Contacts of the helix formed by residues 143 - 158 (chain B) in PDB entry 3BRS
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 SER 143 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LYS* 3.7 25.4 - - - -
73B ALA 5.2 0.2 - - - -
74B ALA 4.1 16.6 - - - -
76B TYR 4.5 1.6 - - - +
98B SER* 4.1 2.2 - - - -
139B PHE* 3.7 8.5 - - - -
140B VAL* 2.6 29.7 + - - +
142B ASN* 1.4 77.8 - - - +
144B LYS* 1.3 64.2 + - - +
145B THR* 3.9 2.7 - - - -
146B ALA* 3.2 13.7 + - - +
147B MET* 3.1 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ALA 5.5 0.6 + - - -
76B TYR* 3.6 38.0 - - + +
98B SER* 3.7 7.3 + - - +
99B GLY* 3.6 37.4 + - - +
100B MET 4.8 4.0 - - - -
142B ASN 3.7 2.4 + - - -
143B SER* 1.3 71.8 - - - +
145B THR* 1.3 58.5 + - + +
147B MET* 4.1 11.9 - - + -
148B ASP* 2.8 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LYS* 3.1 20.3 + - - -
97B ASP* 3.2 38.4 - - - +
98B SER* 3.3 13.1 + - - +
113B ASN* 3.6 20.4 - - - +
139B PHE* 3.3 12.6 - - - -
143B SER* 3.7 0.5 + - - -
144B LYS* 1.3 79.1 - - - +
146B ALA* 1.4 58.7 + - - +
148B ASP* 4.1 0.4 - - - -
149B ARG* 2.8 53.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B SER* 3.8 19.0 + - - +
139B PHE* 3.6 20.2 - - + -
140B VAL 3.1 31.0 - - - +
141B LYS* 4.4 5.2 - - - -
143B SER* 3.1 5.8 + - - +
145B THR* 1.4 78.0 + - - +
147B MET* 1.3 67.2 + - - +
149B ARG* 3.4 2.2 + - - +
150B GLU* 3.0 29.0 + - - +
169B TYR* 5.5 0.9 - - + -
197B LEU* 4.5 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR* 3.7 55.4 - - + -
141B LYS 3.4 17.0 + - - +
142B ASN* 4.1 8.7 - - - +
143B SER 3.1 19.9 + - - +
144B LYS* 3.8 5.8 - - + +
146B ALA* 1.3 76.5 - - - +
148B ASP* 1.3 65.2 + - - +
150B GLU* 3.9 6.4 - - - +
151B GLU* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ASN* 3.5 25.7 + - + +
114B ILE* 3.5 37.4 + - + +
144B LYS* 2.8 58.8 + - - +
145B THR* 5.4 0.2 - - - -
147B MET* 1.3 76.9 - - - +
149B ARG* 1.3 57.0 + - - +
151B GLU* 3.7 8.1 - - - +
152B GLY* 2.8 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASP* 4.5 4.4 + - - -
113B ASN* 2.9 43.0 + - + +
116B ALA* 5.4 0.4 - - - +
117B GLY* 3.5 6.8 - - - -
139B PHE* 3.5 17.4 - - - -
145B THR* 2.8 36.5 + - - +
146B ALA* 3.9 3.8 - - - +
147B MET 3.3 0.2 - - - -
148B ASP* 1.3 76.7 - - - +
150B GLU* 1.3 51.7 - - - +
153B LEU* 2.8 34.0 + - - +
197B LEU* 2.9 43.1 + - + +
198B ASN* 3.7 9.5 - - - +
223B ILE* 3.5 36.5 - - + +
244B GLN* 3.4 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B VAL* 6.2 0.2 - - + -
138B SER* 4.7 1.2 + - - -
141B LYS* 5.6 0.5 - - - +
146B ALA 3.0 19.0 + - - +
147B MET* 3.9 6.2 - - - +
149B ARG* 1.3 75.4 - - - +
