Contacts of the helix formed by residues 144 - 166 (chain B) in PDB entry 2B4J
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 144 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B GLY* 4.9 4.4 + - - -
142B PRO 3.4 5.5 + - - +
143B TYR* 1.3 77.3 - - - +
145B PRO* 1.3 70.6 - - - +
146B GLN* 3.2 20.2 + - - +
147B SER* 2.7 41.8 + - - -
148B GLN* 3.0 22.2 + - - +
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Residues in contact with PRO 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TYR* 3.5 35.0 - - + +
144B ASN* 1.3 85.1 - - - +
146B GLN* 1.3 57.3 + - + +
148B GLN* 3.3 2.0 + - + +
149B GLY* 2.8 31.7 + - - -
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Residues in contact with GLN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ASN* 3.2 14.8 + - - +
145B PRO* 1.3 79.8 - - + +
147B SER* 1.3 56.8 + - - +
149B GLY* 3.1 16.9 + - - -
150B VAL* 3.2 18.6 + - - +
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Residues in contact with SER 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLN* 3.0 36.4 + - - +
114B HIS* 5.5 4.9 - - - +
144B ASN* 2.7 34.1 + - - -
146B GLN* 1.3 74.2 - - - +
148B GLN* 1.3 59.2 + - - -
150B VAL* 3.4 19.5 - - - +
151B ILE 3.5 2.4 + - - -
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Residues in contact with GLN 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLN* 5.4 1.4 + - - -
64B ASP* 4.9 2.8 - - - +
116B ASP* 5.1 15.2 + - - +
143B TYR* 3.2 40.0 - - + +
144B ASN 3.0 16.5 + - - +
145B PRO 3.8 2.7 - - - +
147B SER* 1.3 73.7 - - - +
149B GLY* 1.3 60.0 + - - +
150B VAL 3.2 0.4 - - - -
151B ILE* 3.2 21.0 - - - +
152B GLU* 2.9 65.7 + - + +
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Residues in contact with GLY 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PRO 2.8 18.5 + - - -
146B GLN* 3.1 6.2 + - - -
148B GLN* 1.3 72.7 - - - +
150B VAL* 1.3 53.0 + - - +
152B GLU* 3.8 6.5 - - - +
153B SER* 2.8 36.4 + - - -
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLN* 4.0 15.9 - - - +
77B VAL* 5.4 12.8 - - + -
79B VAL* 5.6 9.9 - - + -
146B GLN 3.2 16.4 + - - +
147B SER* 3.4 14.6 - - - +
148B GLN 3.2 0.2 - - - -
149B GLY* 1.3 77.3 - - - +
151B ILE* 1.3 56.6 + - - +
153B SER* 3.5 5.9 - - - -
154B MET* 3.1 29.2 + - + +
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLN* 3.9 38.4 - - + +
63B LEU 4.2 2.5 - - - -
64B ASP* 3.0 50.5 - - + +
75B VAL* 4.6 2.9 - - + +
77B VAL* 3.8 28.0 - - + -
147B SER 3.5 1.0 + - - -
148B GLN* 3.2 38.8 - - - +
150B VAL* 1.3 77.3 - - + +
152B GLU* 1.3 64.3 + - - +
153B SER 3.1 1.3 - - - -
154B MET* 3.2 4.4 + - + +
155B ASN* 2.9 30.2 + - - +
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Residues in contact with GLU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASP* 5.0 1.0 - - - +
148B GLN* 2.9 54.9 + - + +
149B GLY* 3.8 6.5 - - - +
151B ILE* 1.3 72.1 - - - +
153B SER* 1.3 57.8 + - - +
155B ASN* 3.5 15.4 + - - +
156B LYS* 3.0 48.2 + - - +
302B PO4 4.8 10.5 + - - -
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLY 2.8 20.7 + - - -
150B VAL* 3.5 8.1 - - - -
152B GLU* 1.3 75.3 - - - +
154B MET* 1.3 60.0 + - - +
156B LYS* 3.4 7.5 + - - +
157B GLU* 2.9 29.3 + - - +
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Residues in contact with MET 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 4.6 6.3 - - + -
77B VAL* 3.7 28.9 - - + -
82B GLY* 3.9 24.7 - - - +
84B ILE* 3.7 31.9 - - + -
150B VAL* 3.1 16.2 + - + +
151B ILE* 3.2 5.6 + - + +
153B SER* 1.3 77.6 - - - +
155B ASN* 1.3 56.3 + - - +
157B GLU* 3.3 8.3 + - - +
