Contacts of the helix formed by residues 146 - 161 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASP* 3.2 16.6 + - - +
144B PRO 3.2 7.0 - - - +
145B ALA* 1.3 80.2 - - - +
147B ARG* 1.3 64.2 + - - +
148B GLU* 3.2 1.6 - - - +
149B GLY* 2.9 23.1 + - - -
150B HIS* 2.9 21.3 + - - +
4H A 3.4 17.8 + - - -
5H G 3.3 34.6 + - - +
43Q T 3.0 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 4.6 2.5 - - + -
135B MET* 3.5 40.8 - - + +
138B GLU* 3.3 46.6 + - - +
139B LEU* 4.0 11.7 - - + -
140B ARG 5.7 0.2 - - - +
143B ASP* 2.8 19.7 + - - +
145B ALA* 3.3 33.7 + - + +
146B ASN* 1.3 71.5 - - - +
148B GLU* 1.3 60.0 + - - +
150B HIS* 3.3 5.1 + - - +
151B ALA* 2.8 34.1 + - - +
44Q C 4.1 1.8 - - - -
45Q G 2.8 48.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B TRP* 3.9 17.1 - - + -
109B ILE* 4.0 28.4 - - + +
112B LYS* 3.4 20.1 + - - +
113B ILE* 4.1 14.1 - - + +
116B GLN* 4.8 1.9 - - - +
143B ASP* 2.8 16.0 + - - +
146B ASN* 4.5 1.4 - - - +
147B ARG* 1.3 78.8 - - - +
149B GLY* 1.3 57.4 + - - +
151B ALA* 3.4 2.8 + - - +
152B ALA* 2.9 27.5 + - - +
203B LYS* 5.1 3.6 + - - -
219B GLU* 3.3 19.4 - - - +
5H G 2.9 42.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ASN* 2.9 25.0 + - - -
148B GLU* 1.3 76.2 - - - +
150B HIS* 1.3 65.2 + - - +
153B ARG* 3.1 18.5 + - - +
4H A 3.4 22.7 + - - +
5H G 3.2 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B MET* 3.5 23.4 - - + +
145B ALA 4.1 1.6 + - - -
146B ASN* 2.9 26.9 + - - +
147B ARG* 3.9 3.3 + - - +
149B GLY* 1.3 74.5 - - - +
151B ALA* 1.3 67.4 + - - +
153B ARG* 3.4 5.7 + - + +
154B SER* 3.2 23.7 + - - -
3H G 3.5 14.5 + - - -
43Q T 3.8 13.0 - - - -
44Q C 2.7 56.1 + - - -
45Q G 3.3 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 4.3 16.6 - - + -
116B GLN* 4.3 11.2 - - - +
132B LEU* 4.1 19.6 - - + +
135B MET* 3.6 20.3 - - + -
147B ARG 2.8 19.8 + - - +
148B GLU 3.5 4.7 - - - +
150B HIS* 1.3 79.5 - - - +
152B ALA* 1.3 56.5 + - - +
154B SER* 3.4 2.1 + - - -
155B TYR* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LYS* 4.7 2.5 - - - +
116B GLN* 4.1 17.5 + - - +
148B GLU 2.9 17.4 + - - +
149B GLY 3.8 3.4 - - - +
150B HIS 3.3 0.2 - - - -
151B ALA* 1.3 73.9 - - - +
153B ARG* 1.3 68.2 + - - +
155B TYR* 3.3 7.3 + - - +
156B PHE* 2.9 32.1 + - + -
4H A 3.5 20.2 - - - +
5H G 3.9 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLY 3.1 14.9 + - - +
150B HIS* 3.9 7.6 - - + +
151B ALA 3.3 0.2 - - - -
152B ALA* 1.3 77.5 - - - +
154B SER* 1.3 64.1 + - - +
156B PHE* 3.5 1.6 + - - +
157B ASN* 3.0 47.6 + - - +
162B ASN* 5.7 1.8 + - - -
2H C 2.7 33.2 + - - -
3H G 2.9 57.8 + - - +
4H A 3.4 33.8 - - - +
