Contacts of the helix formed by residues 141 - 159 (chain A) in PDB entry 5J3V
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 ASP 141 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLY 4.1 4.2 - - - +
139A SER* 3.2 13.4 + - - +
140A GLU* 1.3 75.4 - - - +
142A TYR* 1.3 66.7 + - - +
143A ASN* 3.4 13.2 + - - +
144A THR* 3.1 36.4 + - - +
145A CYS* 3.1 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 5.6 0.4 - - - -
139A SER 5.4 0.2 - - - -
140A GLU 3.2 7.2 + - - +
141A ASP* 1.3 72.9 + - - +
143A ASN* 1.3 67.0 + - - +
145A CYS* 3.1 8.9 + - + +
146A GLU* 2.8 63.3 + - + +
185A HIS* 4.6 9.6 - + - -
187A SER* 2.7 40.8 + - - -
189A LYS* 3.7 12.0 - - - +
190A ILE* 3.6 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLY* 3.3 24.5 + - - +
101A ASP 3.3 13.9 + - - -
102A SER* 3.9 9.3 + - - +
107A ARG* 3.0 41.1 + - - +
141A ASP* 3.3 11.1 + - - +
142A TYR* 1.3 91.1 - - - +
144A THR* 1.3 57.9 + - - +
146A GLU* 4.0 1.6 - - - +
147A GLY* 2.8 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 3.5 19.3 + - + +
100A GLY* 3.5 11.1 + - - +
136A LEU* 4.0 38.5 - - + +
139A SER* 4.0 14.6 - - - +
141A ASP* 3.1 26.2 + - - +
143A ASN* 1.3 76.5 - - - +
145A CYS* 1.3 60.6 + - - +
148A ALA* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU 3.9 10.0 + - - +
137A LEU* 3.7 24.3 - - - +
139A SER 4.2 11.4 - - - +
141A ASP 3.1 12.8 + - - +
142A TYR* 3.1 14.1 + - + +
144A THR* 1.3 75.9 - - - +
146A GLU* 1.3 59.7 + - - +
148A ALA* 3.9 1.6 - - - +
149A PHE* 2.9 34.4 + - - +
182A PHE* 4.3 14.8 - - - -
185A HIS* 5.0 7.4 - - - -
190A ILE* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 3.5 22.8 + - - +
142A TYR* 2.8 51.9 + - + +
143A ASN* 4.0 3.4 - - - +
145A CYS* 1.3 70.6 - - - +
147A GLY* 1.3 58.2 + - - +
149A PHE* 4.3 0.9 - - - -
150A GLY* 2.6 34.2 + - - -
189A LYS* 4.1 27.5 + - + +
190A ILE* 3.8 19.5 - - + +
193A HIS* 4.4 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 4.0 16.3 - - - +
100A GLY 4.9 0.2 - - - -
107A ARG* 4.6 15.0 - - - +
111A GLY* 5.3 5.9 - - - -
114A ILE* 6.0 0.5 - - - +
133A LEU* 5.2 0.2 - - - +
143A ASN 2.8 21.0 + - - -
144A THR 4.2 0.4 - - - -
146A GLU* 1.3 73.5 - - - +
148A ALA* 1.3 59.2 + - - +
150A GLY* 4.2 1.2 - - - -
151A ALA* 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 3.9 4.3 - - + +
133A LEU* 3.8 43.1 - - + +
136A LEU* 4.0 10.3 - - + -
137A LEU* 3.9 9.9 - - + -
144A THR 3.1 19.4 + - - +
145A CYS 3.9 0.2 - - - +
147A GLY* 1.3 74.0 - - - +
149A PHE* 1.3 60.3 + - - +
151A ALA* 3.4 2.4 + - - +
152A LEU* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 3.9 18.3 - - + +
145A CYS* 2.9 20.9 + - - +
146A GLU* 3.8 3.8 - - - +
148A ALA* 1.3 75.9 - - - +
150A GLY* 1.3 63.3 + - - +
152A LEU* 3.4 3.3 + - + -
153A GLN* 3.1 23.6 + - - +
179A PHE* 3.8 34.8 - + - -
182A PHE* 3.5 39.3 - + + -
190A ILE* 3.8 22.0 - - + -
193A HIS* 3.8 21.3 - - + -
194A ALA* 3.8 31.4 - - + -
197A CYS* 4.2 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A THR* 4.8 0.5 - - - +
146A GLU* 2.6 21.0 + - - -
147A GLY* 4.3 1.3 - - - -
149A PHE* 1.3 73.4 - - - +
151A ALA* 1.3 58.4 + - - +