151B GLU* 1.3 64.5 + - - +
153B LEU* 3.3 7.8 - - + +
154B LYS* 3.0 57.3 + - + +
167B ILE* 3.4 22.8 - - + +
169B TYR* 2.7 38.7 + - - -
197B LEU* 3.9 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ILE* 3.5 29.9 - - - +
147B MET 3.1 16.8 + - - +
148B ASP* 3.7 8.6 - - - +
150B GLU* 1.3 72.0 - - - +
152B GLY* 1.3 66.4 + - - +
154B LYS* 3.3 10.0 + - - +
155B ILE* 3.0 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ILE* 3.5 29.3 - - - +
118B ILE* 3.2 22.2 - - - +
148B ASP 2.8 14.7 + - - -
149B ARG 3.9 0.7 - - - -
151B GLU* 1.3 78.5 - - - +
153B LEU* 1.3 63.4 + - - +
155B ILE* 3.3 1.1 + - - -
156B GLY 2.9 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLY* 3.3 10.1 - - - +
120B ILE* 3.6 20.9 - - + +
121B GLY* 3.6 26.2 - - - -
124B THR* 4.4 2.0 - - - +
134B ILE* 5.6 0.2 - - + -
136B VAL* 3.9 35.9 - - + -
149B ARG 2.8 19.3 + - - +
150B GLU* 3.3 11.7 - - + +
152B GLY* 1.3 76.0 - - - +
154B LYS* 1.3 62.0 + - + +
156B GLY 3.3 0.5 + - - -
157B LEU* 3.1 36.8 + - + +
164B ILE* 4.3 11.9 - - + -
167B ILE* 5.8 0.7 - - + -
195B VAL* 4.2 21.8 - - + -
197B LEU* 4.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLU* 3.0 45.3 + - + +
151B GLU* 3.3 8.9 + - - +
153B LEU* 1.3 71.7 - - + +
155B ILE* 1.3 67.2 + - + +
157B LEU* 3.0 15.5 + - - +
158B SER* 3.3 9.5 + - - +
161B SER* 3.8 22.4 - - - +
164B ILE* 4.3 17.5 - - + -
167B ILE* 4.1 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ILE* 4.2 14.6 - - + -
118B ILE* 3.9 19.3 - - + -
151B GLU* 3.0 45.0 + - + +
152B GLY 3.5 7.2 - - - +
154B LYS* 1.3 74.7 - - + +
156B GLY* 1.3 63.6 + - - +
157B LEU 3.0 1.0 + - - -
158B SER* 3.1 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ILE* 3.8 31.0 - - - -
121B GLY 3.5 18.7 - - - +
122B ALA* 3.5 11.7 + - - +
125B LYS* 3.7 9.2 - - - +
152B GLY 2.9 16.7 + - - -
153B LEU 3.3 1.7 + - - -
155B ILE* 1.3 74.3 - - - +
157B LEU* 1.3 58.0 + - - +
158B SER* 3.4 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLY* 3.5 19.7 - - - +
124B THR* 4.1 4.9 - - + -
125B LYS* 3.2 28.4 + - + +
134B ILE* 3.6 25.4 - - + -
153B LEU* 3.1 27.7 + - + +
154B LYS* 3.0 8.4 + - - +
155B ILE 3.0 1.2 - - - -
156B GLY* 1.3 77.3 - - - +
158B SER* 1.3 72.9 + - - +
160B ASP* 2.9 25.0 + - + +
161B SER* 3.8 14.1 - - - +
164B ILE* 3.5 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LYS* 2.8 31.1 + - - +
154B LYS 3.3 4.3 + - - +
155B ILE* 3.1 15.2 + - - +
156B GLY 4.2 2.6 + - - -
157B LEU* 1.3 74.9 - - - +
159B ASP* 1.3 66.4 + - - +
161B SER* 3.3 18.7 + - - -
----------------------------------------------------------
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