Contacts of the helix formed by residues 180 - 193 (chain A) in PDB entry 2H5X
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 THR 180 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 4.5 1.6 - - - -
178A ASP 4.6 4.7 - - - +
179A ALA* 1.3 76.7 - - - +
181A THR* 1.3 64.8 + - - +
182A SER* 3.0 22.9 + - - -
183A SER* 3.1 17.6 + - - +
184A ALA* 3.0 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 3.6 31.6 + - - +
150A PRO* 3.7 14.4 - - + +
151A VAL* 3.4 20.5 - - - +
180A THR* 1.3 74.2 - - - +
182A SER* 1.3 68.2 + - - +
184A ALA* 4.4 0.7 - - - -
185A LEU* 3.2 18.9 + - - +
14D LEU* 3.2 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A THR* 3.0 11.7 + - - -
181A THR* 1.3 82.7 - - - +
183A SER* 1.3 72.6 + - - +
185A LEU* 3.1 14.0 + - - +
186A ARG* 3.1 29.5 + - - +
13D ALA 6.0 1.3 - - - -
14D LEU* 3.9 15.0 - - - -
32D PRO* 5.5 0.7 - - - +
35D LEU* 6.6 0.2 - - - -
36D ALA* 6.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ALA* 3.7 9.4 - - - +
180A THR* 3.1 28.9 + - - +
182A SER* 1.3 82.9 + - - +
184A ALA* 1.3 65.2 + - - +
186A ARG* 3.2 31.6 + - - +
187A SER* 2.9 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 4.8 0.2 - - + -
151A VAL* 3.9 17.7 - - + +
169A THR* 5.6 0.8 - - + +
172A VAL* 3.6 18.4 - - + +
173A LEU* 4.4 17.0 - - + -
179A ALA* 4.3 11.7 - - + -
180A THR 3.0 17.2 + - - +
181A THR* 3.5 6.1 - - - +
182A SER 3.2 0.2 - - - -
183A SER* 1.3 85.0 + - - +
185A LEU* 1.3 55.9 + - - +
187A SER* 3.4 3.1 + - - -
188A ALA* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 3.9 15.2 - - + +
154A ALA* 3.3 34.1 - - + -
155A LEU* 4.2 11.7 - - + -
158A LEU* 4.8 4.0 - - + -
181A THR 3.2 8.8 + - - +
182A SER 3.1 10.8 + - - +
184A ALA* 1.3 76.8 - - - +
186A ARG* 1.3 66.4 + - - +
188A ALA* 3.3 3.0 + - - +
189A LEU* 3.0 49.0 + - + +
14D LEU* 3.5 31.9 - - + +
32D PRO* 3.6 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A SER* 3.1 19.6 + - - +
183A SER* 3.2 42.9 + - - +
185A LEU* 1.3 79.0 - - - +
187A SER* 1.3 63.6 + - - +
189A LEU* 3.3 9.4 + - - +
190A SER* 3.1 21.0 + - - -
32D PRO* 4.1 31.2 + - + +
33D ALA* 4.7 5.4 - - - +
36D ALA* 3.7 27.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A VAL* 3.3 31.7 - - - +
183A SER* 2.9 15.2 + - - -
184A ALA* 3.4 2.4 - - - -
186A ARG* 1.3 74.0 - - - +
188A ALA* 1.3 67.3 + - - +
190A SER* 2.9 19.0 + - - -
191A LEU* 3.1 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 4.8 3.4 - - + -
155A LEU* 3.7 27.8 - - + -
168A ALA* 4.0 16.3 - - + +
169A THR* 4.6 1.6 - - - +
172A VAL* 3.6 15.4 - - + +
184A ALA 3.0 10.8 + - - +
185A LEU* 3.6 9.4 - - - +
187A SER* 1.3 78.2 - - - +
189A LEU* 1.3 57.5 + - - +
191A LEU* 3.1 6.0 + - - +
192A LEU* 2.8 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 3.7 19.3 - - + -
158A LEU* 4.1 11.4 - - + -
160A PHE* 3.9 19.3 - - + -
185A LEU* 3.0 39.2 + - + +
186A ARG* 3.4 10.5 - - - +
188A ALA* 1.3 77.8 - - - +
190A SER* 1.3 53.9 + - - +
192A LEU* 3.4 3.0 - - - +
193A GLY* 2.5 35.7 + - - -
32D PRO* 3.8 20.9 - - + -
90D ALA 3.9 19.7 - - - +
91D VAL* 4.4 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ARG 3.1 10.8 + - - -
187A SER* 2.9 13.1 + - - -
189A LEU* 1.3 77.4 - - - +
191A LEU* 1.3 64.6 + - - +
193A GLY* 3.7 2.9 + - - -
194A LYS 3.6 10.6 + - - -
195A ALA* 3.8 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ALA* 4.6 8.7 - - + +
171A THR* 4.3 23.3 - - + -
172A VAL* 3.8 28.0 - - + -
187A SER 3.1 12.2 + - - +
188A ALA* 3.5 7.0 - - - +
190A SER* 1.3 79.7 - - - +
192A LEU* 1.3 60.4 + - + +
194A LYS* 3.2 20.3 + - - +
195A ALA 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 4.0 25.1 - - + -
160A PHE* 3.7 51.1 - - + -
164A GLN* 3.8 32.5 - - + +
165A ALA* 5.1 2.9 - - - -
168A ALA* 4.1 17.7 - - + -
188A ALA 2.8 19.6 + - - +
189A LEU* 3.7 4.3 - - - +
191A LEU* 1.3 73.6 - - - +
193A GLY* 1.3 59.4 + - - +
194A LYS* 2.7 27.2 + - - +
111D ARG* 4.3 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PHE* 5.5 0.2 - - - -
189A LEU 2.5 21.6 + - - -
190A SER* 3.7 3.3 + - - -
191A LEU 3.3 0.2 - - - -
192A LEU* 1.3 71.1 - - - +
194A LYS* 1.3 74.7 + - - +
195A ALA* 3.8 1.1 - - - -
91D VAL* 4.0 29.8 - - - +
92D HIS* 4.4 7.0 - - - -
111D ARG* 3.2 15.4 + - - -
----------------------------------------------------------
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