Contacts of the helix formed by residues 179 - 191 (chain B) in PDB entry 2HDH
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 GLN 179 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LYS* 2.9 28.9 + - - +
177B THR 4.0 0.4 + - - -
178B SER* 1.3 71.9 - - - +
180B LYS* 1.3 61.2 + - - +
182B PHE* 3.1 15.9 + - - +
183B GLU* 2.7 73.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 5.5 7.4 - - + +
13B ILE* 4.2 30.6 - - + +
129B HIS* 6.0 4.8 - - - +
153B ARG* 6.5 0.7 - - + -
178B SER* 3.8 9.2 - - - +
179B GLN* 1.3 79.8 - - - +
181B THR* 1.3 62.7 + - - +
183B GLU* 4.1 6.4 - - - +
184B SER* 3.1 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 5.6 0.2 - - - -
131B ILE* 3.8 36.0 - - + +
152B ASP 2.7 20.3 + - - +
153B ARG* 3.3 28.1 - - - +
155B ALA* 4.5 2.0 - - + -
177B THR* 4.0 11.4 - - + -
178B SER* 2.7 20.1 + - - -
180B LYS* 1.3 77.5 - - - +
182B PHE* 1.3 62.1 + - - +
184B SER* 3.4 2.8 + - - -
185B LEU* 3.1 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL* 3.7 31.2 - - + -
173B LYS* 3.9 28.5 - - + -
177B THR* 4.5 2.9 - - - +
178B SER 3.2 11.2 + - - +
179B GLN* 3.1 33.6 + - - +
181B THR* 1.3 77.0 - - - +
183B GLU* 1.3 64.7 + - + +
185B LEU* 3.1 8.8 + - - +
186B VAL* 2.9 50.0 + - + +
197B VAL 6.0 0.2 - - - -
198B SER* 3.6 34.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 3.3 34.8 + - + +
179B GLN* 2.7 55.6 + - - +
180B LYS* 4.1 5.8 - - - +
182B PHE* 1.3 77.7 - - + +
184B SER* 1.3 63.1 + - - +
186B VAL* 3.2 8.6 + - - +
187B ASP* 2.9 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 6.1 1.7 - - - +
13B ILE* 3.0 39.8 + - - +
15B VAL* 3.7 12.5 + - - +
131B ILE* 3.5 14.5 - - - +
180B LYS 3.1 18.8 + - - -
181B THR 3.4 6.5 - - - -
182B PHE 3.2 0.2 - - - -
183B GLU* 1.3 77.2 - - - +
185B LEU* 1.3 58.4 + - - +
187B ASP* 3.4 7.8 + - - +
188B PHE* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 5.5 1.1 - - + -
103B LEU* 4.0 37.0 - - + -
131B ILE* 4.2 11.9 - - + -
133B ALA* 4.8 5.2 - - + -
155B ALA* 3.5 32.5 - - + -
156B GLY 4.5 5.8 - - - +
157B LEU* 4.3 19.5 - - + +
171B VAL* 4.1 19.7 - - + -
181B THR* 3.1 17.9 + - + +
182B PHE* 3.1 7.9 + - - +
184B SER* 1.3 73.8 - - - +
186B VAL* 1.3 60.7 + - - +
188B PHE* 3.6 5.9 - - + +
189B SER* 2.8 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL* 4.5 10.3 - - + -
182B PHE* 2.9 52.0 + - + +
183B GLU* 3.2 9.6 + - - +
185B LEU* 1.3 76.3 - - - +
187B ASP* 1.3 67.4 + - - +
189B SER* 3.4 7.7 + - - -
190B LYS* 3.2 47.4 + - + +
196B PRO* 3.9 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 3.4 31.2 + - - +
183B GLU* 2.9 24.7 + - - +
184B SER* 3.7 6.9 - - - +
186B VAL* 1.3 77.9 - - - +
188B PHE* 1.3 60.8 + - - +
190B LYS* 3.2 14.5 + - - +
191B ALA* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 3.7 30.5 - - + -
18B VAL* 3.9 19.3 - - + -
30B ILE* 5.9 3.1 - - + -
34B ALA* 4.6 5.2 - - + -
39B HIS* 3.4 35.7 - + - -
103B LEU* 3.5 24.0 - - + -
105B VAL* 4.8 4.5 - - + -
157B LEU* 4.2 18.4 - - + -
159B PHE* 5.0 1.6 - + - -
184B SER 2.9 17.2 + - - +
185B LEU* 3.6 7.9 - - + +
187B ASP* 1.3 77.4 - - - +
189B SER* 1.3 63.8 + - - +
191B ALA* 2.9 8.4 + - + +
192B LEU* 2.9 58.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 3.9 14.7 - - - +
169B VAL* 3.4 31.2 - - - +
171B VAL* 4.0 1.4 - - - +
185B LEU 2.8 24.4 + - - -
186B VAL 3.5 6.3 - - - -
187B ASP 3.2 0.2 - - - -
188B PHE* 1.3 76.8 - - - +
190B LYS* 1.3 59.9 + - - +
192B LEU* 3.1 18.6 + - - +
194B LYS* 2.9 29.1 + - - +
196B PRO* 3.6 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B VAL* 3.2 34.7 + - + +
187B ASP* 3.2 15.0 + - - +
189B SER* 1.3 76.2 - - - +
191B ALA* 1.3 58.2 + - - +
193B GLY* 2.9 19.4 + - - -
194B LYS 3.6 10.3 - - - +
195B HIS* 6.4 0.4 - - - -
196B PRO* 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B THR* 3.3 20.4 - - - +
39B HIS* 3.8 23.2 - - + +
187B ASP 2.9 13.5 + - - +
188B PHE* 2.9 13.9 + - - +
190B LYS* 1.3 71.5 - - - +
192B LEU* 1.3 58.6 - - - +
193B GLY 3.0 5.5 + - - -
----------------------------------------------------------
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