Contacts of the helix formed by residues 169 - 177 (chain A) in PDB entry 2E52
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 TRP 169 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 3.4 37.2 - - + +
44A ARG* 5.5 2.0 - - - -
46A ILE* 3.7 29.2 - - + -
47A GLY* 3.6 20.6 - - - -
67A GLY* 3.6 14.8 - - - -
70A VAL* 4.2 7.4 - - + -
71A LEU* 4.1 15.7 - - + -
109A ALA* 3.5 34.8 - - + -
110A LYS 2.9 24.2 + - - -
111A SER* 5.0 2.7 - - - -
142A THR* 3.6 24.5 + - + +
143A ALA 3.2 25.7 + - - -
144A PRO* 3.6 4.3 - - + -
168A SER* 1.3 74.0 - - - +
170A GLU* 1.3 66.3 + - - +
172A LEU* 3.4 10.4 + - + -
173A ALA* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG 5.7 0.9 - - - +
144A PRO* 3.8 9.0 - - - +
145A PHE* 2.9 42.3 + - + +
146A PHE* 4.3 11.2 - - + -
168A SER* 3.1 6.9 - - - +
169A TRP* 1.3 79.3 + - - +
171A HIS* 1.3 66.2 + - - +
173A ALA* 3.4 6.5 + - - +
174A ILE* 3.0 29.9 + - - +
234A LEU* 4.5 11.2 - - + -
237A GLU* 4.1 33.9 - - + +
241A ILE* 4.0 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE* 3.6 37.9 - + - -
167A PHE* 3.6 24.0 - - + -
168A SER* 2.7 30.4 + - - +
170A GLU* 1.3 75.8 - - - +
172A LEU* 1.3 61.9 + - - +
174A ILE* 3.3 13.7 + - + +
175A LEU* 3.1 27.0 + - - +
212A MET* 5.6 0.2 - - - -
215A PHE* 3.7 27.6 - + - -
216A ASN* 2.8 26.0 + - - -
219A PHE* 3.7 27.1 - + + -
230A LEU* 5.3 1.8 - - + -
234A LEU* 5.3 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 4.3 9.2 - - + -
71A LEU* 3.6 25.6 - - + -
74A ALA* 3.5 32.8 - - + -
75A PHE* 5.2 2.7 - - + +
78A LEU* 4.1 27.8 - - + -
142A THR* 4.5 2.5 - - + -
167A PHE* 4.0 19.2 - - + -
168A SER 3.1 14.8 + - - +
169A TRP* 3.5 27.4 - - + +
171A HIS* 1.3 74.9 - - - +
173A ALA* 1.3 64.2 + - - +
175A LEU* 3.2 6.6 + - + +
176A LEU* 3.0 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 4.5 9.4 - - + +
43A VAL* 3.9 15.7 - - + +
44A ARG* 4.3 18.4 - - + +
169A TRP 2.9 21.1 + - - +
170A GLU 3.4 5.6 + - - +
172A LEU* 1.3 72.8 - - - +
174A ILE* 1.3 57.5 + - - +
176A LEU* 3.4 8.2 + - - +
177A GLN* 2.9 33.3 + - - +
237A GLU* 4.0 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLU 3.0 20.9 + - - +
171A HIS* 3.6 12.8 - - + +
172A LEU 3.1 0.4 - - - -
173A ALA* 1.3 74.7 - - - +
175A LEU* 1.3 65.0 + - - +
177A GLN* 3.3 6.1 + - - +
178A LEU* 3.0 47.8 + - + +
219A PHE* 4.0 20.0 - - + -
225A ILE* 4.3 2.9 - - + -
230A LEU* 3.8 24.0 - - + -
233A LEU* 4.0 31.4 - - + -
234A LEU* 3.9 23.1 - - + +
237A GLU* 4.8 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 4.0 22.0 - - + -
167A PHE* 4.1 23.8 - - + -
171A HIS 3.1 16.5 + - - +
172A LEU* 3.6 7.2 - - - +
174A ILE* 1.3 75.5 - - - +
176A LEU* 1.3 63.4 + - - +
178A LEU 3.4 0.5 + - - -
179A ASP 3.2 3.1 + - - -
180A LEU* 3.0 56.7 + - + +
188A PHE* 4.0 19.5 - - + -
191A LEU* 4.2 11.0 - - + -
219A PHE* 3.6 23.8 - - + -
223A PHE* 3.9 17.0 - - + -
225A ILE* 5.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 3.0 29.7 + - + +
39A VAL* 4.3 9.9 - - + -
40A ILE* 3.5 26.9 - - + -
43A VAL* 4.1 17.9 - - + -
74A ALA* 3.8 32.5 - - + +
77A LEU* 3.6 32.3 - - + -
78A LEU* 3.8 15.0 - - + -
172A LEU* 3.0 25.0 + - + +
173A ALA* 3.7 3.4 - - - +
175A LEU* 1.3 75.3 - - - +
177A GLN* 1.3 63.4 + - - +
179A ASP* 3.0 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 5.9 0.5 + - - -
40A ILE* 3.7 17.8 - - + +
44A ARG* 2.7 32.7 + - - +
173A ALA 2.9 18.8 + - - +
174A ILE* 3.3 6.4 + - - +
176A LEU* 1.3 75.9 - - - +
178A LEU* 1.3 67.4 + - + +
179A ASP* 3.2 11.5 + - - +
233A LEU* 3.1 33.9 - - + +
236A LYS* 5.5 5.1 - - - +
237A GLU* 5.2 1.6 + - - -
----------------------------------------------------------
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