Contacts of the helix formed by residues 158 - 170 (chain E) in PDB entry 3N1Q
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 LYS 158 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E TRP* 3.3 65.2 - - + +
121E VAL* 5.1 2.7 - - + -
151E THR* 4.2 13.2 - - + -
153E ASP* 2.9 31.8 + - - +
155E ASP* 2.8 40.1 + - + +
156E ARG 3.1 1.0 - - - -
157E ASN* 1.3 76.2 - - + +
159E TYR* 1.3 61.8 + - - +
160E GLY 3.3 1.3 - - - -
161E LEU* 3.3 5.8 + - + +
162E LEU* 2.9 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E THR* 3.5 38.7 - - + +
151E THR* 3.7 15.7 - - + -
154E ARG* 3.7 21.0 - - - +
155E ASP 3.1 16.8 - - - -
156E ARG* 3.1 41.3 + - - +
158E LYS* 1.3 76.3 - - - +
160E GLY* 1.3 66.5 + - - +
162E LEU* 3.4 11.2 - - + +
163E ALA* 2.9 25.8 + - - +
176E TYR* 3.2 23.5 - + + +
179E ARG 3.8 11.2 - - - -
180E ASN 3.5 21.2 + - - -
181E HIS* 4.0 5.2 - - - -
182E VAL* 4.0 13.3 - - + +
870F ASP* 5.4 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E PRO* 3.4 12.9 - - - +
43E LEU 3.1 37.9 + - - -
156E ARG 4.4 0.2 + - - -
157E ASN 4.0 6.9 + - - -
158E LYS 3.3 0.8 - - - -
159E TYR* 1.3 79.9 - - - +
161E LEU* 1.3 59.8 + - - +
163E ALA* 3.5 6.8 + - - +
164E ARG 3.5 3.3 + - - -
176E TYR* 3.5 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 161 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E LEU* 4.7 13.0 - - + +
42E PRO* 3.5 36.5 - - + +
117E MET* 5.1 11.9 - - + -
118E TRP* 3.5 37.5 - - + +
157E ASN 4.7 4.8 + - - +
158E LYS* 3.3 7.1 + - + +
159E TYR 3.3 0.2 - - - -
160E GLY* 1.3 72.6 - - - +
162E LEU* 1.3 62.0 + - - +
164E ARG* 2.9 7.0 + - + +
165E LEU* 2.8 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E LEU* 4.3 8.7 - - + -
114E VAL* 3.7 29.8 - - + -
118E TRP* 3.8 13.2 - - + -
123E LEU* 4.3 9.2 - - + -
149E ILE* 3.9 22.0 - - + +
150E THR* 3.7 37.9 - - - +
151E THR* 4.2 9.0 - - + -
158E LYS 2.9 14.7 + - - +
159E TYR* 3.4 15.5 - - + +
161E LEU* 1.3 76.3 - - - +
163E ALA* 1.3 57.7 + - - +
165E LEU* 3.1 5.8 + - + +
166E ALA* 2.8 28.5 + - - +
182E VAL* 4.7 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LEU* 3.7 27.8 - - + -
149E ILE* 5.9 0.2 - - - -
159E TYR 2.9 12.0 + - - +
160E GLY 3.6 10.3 - - - +
162E LEU* 1.3 75.4 - - - +
164E ARG* 1.3 62.6 + - - +
166E ALA* 2.9 16.8 + - - +
167E VAL* 3.0 16.9 + - - +
174E VAL* 3.8 17.0 - - + +
176E TYR* 4.7 5.8 - - + -
182E VAL* 4.1 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E LEU* 3.7 31.4 - - + -
41E VAL* 2.8 38.0 + - - +
42E PRO* 4.1 9.9 - - + -
43E LEU* 3.2 31.6 - - - +
47E GLN* 4.7 3.0 - - - +
49E VAL* 4.7 9.5 - - - +
160E GLY 3.5 2.2 + - - -
161E LEU* 2.9 11.5 + - + +
163E ALA* 1.3 77.0 - - - +
165E LEU* 1.3 59.1 + - - +
167E VAL* 2.9 43.6 + - - +
168E GLU* 3.0 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E LEU* 3.5 29.8 - - + -
110E LEU* 3.3 20.1 - - + +
113E ALA* 4.2 22.0 - - + +
114E VAL* 4.4 6.7 - - + -
117E MET* 3.6 31.2 - - + -
118E TRP* 3.6 34.1 - - + -
161E LEU* 2.8 17.7 + - + +
162E LEU* 3.1 8.5 + - - +
164E ARG* 1.3 74.3 - - - +
166E ALA* 1.3 56.3 + - - +
168E GLU* 3.5 8.3 + - + +
169E ALA* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 166 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E LEU* 3.6 21.7 - - + +
149E ILE* 4.6 1.8 - - + -
162E LEU 2.8 12.6 + - - +
163E ALA* 2.9 15.2 + - - +
165E LEU* 1.3 76.1 - - - +
167E VAL* 1.3 60.7 + - - +
169E ALA* 3.4 7.2 + - - +
171E PHE* 3.2 26.8 + - + +
174E VAL* 3.8 5.6 - - + -
184E VAL* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LEU* 4.6 5.2 - - + -
49E VAL* 4.2 29.2 - - + +
163E ALA 3.0 17.4 + - - +
164E ARG* 2.9 34.8 + - - +
166E ALA* 1.3 75.8 - - - +
168E GLU* 1.3 69.5 + - - +
170E GLY* 3.3 14.0 + - - -
171E PHE 4.5 6.3 - - - +
174E VAL* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 168 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E LEU* 3.8 34.1 - - + +
113E ALA* 6.4 1.3 - - + -
164E ARG* 3.0 31.3 + - - +
165E LEU* 3.9 11.9 - - + +
167E VAL* 1.3 76.8 - - - +
169E ALA* 1.3 66.2 + - - +
170E GLY* 3.4 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 169 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E ARG* 3.8 20.0 - - - +
109E ALA* 4.1 15.1 - - - +
110E LEU* 3.8 31.0 - - + +
113E ALA* 5.9 2.2 - - + -
165E LEU 3.0 17.3 + - - +
166E ALA* 3.4 10.1 - - - +
167E VAL 3.2 0.4 - - - -
168E GLU* 1.3 78.8 - - - +
170E GLY* 1.3 56.9 + - - +
171E PHE* 3.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 170 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E ARG* 2.7 30.5 + - - -
167E VAL 3.3 9.3 + - - -
168E GLU 3.2 3.6 - - - -
169E ALA* 1.3 79.7 - - - +
171E PHE* 1.3 68.0 + - - +
172E ASP* 3.2 8.1 + - - +
----------------------------------------------------------
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