Contacts of the helix formed by residues 153 - 163 (chain B) in PDB entry 2Q53
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 PRO 153 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 4.3 4.0 - - + -
80B TRP* 3.4 60.1 - - + +
115B GLN* 4.5 15.2 - - - +
152B LEU* 1.3 90.7 - - + +
154B LEU* 1.3 65.9 + - - +
155B GLU* 3.1 9.6 - - + +
156B TYR* 3.1 14.7 + - + +
157B GLN* 3.0 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU 3.3 2.7 + - - +
153B PRO* 1.3 72.2 - - - +
155B GLU* 1.3 72.3 + - - +
157B GLN* 3.7 16.7 + - + +
158B GLU* 2.9 63.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU* 6.1 1.3 - - - +
153B PRO* 3.1 8.5 - - + +
154B LEU* 1.3 90.5 + - - +
156B TYR* 1.3 65.5 + - - +
158B GLU* 3.1 17.4 + - - +
159B LYS* 3.2 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 5.4 3.1 + - - +
26B LEU* 5.6 1.3 - - + -
51B LEU* 3.8 22.5 - - + +
78B GLU* 4.0 22.7 - - + +
79B VAL* 3.7 19.2 - - - +
80B TRP* 3.6 54.3 + + + +
152B LEU* 3.7 20.9 - - + -
153B PRO* 3.1 15.1 + - + +
155B GLU* 1.3 75.8 - - - +
157B GLN* 1.3 62.8 + - - +
159B LYS* 2.8 41.1 + - + +
160B LEU* 3.0 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA* 3.7 16.8 - - + +
148B LYS* 3.2 28.8 + - - +
151B GLY* 3.7 8.5 - - - -
152B LEU* 2.5 44.7 + - + +
153B PRO 3.0 16.3 + - - +
154B LEU* 3.8 18.5 - - + +
156B TYR* 1.3 77.2 - - - +
158B GLU* 1.3 67.2 + - - +
160B LEU* 3.3 12.2 + - - +
161B LYS* 2.9 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 2.9 44.8 + - + +
155B GLU* 3.1 11.2 + - - +
156B TYR 3.1 0.6 - - - -
157B GLN* 1.3 77.6 - - - +
159B LYS* 1.3 63.1 + - + +
161B LYS* 3.0 55.7 + - - +
162B ALA* 3.4 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASP* 5.8 1.8 + - - -
78B GLU* 5.1 17.4 + - - +
155B GLU* 3.2 12.1 + - - +
156B TYR* 2.8 27.1 + - + +
158B GLU* 1.3 74.7 - - + +
160B LEU* 1.3 65.4 + - + +
161B LYS 2.8 6.0 + - - -
162B ALA* 2.8 18.2 + - - +
163B ILE* 3.3 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR 5.9 0.7 - - - +
26B LEU* 4.6 3.4 - - + -
51B LEU* 4.1 18.2 - - + -
140B LYS* 3.4 9.4 - - - +
143B ILE* 4.0 24.7 - - + +
144B CYS* 5.3 10.4 - - + +
147B ALA* 3.4 33.4 - - + -
156B TYR* 3.0 43.0 + - + +
157B GLN* 3.8 8.5 - - - +
159B LYS* 1.3 77.0 - - + +
161B LYS* 1.3 61.9 - - + +
163B ILE* 3.0 43.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LYS* 2.7 29.0 + - - +
144B CYS* 5.4 14.8 - - - -
154B LEU* 5.5 0.2 - - - +
157B GLN* 2.9 27.7 + - - +
158B GLU* 3.0 49.9 + - - +
159B LYS 2.8 1.2 + - - -
160B LEU* 1.3 77.8 - - - +
162B ALA* 1.3 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LYS* 4.2 0.2 - - - -
158B GLU 3.4 6.0 + - - +
159B LYS* 2.8 13.0 + - - +
161B LYS* 1.3 73.1 - - - +
163B ILE* 1.3 65.1 + - - +
164B GLU* 3.0 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 4.7 2.5 - - + -
53B PHE* 4.1 25.1 - - + -
135B PRO* 3.6 32.3 - - + -
140B LYS* 2.5 38.6 + - + -
143B ILE* 5.4 2.7 - - + -
159B LYS 3.3 3.7 + - - +
160B LEU* 3.0 58.3 - - + +
161B LYS 3.1 2.2 - - - -
162B ALA* 1.3 74.4 - - - +
164B GLU* 1.3 61.1 + - - +
165B PRO* 3.0 7.3 - - - +
----------------------------------------------------------
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