Contacts of the helix formed by residues 146 - 164 (chain B) in PDB entry 2E9D
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 GLY 146 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B TYR* 1.3 80.9 - - - +
147B GLY* 1.3 65.4 + - - -
148B ARG 3.4 2.2 - - - -
149B TRP* 3.4 15.4 + - - +
150B ASP* 3.1 23.2 + - - +
203B ASN* 3.3 21.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B TYR* 3.5 13.1 - - - -
146B GLY* 1.3 69.8 - - - -
148B ARG* 1.3 66.0 + - - +
150B ASP* 3.3 4.2 + - - +
151B ILE* 3.3 25.1 + - - +
203B ASN* 2.6 18.5 + - - -
204B PHE 3.3 19.7 - - - -
206B LEU* 4.0 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLU* 3.7 25.0 + - + +
178A ASN* 4.2 8.5 + - - +
188A PRO* 6.2 2.4 - - - +
207A TRP* 3.1 78.1 + - + +
208A GLN* 4.3 8.5 + - - +
210A ALA* 3.8 12.9 - - - +
211A TYR* 3.9 22.8 - - - +
147B GLY* 1.3 75.3 - - - +
149B TRP* 1.3 57.3 + - - +
151B ILE* 3.2 3.6 + - - +
152B VAL* 2.9 32.6 + - - +
203B ASN* 2.9 17.0 + - - +
206B LEU* 3.6 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLU* 4.0 20.9 - - - +
111B GLY* 3.4 40.6 - - - -
112B ASP* 3.8 37.5 + - + +
144B ASN 5.4 0.7 - - - -
145B TYR* 4.2 2.9 - + - -
146B GLY* 3.4 26.8 + - - +
147B GLY 3.2 0.4 - - - -
148B ARG* 1.3 79.4 - - - +
150B ASP* 1.3 77.4 + - + +
152B VAL* 3.2 7.0 + - + +
153B GLN* 2.8 55.2 + - + +
156B ARG* 4.7 14.2 - - - +
182B CYS* 4.1 15.0 - - - -
203B ASN* 5.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B TYR* 2.7 34.3 + - + +
146B GLY 3.1 5.8 + - - +
147B GLY 3.4 7.2 - - - +
149B TRP* 1.3 88.2 - - + +
151B ILE* 1.3 59.7 - - - +
153B GLN* 2.5 39.7 + - - +
154B GLY* 3.2 1.0 + - - -
181B VAL* 3.4 6.7 - - - +
182B CYS* 2.9 38.0 + - - +
208B GLN* 2.8 23.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 3.8 47.1 - - + -
177A LEU* 4.4 7.4 - - + -
207A TRP* 3.9 23.1 - - + -
147B GLY 3.4 14.4 - - - +
148B ARG* 3.2 7.9 + - - +
150B ASP* 1.3 76.8 - - + +
152B VAL* 1.3 59.3 + - - +
154B GLY* 3.2 1.9 + - - -
155B VAL* 2.8 30.5 + - + +
177B LEU* 4.6 9.8 - - + +
181B VAL* 4.5 11.4 - - + -
206B LEU* 4.4 8.3 - - + -
207B TRP* 4.1 31.6 - - + +
208B GLN* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ILE* 3.6 29.6 - - + +
173A ASP* 3.9 12.1 - - - +
174A GLU* 3.6 31.2 - - + +
177A LEU* 4.5 7.2 - - + -
207A TRP* 4.0 11.4 - - + -
148B ARG 2.9 20.4 + - - +
149B TRP* 3.6 9.9 - - + +
151B ILE* 1.3 72.3 - - - +
153B GLN* 1.3 62.1 + - - +
155B VAL* 3.1 9.3 + - - +
156B ARG* 2.9 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TRP* 2.8 47.3 + - + +
150B ASP* 2.5 42.5 + - - +
152B VAL* 1.3 72.9 - - - +
154B GLY* 1.3 71.6 + - - +
156B ARG* 3.2 17.4 + - - +
157B GLN* 2.4 52.7 + - - +
180B HIS 2.7 24.2 + - - -
181B VAL* 3.8 1.2 - - - +
182B CYS* 4.1 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ASP 3.2 5.3 + - - -
151B ILE* 3.6 3.6 - - - -
152B VAL 3.2 0.4 - - - -
153B GLN* 1.3 84.4 - - - +
155B VAL* 1.3 63.5 + - - +
157B GLN* 3.0 18.6 + - - +
158B LEU* 3.1 16.1 + - - +
177B LEU* 4.5 10.1 - - - -
180B HIS* 3.5 30.3 - - - +
181B VAL* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 3.6 41.3 - - + -
