Contacts of the helix formed by residues 178 - 193 (chain B) in PDB entry 1H24
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 TYR 178 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ALA* 3.8 7.6 - - + -
119A HIS* 3.4 46.5 - + + +
120A SER* 3.5 30.5 - - - -
182A THR* 4.3 13.7 - - + -
276A SER* 4.1 8.5 - - - -
277A ALA* 3.3 17.5 + - - +
278A LYS* 3.1 51.3 + - + -
175B VAL* 3.1 9.7 + - + +
177B ASP* 1.3 96.2 - - + +
179B HIS* 1.3 63.4 + - - +
180B GLU 3.2 3.5 + - - -
181B ASP* 3.2 7.6 + - + +
182B ILE* 2.9 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A VAL* 3.4 28.5 - - + +
155A PRO* 5.7 0.4 - - + -
175B VAL* 2.1 50.9 + - + +
176B PRO* 3.0 35.9 - - + +
177B ASP 3.7 1.8 - - - -
178B TYR* 1.3 75.3 - - - +
180B GLU* 1.3 69.1 + - - +
182B ILE* 3.5 3.4 + - - +
183B HIS* 3.1 23.0 + - - +
317B GLN* 3.6 9.3 + - - +
320B LEU* 3.9 23.4 - - + +
379B LYS* 5.2 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B PRO 5.7 0.2 + - - -
177B ASP 5.5 0.4 + - - -
178B TYR 3.3 0.6 - - - -
179B HIS* 1.3 79.1 - - - +
181B ASP* 1.3 70.6 + - - +
183B HIS* 3.2 10.9 + - + +
184B THR* 2.9 32.2 + - - +
379B LYS* 2.4 53.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A SER* 3.0 29.7 + - - +
278A LYS* 2.5 35.7 + - - -
177B ASP 5.0 1.7 - - - +
178B TYR* 3.2 11.1 + - - +
180B GLU* 1.3 76.7 - - - +
182B ILE* 1.3 64.3 + - - +
184B THR* 3.3 6.3 + - - -
185B TYR* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A HIS 3.3 21.1 - - - +
120A SER 3.5 20.0 - - - +
122A ARG* 3.6 26.9 - - + +
152A PHE* 3.8 24.9 - - + +
154A VAL* 4.0 22.7 - - + -
175B VAL* 5.8 1.3 - - + -
178B TYR* 2.9 29.9 + - + +
179B HIS 4.2 2.2 - - - +
181B ASP* 1.3 73.1 - - - +
183B HIS* 1.3 57.9 + - - +
185B TYR* 3.1 3.6 + - + +
186B LEU* 2.7 59.1 + - + +
317B GLN* 5.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B HIS 3.1 14.7 + - - +
180B GLU* 3.5 18.4 - - + +
182B ILE* 1.3 75.6 - - - +
184B THR* 1.3 64.0 + - - +
186B LEU* 3.3 4.3 + - - +
187B ARG* 3.0 67.0 + - + +
314B PHE* 4.4 8.8 - + - -
317B GLN* 3.8 24.5 + - - +
318B TYR* 4.3 9.6 - + - -
379B LYS* 3.6 37.2 + - - -
380B THR* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B GLU* 2.9 22.9 + - - +
181B ASP* 3.5 8.5 - - - +
183B HIS* 1.3 81.2 - - - +
185B TYR* 1.3 66.5 + - - +
187B ARG* 3.1 8.2 + - + +
188B GLU* 3.0 23.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 2.6 48.3 + - - +
120A SER 4.2 7.9 - - - +
121A HIS* 3.3 49.3 - + + +
122A ARG* 3.7 20.6 - - + -
181B ASP 3.0 16.6 + - - +
182B ILE* 3.6 3.4 - - - +
184B THR* 1.3 79.0 - - - +
186B LEU* 1.3 63.5 + - + +
188B GLU* 3.3 21.1 + - - +
189B MET* 2.9 53.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 4.0 35.2 - - + +
154A VAL* 5.9 0.9 - - + -
182B ILE* 2.7 44.1 + - + +
183B HIS 3.7 3.8 - - - +
185B TYR* 1.3 76.0 - - + +
187B ARG* 1.3 57.7 + - - +
189B MET* 4.3 0.9 - - + +
190B GLU* 2.7 37.4 + - - +
309B PRO* 3.5 19.1 - - + +
313B GLN* 4.1 29.8 - - + +
314B PHE* 3.9 19.9 - - + -
317B GLN* 3.9 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B HIS* 3.0 44.0 + - + +
184B THR* 3.1 11.2 + - + +
186B LEU* 1.3 78.6 - - - +
188B GLU* 1.3 63.8 + - - +
190B GLU* 3.1 37.5 + - - +
191B VAL* 3.7 10.0 + - - +
314B PHE* 3.9 15.0 - - - -
353B SER* 4.1 2.5 - - - -
380B THR* 3.2 26.5 + - - -
382B TYR* 3.2 39.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B THR* 3.0 14.6 + - + +
185B TYR* 3.9 26.4 - - - +
187B ARG* 1.3 78.2 - - - +
189B MET* 1.3 68.6 + - - +
191B VAL* 3.2 15.6 + - - +
192B LYS* 3.4 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 4.2 18.8 - - + +
122A ARG* 5.0 0.9 - - - +
185B TYR* 2.9 62.7 + - + +
186B LEU* 4.4 2.0 - - + -
188B GLU* 1.3 78.2 - - - +
190B GLU* 1.3 61.6 + - - +
192B LYS* 3.0 49.2 + - + +
193B CYS* 3.1 25.7 + - - +
305B ASP* 6.3 3.4 - - + -
307B ALA 5.3 1.8 - - - +
309B PRO* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU 2.7 18.8 + - - +
187B ARG* 3.1 34.2 + - - +
189B MET* 1.3 72.2 - - - +
191B VAL* 1.3 62.8 + - + +
193B CYS* 4.0 2.7 - - - +
194B LYS* 3.3 16.1 + - - +
309B PRO* 3.4 21.4 - - + +
314B PHE* 3.5 8.6 - - - -
351B LEU* 3.4 26.4 - - + +
352B PRO* 3.0 19.7 - - + +
353B SER* 2.6 50.1 + - - -
382B TYR* 4.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ARG 4.0 11.2 - - - +
188B GLU* 3.2 9.2 + - - +
189B MET 3.1 0.8 - - - -
190B GLU* 1.3 78.9 - - + +
192B LYS* 1.3 64.8 + - + +
193B CYS 3.4 0.5 + - - -
194B LYS* 3.5 16.4 + - + +
351B LEU* 4.1 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLU* 3.4 45.8 + - - +
189B MET* 3.0 31.4 + - + +
191B VAL* 1.3 79.5 - - + +
193B CYS* 1.3 61.6 + - - +
194B LYS 3.4 3.5 - - - +
241B ARG* 5.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B MET* 3.1 31.6 + - - +
190B GLU* 4.0 3.6 - - - +
192B LYS* 1.3 79.7 - - - +
194B LYS* 1.3 66.7 + - - +
195B PRO* 3.5 1.2 - - - +
237B ASN* 3.2 29.5 + - - +
241B ARG* 3.4 29.8 - - - +
305B ASP* 5.1 7.9 - - - -
307B ALA 5.0 1.8 - - - -
308B ALA* 4.1 27.4 - - + -
309B PRO* 4.3 6.3 - - + +
----------------------------------------------------------
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