153A GLN* 3.9 4.4 + - - +
154A LYS* 3.7 17.2 + - - +
193A HIS* 3.6 23.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 6.1 0.2 - - + -
111A GLY* 4.7 8.3 - - - +
114A ILE* 4.9 12.3 - - + -
115A THR* 3.7 23.3 - - + +
133A LEU* 4.4 15.9 - - + -
147A GLY 3.3 19.0 + - - +
148A ALA* 3.7 4.7 - - - +
149A PHE 3.2 0.2 - - - -
150A GLY* 1.3 75.6 - - - +
152A LEU* 1.3 59.0 + - - +
153A GLN 3.1 1.6 - - - -
154A LYS 3.2 2.6 + - - -
155A ILE* 3.0 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 4.8 10.8 - - + -
133A LEU* 3.7 38.4 - - + +
134A CYS* 4.4 5.4 - - + +
137A LEU* 3.9 33.7 - - + -
148A ALA 2.9 21.0 + - - +
149A PHE* 3.4 10.7 + - + +
151A ALA* 1.3 78.1 - - - +
153A GLN* 1.3 57.0 + - - +
155A ILE* 3.4 13.8 + - + +
156A CYS* 3.0 34.9 + - - -
175A MET* 4.6 15.3 - - + -
179A PHE* 4.2 15.5 - - + -
197A CYS* 4.2 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE 3.1 15.7 + - - +
150A GLY 3.9 5.6 - - - +
151A ALA 3.1 0.4 - - - -
152A LEU* 1.3 77.8 - - - +
154A LYS* 1.3 58.2 + - - +
156A CYS* 3.2 4.8 + - - +
157A GLU* 3.0 56.5 + - + +
192A SER 4.8 0.2 - - - +
193A HIS* 2.4 41.2 + - - +
196A ALA* 3.5 30.3 - - + +
197A CYS* 3.6 16.5 - - - +
200A GLN* 5.2 0.2 - - - +
234A ASN* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 5.8 4.9 - - - +
115A THR* 3.6 39.1 + - + +
150A GLY 3.7 7.6 + - - +
151A ALA 3.2 1.8 + - - +
153A GLN* 1.3 80.1 - - - +
155A ILE* 1.3 58.1 + - - +
157A GLU* 3.6 18.8 - - - +
158A ASP* 2.8 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ILE* 5.3 3.4 - - + -
115A THR* 4.9 9.9 - - + +
118A ALA* 4.8 10.1 - - + -
123A LEU* 4.2 25.8 - - + -
129A LEU* 4.0 22.0 - - + -
130A LEU* 4.5 10.8 - - + -
133A LEU* 3.9 28.5 - - + -
151A ALA* 3.0 17.9 + - + +
152A LEU* 3.6 16.6 - - + +
154A LYS* 1.3 77.4 - - - +
156A CYS* 1.3 56.9 + - - +
158A ASP* 4.7 3.1 - - - -
159A SER* 2.6 43.5 + - - +
175A MET* 6.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU 3.0 26.0 + - - +
153A GLN 3.2 5.1 + - - +
155A ILE* 1.3 80.4 - - - +
157A GLU* 1.3 57.3 + - - +
159A SER 4.0 6.1 - - - -
160A ALA* 3.2 26.2 - - - -
175A MET* 4.5 19.5 - - - -
179A PHE* 4.5 1.3 - - - -
197A CYS* 4.2 19.3 - - - +
200A GLN* 3.6 21.3 - - + +
201A PHE* 3.8 32.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLN* 3.0 49.7 + - + +
154A LYS* 3.6 23.5 - - - +
156A CYS* 1.3 77.2 - - - +
158A ASP* 1.3 68.9 + - - +
160A ALA* 3.8 10.6 + - - +
196A ALA* 5.0 2.6 - - - +
200A GLN* 3.4 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A THR 4.0 5.5 - - - +
119A SER* 3.2 35.9 + - - +
154A LYS* 2.8 48.2 + - - +
155A ILE* 4.1 2.9 - - - +
157A GLU* 1.3 79.5 - - - +
159A SER* 1.3 63.0 + - - +
160A ALA 3.6 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA 4.7 9.0 + - - -
119A SER* 5.8 0.9 - - - -
123A LEU* 4.1 22.6 - - - +
155A ILE* 2.6 23.7 + - - +
156A CYS* 3.5 10.7 - - - +
158A ASP* 1.3 74.7 + - - +
160A ALA* 1.3 59.3 + - - +
161A GLU* 2.8 17.5 - - - +
162A ILE* 4.1 22.1 - - - +
201A PHE* 4.5 4.5 - - - -
----------------------------------------------------------
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