Contacts of the helix formed by residues 146 - 161 (chain J) in PDB entry 5XVO
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 ASN 146 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J ASP* 3.2 16.1 + - - -
144J PRO 3.2 7.2 - - - +
145J ALA* 1.3 80.9 - - - +
147J ARG* 1.3 65.7 + - - +
148J GLU* 3.2 5.8 + - - +
149J GLY* 3.4 26.9 - - - +
150J HIS* 3.1 27.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 147 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J ILE* 4.6 2.5 - - + -
135J MET* 3.0 53.5 - - + +
138J GLU* 3.3 44.2 + - - +
139J LEU* 3.8 15.3 - - + -
140J ARG 5.8 0.2 - - - +
143J ASP* 2.9 16.3 + - - +
145J ALA* 3.5 24.6 + - + +
146J ASN* 1.3 74.8 - - - +
148J GLU* 1.3 59.3 + - - +
150J HIS* 3.4 26.4 + - - +
151J ALA* 2.8 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J TRP* 3.9 20.9 - - - -
109J ILE* 4.0 24.3 - - + +
112J LYS* 3.5 23.1 + - - +
113J ILE* 4.1 13.9 - - + +
116J GLN* 4.8 1.6 - - - +
143J ASP* 2.9 14.3 + - - +
146J ASN* 4.9 4.3 + - - +
147J ARG* 1.3 79.2 - - - +
149J GLY* 1.3 58.8 + - - +
151J ALA* 3.4 2.4 + - - +
152J ALA* 2.9 27.7 + - + +
219J GLU* 3.3 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J ASN* 3.3 26.2 + - - +
147J ARG 3.3 0.4 - - - -
148J GLU* 1.3 78.1 - - - +
150J HIS* 1.3 61.4 + - - +
152J ALA* 3.8 6.0 - - - +
153J ARG* 3.1 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 150 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J MET* 3.4 23.7 - - + +
145J ALA 3.7 15.9 + - - -
146J ASN* 3.1 26.7 + - + +
147J ARG* 3.4 24.7 + - - +
149J GLY* 1.3 74.3 - - - +
151J ALA* 1.3 63.9 + - - +
153J ARG* 3.4 40.3 + - - +
154J SER* 3.1 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J ILE* 4.3 17.3 - - + -
116J GLN* 4.3 10.5 - - - +
132J LEU* 4.1 17.4 - - + +
135J MET* 3.6 21.2 - - + -
147J ARG 2.8 18.4 + - - +
148J GLU 3.5 5.4 - - - +
150J HIS* 1.3 78.0 - - - +
152J ALA* 1.3 56.5 + - - +
154J SER* 3.6 2.4 - - - -
155J TYR* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J LYS* 4.7 9.9 - - - +
116J GLN* 4.2 15.9 + - - +
148J GLU* 2.9 17.7 + - + +
149J GLY* 3.8 8.3 - - - +
151J ALA* 1.3 74.9 - - - +
153J ARG* 1.3 59.8 + - - +
155J TYR* 3.3 6.6 + - - +
156J PHE* 2.9 47.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149J GLY 3.1 20.1 + - - +
150J HIS* 3.4 41.2 + - - +
152J ALA* 1.3 76.9 - - - +
154J SER* 1.3 59.8 + - - +
156J PHE* 3.9 3.9 - - - +
157J ASN* 3.0 51.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 154 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J LYS* 4.6 10.4 - - - +
131J ALA* 5.6 2.4 - - - +
132J LEU* 4.0 15.8 - - - +
135J MET* 5.2 4.5 - - - -
150J HIS 3.1 15.3 + - - -
151J ALA* 3.6 4.9 - - - -
153J ARG* 1.3 77.4 - - - +
155J TYR* 1.3 61.5 + - - +
157J ASN* 3.2 6.5 + - - +
158J THR* 2.8 38.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 155 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J GLN* 3.2 61.5 - - + +
119J HIS* 2.8 28.8 + - - +
120J LEU* 3.8 24.3 - - + +
132J LEU* 4.2 6.2 - - + +
151J ALA 2.9 19.3 + - - +
152J ALA* 3.4 4.9 - - - +
154J SER* 1.3 77.2 + - - +
156J PHE* 1.3 90.0 + + - +
158J THR* 3.5 3.1 + - - -
159J LEU* 3.1 40.7 + - + +
223J PRO* 4.3 3.3 - - - +
226J ASP* 2.8 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J GLN* 4.9 3.1 - - - -
152J ALA* 2.9 38.3 + - + +
153J ARG* 4.1 4.0 - - - +
155J TYR* 1.3 96.8 - + - +
157J ASN* 1.3 61.7 + - - +
159J LEU* 4.5 1.8 - - + +
160J PHE* 2.9 56.7 + + - +
164J PHE* 4.0 22.6 - + + -
166J ARG* 3.9 27.8 - - + -
176J LEU* 3.8 19.5 - - + -
180J TYR* 3.7 22.4 - - - -
226J ASP* 4.4 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 157 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153J ARG* 3.0 40.4 + - - +
154J SER* 3.2 6.3 + - - +
156J PHE* 1.3 76.3 - - - +
158J THR* 1.3 58.5 + - - +
161J GLY* 2.6 43.5 + - - +
162J ASN* 3.3 34.6 + - - +
164J PHE* 3.0 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120J LEU* 3.8 16.1 - - + +
125J TYR* 3.5 55.2 + - + -
128J LYS* 3.3 39.2 + - + +
154J SER* 2.8 22.0 + - - -
155J TYR* 3.6 5.5 - - - -
157J ASN* 1.3 79.4 - - - +
159J LEU* 1.3 59.8 + - - +
161J GLY* 4.4 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J HIS* 3.7 18.6 - - + +
120J LEU* 3.8 20.2 - - + -
123J ARG* 4.2 19.1 - - + -
125J TYR* 4.6 7.6 + - + -
155J TYR* 3.1 50.3 + - + +
156J PHE 4.5 0.2 - - - -
157J ASN 3.3 0.2 - - - -
158J THR* 1.3 81.9 - - - +
160J PHE* 1.3 88.3 + - + +
161J GLY 3.6 0.6 + - - -
226J ASP* 5.1 2.0 - - + -
230J TYR* 3.4 39.7 + - + -
233J ARG* 4.9 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 160 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156J PHE* 2.9 45.3 + + - +
159J LEU* 1.3 91.5 - - + +
161J GLY* 1.3 63.3 + - - +
163J ASP* 5.5 0.7 - - - +
164J PHE* 3.5 38.3 + + + +
172J ILE* 3.7 41.5 - - + -
176J LEU* 4.7 4.7 - - + -
226J ASP* 5.1 3.4 - - + -
229J ILE* 4.5 6.5 - - + -
230J TYR* 3.9 34.1 - + + -
233J ARG* 4.1 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 161 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157J ASN* 2.6 31.0 + - - +
158J THR 4.4 1.2 + - - -
159J LEU 3.6 1.8 + - - -
160J PHE* 1.3 74.6 - - - +
162J ASN* 1.3 63.8 + - - -
163J ASP* 3.2 4.0 - - - -
164J PHE* 3.2 16.1 + - - +
----------------------------------------------------------
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