45Q G 3.4 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 5.8 0.2 - - - +
128B LYS* 4.3 15.6 + - - +
131B ALA* 5.6 2.3 - - - +
132B LEU* 4.0 15.8 - - - +
135B MET* 5.3 3.8 - - - -
150B HIS 3.2 14.3 + - - -
151B ALA* 3.6 4.5 - - - -
153B ARG* 1.3 78.0 - - - +
155B TYR* 1.3 61.7 + - - +
157B ASN* 3.2 5.3 + - - +
158B THR* 2.8 38.1 + - - -
46Q G 5.9 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLN* 3.3 60.8 - - + +
119B HIS* 2.8 29.0 + - - +
120B LEU* 3.8 24.1 - - + +
132B LEU* 4.2 6.2 - - + +
151B ALA 2.9 19.1 + - - +
152B ALA* 3.4 5.2 - - - +
154B SER* 1.3 76.5 - - - +
156B PHE* 1.3 85.7 + + - +
158B THR* 3.5 2.8 + - - -
159B LEU* 3.1 44.6 + - + +
223B PRO* 4.2 3.8 - - - +
226B ASP* 2.8 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLN* 5.1 3.1 - - - -
152B ALA* 2.9 31.8 + - + +
153B ARG* 4.1 3.6 - - - +
155B TYR* 1.3 96.7 - + - +
157B ASN* 1.3 62.3 + - - +
159B LEU* 4.5 1.6 - - - +
160B PHE* 2.9 56.1 + + - +
161B GLY 4.3 0.2 - - - +
164B PHE* 4.1 22.3 - + + -
166B ARG* 4.0 21.1 - - + -
176B LEU* 3.9 19.5 - - + -
180B TYR* 3.7 22.7 - + - -
226B ASP* 4.5 5.2 - - - -
4H A 4.4 12.1 - - - -
5H G 3.8 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ARG* 3.0 46.9 + - - +
154B SER* 3.8 4.9 - - - +
156B PHE* 1.3 77.2 - - - +
158B THR* 1.3 58.2 + - - +
161B GLY* 2.6 44.9 + - - +
162B ASN* 3.5 34.1 + - + +
164B PHE 3.3 20.8 + - - +
4H A 6.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 3.8 15.0 - - + -
125B TYR* 3.5 52.3 + - + -
128B LYS* 3.7 37.4 + - + +
154B SER* 2.8 23.0 + - - -
155B TYR* 3.5 5.6 - - - -
157B ASN* 1.3 79.3 - - - +
159B LEU* 1.3 59.8 + - - +
161B GLY 4.4 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B HIS* 3.7 19.1 - - + +
120B LEU* 3.8 20.0 - - + -
123B ARG* 4.2 18.8 - - + -
125B TYR* 4.5 7.4 + - + -
155B TYR* 3.1 48.8 + - + +
156B PHE* 4.4 0.4 - - + -
157B ASN 3.3 0.2 - - - -
158B THR* 1.3 82.8 - - - +
160B PHE* 1.3 86.3 + - + +
226B ASP* 5.0 2.0 - - + -
230B TYR* 3.4 38.9 + - + -
233B ARG* 5.0 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B PHE* 2.9 44.6 + + - +
159B LEU* 1.3 90.6 - - + +
161B GLY* 1.3 63.3 + - - +
163B ASP* 5.2 0.9 + - - +
164B PHE* 3.5 38.8 + + + +
172B ILE* 3.7 42.8 - - + -
176B LEU* 4.6 4.7 - - + -
226B ASP* 5.1 3.1 - - + -
229B ILE* 4.5 7.2 - - + -
230B TYR* 3.9 34.5 - + + -
233B ARG* 4.2 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ASN* 2.6 32.3 + - - +
158B THR 4.4 1.8 + - - -
159B LEU 3.7 1.8 + - - -
160B PHE* 1.3 75.7 - - - +
162B ASN* 1.3 61.6 + - - -
163B ASP* 3.1 7.2 - - - -
164B PHE* 3.2 15.2 + - - +
----------------------------------------------------------
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