Contacts of the helix formed by residues 147 - 158 (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 VAL 147 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA* 1.3 74.7 - - - +
148A ARG* 1.3 67.7 + - - +
150A PRO* 3.1 9.8 - - - +
151A VAL* 3.2 18.9 + - - +
173A LEU* 3.4 32.1 - - + -
177A HIS 5.6 0.4 - - - +
179A ALA 4.0 18.2 - - - +
180A THR 4.4 2.0 - - - +
181A THR* 3.6 26.9 + - - +
184A ALA* 4.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA 2.5 9.0 + - - +
147A VAL* 1.3 80.5 - - - +
149A SER* 1.3 66.5 - - - +
151A VAL* 3.1 11.4 + - - +
152A VAL* 3.3 16.9 + - + +
166A GLU* 4.4 22.5 + - - +
169A THR* 3.9 7.7 - - + +
170A ASP* 2.6 41.6 + - - +
173A LEU* 3.7 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA* 3.6 7.9 + - - -
148A ARG* 1.3 79.1 - - - +
150A PRO* 1.3 70.2 - - - +
152A VAL* 2.8 31.7 - - - +
153A GLU* 3.0 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA* 3.4 29.8 - - + +
147A VAL 3.1 12.6 - - - +
149A SER* 1.3 95.5 - - - +
151A VAL* 1.3 56.0 + - - +
153A GLU* 3.2 10.4 + - + +
154A ALA 3.0 23.4 + - - -
181A THR* 3.7 16.6 - - + +
14D LEU* 3.5 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 3.2 17.0 - - + +
148A ARG 3.1 7.9 + - - +
150A PRO* 1.3 76.1 - - - +
152A VAL* 1.3 61.0 + - - +
154A ALA* 3.3 7.8 + - - +
155A LEU* 3.1 28.3 + - + +
169A THR* 3.6 26.0 - - + +
181A THR* 3.4 32.1 - - - +
184A ALA* 3.9 15.5 - - + +
185A LEU* 3.9 24.9 - - + +
188A ALA* 4.8 1.6 - - + -
14D LEU* 4.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG* 3.3 14.3 + - + +
149A SER* 2.8 33.2 + - - +
151A VAL* 1.3 73.9 - - - +
153A GLU* 1.3 63.2 + - + +
155A LEU* 3.1 6.6 + - - +
156A VAL* 2.8 37.1 + - + +
162A ALA* 5.7 1.1 - - - +
165A ALA* 4.6 7.2 - - + -
166A GLU* 3.7 29.4 - - + +
169A THR* 3.4 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A SER* 3.0 16.1 + - - +
150A PRO* 3.4 12.6 - - + +
152A VAL* 1.3 85.6 - - + +
154A ALA* 1.3 57.4 + - - +
156A VAL* 3.3 7.2 + - + +
157A GLY* 2.8 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A PRO 3.0 13.6 + - - +
151A VAL 3.4 7.9 - - - +
153A GLU* 1.3 77.5 - - - +
155A LEU* 1.3 61.5 + - - +
157A GLY* 3.2 4.0 + - - -
158A LEU* 3.1 27.6 + - + +
185A LEU* 3.3 33.4 - - + -
14D LEU* 3.7 15.5 - - + +
15D ASP* 6.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 3.1 17.6 + - + +
152A VAL 3.1 6.3 + - - +
154A ALA* 1.3 72.4 - - - +
156A VAL* 1.3 63.5 + - - +
157A GLY 3.1 1.3 - - - -
158A LEU* 3.2 10.6 + - + +
159A GLY 3.3 0.3 + - - -
160A PHE* 2.9 39.9 + - + +
165A ALA* 3.8 32.1 - - + +
168A ALA* 4.8 0.2 - - + -
169A THR* 4.0 5.8 - - - +
185A LEU* 4.2 11.4 - - + -
188A ALA* 3.7 25.6 - - + -
189A LEU* 3.7 34.5 - - + -
192A LEU* 4.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A VAL* 2.8 28.2 + - + +
153A GLU* 3.8 7.4 - - + +
155A LEU* 1.3 73.1 - - - +
157A GLY* 1.3 58.8 + - - +
159A GLY* 3.0 18.2 + - - -
160A PHE 3.5 18.8 + - - +
162A ALA* 4.1 25.6 - - + +
165A ALA* 4.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLU 2.8 14.4 + - - -
154A ALA* 3.2 6.3 + - - -
155A LEU 3.1 0.6 - - - -
156A VAL* 1.3 80.5 - - - +
158A LEU* 1.3 58.5 + - - +
159A GLY 3.0 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ALA 3.1 15.5 + - - +
155A LEU* 3.2 14.5 + - + +
157A GLY* 1.3 77.6 - - - +
159A GLY* 1.3 57.3 + - - +
160A PHE* 3.6 9.0 - - + -
185A LEU* 4.8 5.6 - - + -
189A LEU* 4.1 24.9 - - + -
15D ASP* 6.3 3.6 - - + -
32D PRO* 4.9 6.7 - - + -
83D ARG 5.6 0.9 - - - +
86D MET* 5.0 4.0 - - + +
87D ALA* 3.7 42.7 - - + +
90D ALA* 4.1 21.5 - - + -
91D VAL* 6.0 1.6 - - + -
113D PRO* 3.6 16.6 - - + +
----------------------------------------------------------
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