1.3 64.8 + - - +
310B PHE 3.5 0.2 + - - -
311B LYS* 3.6 23.0 + - - +
312B THR* 4.3 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ALA* 3.7 27.1 - - + -
282B TYR* 3.7 27.1 - + + -
283B HIS* 3.3 33.4 - + - -
286B MET* 4.2 16.4 - - - -
294B ILE* 4.5 3.8 - - + -
297B PRO* 4.3 10.8 - - + -
298B PHE* 3.3 29.6 - + + -
305B ALA 3.1 9.4 + - - +
306B TRP* 3.8 3.4 - - - +
308B HIS* 1.3 81.5 - - + +
310B PHE* 1.3 63.3 + - - +
312B THR* 3.3 5.9 + - - -
313B ALA* 3.1 25.1 + - + +
317B ILE* 3.5 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B TRP 2.9 17.3 + - - +
307B SER 3.9 0.7 - - - +
309B PHE* 1.3 76.7 - - - +
311B LYS* 1.3 69.2 + - + +
312B THR 3.1 1.0 + - - -
313B ALA* 3.5 12.9 + - + +
314B GLY 4.7 2.1 + - - -
315B ILE 4.9 2.7 - - - -
317B ILE* 3.9 16.8 - - + -
337B LYS* 3.4 39.0 - - + +
338B ALA 3.8 5.4 - - - +
339B ALA* 3.7 20.2 - - - -
340B ASP* 3.4 45.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B SER* 3.2 22.6 + - - +
308B HIS* 3.7 17.6 + - - +
309B PHE 3.2 1.4 - - - -
310B PHE* 1.3 82.0 - - + +
312B THR* 1.3 67.9 + - + +
337B LYS* 5.9 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B HIS* 3.6 22.6 + - - -
308B HIS 4.4 5.8 + - - +
309B PHE* 3.3 6.4 + - - -
310B PHE 3.1 0.4 - - - -
311B LYS* 1.3 88.0 - - + +
313B ALA* 1.3 67.0 + - - +
314B GLY* 3.5 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B HIS* 4.1 8.9 - - - -
286B MET* 3.1 25.8 - - + +
309B PHE* 3.1 27.2 + - + +
310B PHE* 3.5 7.8 + - + +
312B THR* 1.3 79.6 - - - +
314B GLY* 1.3 59.6 + - - +
315B ILE* 3.2 7.6 - - + +
317B ILE* 3.9 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PHE 4.7 2.8 + - - -
312B THR 3.5 2.9 - - - -
313B ALA* 1.3 78.0 - - - +
315B ILE* 1.3 64.6 + - - +
----------------------------------------------------------
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