Contacts of the helix formed by residues 152 - 166 (chain A) in PDB entry 2PX7
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 152 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 4.0 16.8 - - + -
81A ALA* 4.1 5.6 - - + +
83A LEU 2.6 28.3 + - - +
84A PRO* 2.9 19.5 + - - -
85A LEU 3.0 9.9 + - - -
86A VAL* 3.5 17.2 - - + +
150A PHE 3.4 2.0 + - - -
151A PHE* 1.3 68.7 - - - +
153A ALA* 1.3 57.6 + - - +
155A LEU* 3.3 3.3 + - - +
156A ARG* 3.0 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PRO* 4.7 1.0 + - - +
151A PHE* 3.3 5.5 - - + +
152A THR* 1.3 78.8 - - - +
154A LEU* 1.3 61.4 + - - +
156A ARG* 3.6 12.1 + - - +
157A GLU* 3.1 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLY* 3.3 25.4 - - - +
113A ALA* 4.2 0.7 - - + -
150A PHE* 4.9 1.3 - - + -
151A PHE* 3.0 20.7 + - + +
153A ALA* 1.3 76.9 - - - +
155A LEU* 1.3 61.5 + - - +
157A GLU* 3.1 10.4 + - + +
158A ALA* 2.9 26.7 + - - +
176A VAL* 3.8 17.3 - - + -
179A LEU* 3.9 20.6 - - + -
181A TYR* 3.6 54.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
74A VAL* 4.4 4.5 - - + -
78A LEU* 3.8 24.7 - - + -
86A VAL* 4.1 6.1 - - + -
88A VAL* 3.9 27.6 - - + -
150A PHE* 4.0 17.9 - - + +
151A PHE 3.1 11.8 + - - +
152A THR 3.3 6.5 + - - +
154A LEU* 1.3 77.6 - - - +
156A ARG* 1.3 56.1 + - - +
158A ALA* 3.3 5.0 + - + +
159A HIS* 2.9 39.9 + - + -
172A ASP* 3.7 35.2 - - + +
175A LEU* 5.3 0.2 - - + -
176A VAL* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 2.6 55.7 + - + -
79A GLU* 4.0 12.0 + - - +
81A ALA 3.5 19.2 + - - -
82A SER 6.0 0.8 - - - -
83A LEU 5.6 0.4 + - - -
152A THR* 3.0 41.6 + - - +
153A ALA* 3.8 9.5 - - - +
155A LEU* 1.3 72.2 - - - +
157A GLU* 1.3 64.5 + - - +
159A HIS* 3.2 3.7 + - - +
160A ALA* 2.9 25.6 + - - +
163A ARG* 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ALA 3.1 21.6 + - - +
154A LEU* 3.1 11.9 + - + +
156A ARG* 1.3 73.4 - - - +
158A ALA* 1.3 57.8 + - - +
160A ALA* 3.3 8.3 + - - +
161A TYR* 3.0 30.7 + - - +
179A LEU* 3.7 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU 2.9 14.1 + - - +
155A LEU* 3.5 10.5 - - + +
157A GLU* 1.3 76.7 - - - +
159A HIS* 1.3 57.3 + - - +
161A TYR* 3.5 2.3 + - - +
162A ALA* 3.0 29.4 + - - +
175A LEU* 3.7 37.1 - - + +
176A VAL* 3.8 17.3 - - + +
179A LEU* 3.5 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 3.5 33.7 + - + +
74A VAL* 3.4 13.0 - - + +
75A ALA* 3.8 15.0 - - + +
78A LEU* 3.7 20.0 - - + -
155A LEU* 2.9 34.5 + - + +
156A ARG* 3.9 2.9 - - - +
158A ALA* 1.3 74.8 - - - +
160A ALA* 1.3 56.7 + - - +
162A ALA* 3.4 5.5 + - - +
163A ARG* 3.0 44.7 + - - +
172A ASP* 2.7 27.0 + - - -
175A LEU* 3.5 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG 2.9 17.6 + - - +
157A GLU* 3.6 10.8 - - - +
158A ALA 3.3 0.2 - - - -
159A HIS* 1.3 73.5 - - - +
161A TYR* 1.3 62.9 + - - +
163A ARG* 3.4 25.0 + - - +
164A ARG* 3.2 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLU 3.0 17.2 + - - +
158A ALA 3.9 3.6 - - - +
160A ALA* 1.3 76.7 - - - +
162A ALA* 1.3 64.5 + - - +
164A ARG* 3.2 41.5 + - - +
165A LYS* 3.1 69.5 + - + +
167A LEU* 5.5 3.4 - - + -
175A LEU 5.3 1.1 - - - -
178A ALA* 3.6 39.0 + - + -
179A LEU* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 4.2 7.2 - - - +
158A ALA 3.0 18.8 + - - +
159A HIS* 3.7 7.9 - - - +
160A ALA 3.3 0.2 - - - -
161A TYR* 1.3 79.6 - - - +
163A ARG* 1.3 56.8 + - - +
165A LYS* 4.7 0.2 - - - -
166A GLY* 2.9 26.9 + - - -
167A LEU* 3.1 39.2 + - + +
175A LEU* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 4.5 15.4 + - - +
159A HIS* 3.0 35.1 + - - +
160A ALA* 3.5 27.9 - - - +
161A TYR 3.3 0.2 - - - -
162A ALA* 1.3 77.5 - - - +
164A ARG* 1.3 62.7 + - + +
165A LYS 3.4 0.2 + - - -
166A GLY* 3.5 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ALA* 3.2 18.7 + - - +
161A TYR* 3.2 55.7 + - - +
163A ARG* 1.3 76.7 - - + +
165A LYS* 1.3 67.0 + - + +
166A GLY 3.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR* 3.1 61.4 + - + +
162A ALA 3.3 2.2 + - - +
164A ARG* 1.3 83.1 - - + +
166A GLY* 1.3 62.9 + - - +
167A LEU* 4.2 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ALA 2.9 7.1 + - - -
163A ARG* 3.5 6.9 + - - -
164A ARG 3.5 3.0 + - - -
165A LYS* 1.3 77.0 - - - +
167A LEU* 1.3 61.8 + - - +
168A GLU* 3.6 13.8 + - - +
----------------------------------------------------------
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