158A LEU* 4.6 12.3 - - + -
172A ILE* 4.2 24.2 - - + -
177A LEU* 3.8 15.9 - - + -
151B ILE* 2.8 22.4 + - + +
152B VAL* 3.1 9.8 + - - +
154B GLY* 1.3 76.3 - - - +
156B ARG* 1.3 57.8 - - - +
158B LEU* 3.2 8.0 + - - +
159B ALA* 2.8 29.8 + - + +
177B LEU* 4.5 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PRO* 3.8 23.2 + - + +
170A ASP* 4.4 17.7 + - - +
172A ILE* 2.7 32.9 + - + +
173A ASP* 3.9 14.1 - - - +
149B TRP* 4.7 17.0 - - - +
152B VAL* 2.9 26.4 + - + +
153B GLN* 3.2 14.6 + - - +
155B VAL* 1.3 76.9 - - - +
157B GLN* 1.3 62.7 + - + +
159B ALA* 3.4 8.0 + - - +
160B GLU* 3.1 27.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
153B GLN* 2.4 43.3 + - - +
154B GLY* 3.0 6.7 + - - +
156B ARG* 1.3 77.5 - - + +
158B LEU* 1.3 64.0 + - - +
160B GLU* 3.2 16.7 + - - +
161B LYS* 3.3 20.1 + - + +
180B HIS* 2.9 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 5.2 5.6 - - + -
154B GLY 3.1 13.5 + - - +
155B VAL* 3.5 8.3 - - - +
157B GLN* 1.3 81.5 - - - +
159B ALA* 1.3 60.6 + - - +
161B LYS* 3.2 17.0 + - + +
162B VAL* 3.2 25.7 + - - +
167B LEU* 3.6 19.3 - - + +
172B ILE* 4.0 32.1 - - + -
176B MET* 4.3 19.1 - - + +
177B LEU* 4.3 26.0 - - + -
180B HIS* 4.1 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU 6.4 0.2 - - - -
159A ALA* 6.2 2.9 - - - +
162A VAL* 3.6 19.0 - - + +
169A PRO* 3.4 32.0 - - + +
172A ILE* 4.7 6.1 - - + -
155B VAL* 2.8 20.0 + - + +
156B ARG* 3.8 7.9 - - - +
157B GLN 3.2 0.2 - - - -
158B LEU* 1.3 73.8 - - - +
160B GLU* 1.3 63.6 + - - +
162B VAL* 3.7 8.7 - - - -
163B GLN* 3.2 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PRO* 3.4 18.3 - - + +
170A ASP* 5.5 2.4 + - - +
156B ARG* 3.1 18.1 + - + +
157B GLN* 3.5 10.3 - - - +
158B LEU 3.1 0.8 - - - -
159B ALA* 1.3 78.5 - - - +
161B LYS* 1.3 50.4 + - - +
162B VAL 3.1 1.1 - - - -
163B GLN* 3.0 24.0 + - - +
164B GLN* 2.7 54.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
157B GLN* 3.3 17.7 - - + +
158B LEU* 3.2 21.2 + - + +
160B GLU* 1.3 76.9 - - + +
162B VAL* 1.3 53.0 + - - +
164B GLN* 3.8 21.5 - - - +
166B ASN* 2.9 22.4 + - + -
167B LEU* 2.7 41.9 + - + -
180B HIS* 4.5 20.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ALA* 3.5 38.6 - - + +
162A VAL* 3.6 15.7 - - + +
163A GLN* 4.0 19.6 + - + +
158B LEU 3.2 10.5 + - - +
159B ALA* 3.8 8.7 - - - +
160B GLU 3.1 0.6 - - - -
161B LYS* 1.3 76.9 - - - +
163B GLN* 1.3 63.3 + - - +
165B GLY* 3.5 9.8 + - - -
167B LEU* 3.6 48.4 - - + +
169B PRO* 4.7 5.4 - - + -
172B ILE* 5.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A VAL* 4.3 13.4 - - + +
167A LEU 5.3 1.2 + - - -
168A GLN* 3.3 28.1 + - - +
169A PRO* 3.8 13.1 - - - +
159B ALA 3.2 12.8 + - - +
160B GLU* 3.0 27.3 + - - +
162B VAL* 1.3 76.7 - - - +
164B GLN* 1.3 56.6 + - + +
165B GLY* 2.6 17.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLU* 2.7 47.9 + - + +
161B LYS* 3.6 17.2 - - - +
163B GLN* 1.3 73.9 - - + +
165B GLY* 1.3 59.4 + - - +
166B ASN* 2.9 30.5 + - - +
----------------------------------------------------------
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