158B LEU* 2.7 37.5 + - + +
183B HIS* 3.8 21.3 - - - +
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Residues in contact with ASN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASP* 2.8 41.0 + - - +
66B THR* 3.6 30.0 + - - +
75B VAL* 3.8 15.8 - - - +
151B ILE* 2.9 24.1 + - - +
152B GLU* 3.8 13.3 + - - +
154B MET* 1.3 74.3 - - - +
156B LYS* 1.3 59.5 + - + +
158B LEU* 3.5 5.8 + - - +
159B LYS* 3.0 37.8 + - - +
302B PO4 3.8 7.9 + - - +
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Residues in contact with LYS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLU* 3.0 34.6 + - + +
153B SER* 3.8 6.5 - - - +
155B ASN* 1.3 73.9 - - + +
157B GLU* 1.3 61.1 + - - +
159B LYS* 3.5 8.2 + - + +
160B LYS* 3.0 27.5 + - - +
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B SER 2.9 18.8 + - - +
154B MET* 3.6 11.7 - - - +
156B LYS* 1.3 74.7 - - - +
158B LEU* 1.3 63.8 + - - +
160B LYS* 3.2 23.6 + - - +
161B ILE* 3.1 40.6 + - + +
183B HIS* 4.5 21.8 - - + +
186B LYS* 5.3 4.5 - - - -
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B THR* 5.1 5.8 - - + -
73B ILE* 4.3 9.9 - - + -
75B VAL* 3.9 28.7 - - + -
84B ILE* 4.0 25.6 - - + -
86B ALA* 4.0 14.1 - - + -
154B MET* 2.7 22.1 + - - +
155B ASN 3.8 4.5 - - - +
156B LYS 3.3 0.2 - - - -
157B GLU* 1.3 73.0 - - - +
159B LYS* 1.3 60.0 + - + +
161B ILE* 3.3 8.0 + - + +
162B ILE* 2.8 44.5 + - + +
176B VAL* 4.6 2.5 - - + +
179B ALA* 3.7 24.5 - - + +
180B VAL* 4.3 12.3 - - + +
183B HIS* 5.7 1.6 - - + -
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Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B THR* 2.9 38.6 + - + -
67B HIS 3.2 17.6 + - - -
68B LEU* 4.2 26.8 - - + +
73B ILE* 6.0 0.2 - - + -
155B ASN* 3.0 22.0 + - - +
156B LYS* 3.8 8.1 - - + +
158B LEU* 1.3 75.2 - - + +
160B LYS* 1.3 60.2 + - - +
162B ILE* 3.4 13.2 + - + +
163B GLY* 3.0 24.3 + - - -
302B PO4 3.0 19.2 + - - -
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Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LYS 3.0 14.4 + - - +
157B GLU* 3.2 30.3 + - - +
159B LYS* 1.3 74.4 - - - +
161B ILE* 1.3 65.2 + - + +
163B GLY* 3.3 3.3 + - - -
164B GLN* 3.1 44.4 + - + +
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Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B GLU* 3.1 31.9 + - + +
158B LEU* 3.7 7.6 - - - +
160B LYS* 1.3 75.2 - - + +
162B ILE* 1.3 67.1 + - - +
164B GLN* 2.9 30.1 + - - +
165B VAL* 3.1 11.6 + - - +
179B ALA* 3.5 27.6 - - + +
182B ILE* 3.8 29.6 - - + -
183B HIS* 3.8 40.2 - - + +
186B LYS* 4.6 8.7 - - - +
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Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 3.6 32.1 - - + -
69B GLU* 5.4 0.2 - - - +
73B ILE* 4.2 7.2 - - + -
158B LEU* 2.8 43.0 + - + +
159B LYS* 3.7 9.4 - - + +
161B ILE* 1.3 72.1 - - - +
163B GLY* 1.3 54.9 + - - +
165B VAL* 3.3 5.9 + - - +
166B ARG* 2.7 49.9 + - - +
172B LEU* 3.8 15.3 - - + -
175B ALA* 4.2 9.0 - - + +
176B VAL* 3.9 22.2 - - + -
179B ALA* 3.6 19.0 - - + +
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Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B LYS 3.0 14.9 + - - -
160B LYS* 3.6 4.9 - - - -
161B ILE 3.1 0.4 - - - -
162B ILE* 1.3 81.1 - - - +
164B GLN* 1.3 60.2 + - - +
166B ARG* 3.7 13.6 + - - +
167B ASP 5.3 0.3 + - - -
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Residues in contact with GLN 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LYS* 3.1 38.8 + - + +
161B ILE* 2.9 31.7 + - - +
163B GLY* 1.3 79.3 - - - +
165B VAL* 1.3 61.7 + - + +
167B ASP* 4.4 6.8 - - - +
168B GLN* 4.3 7.3 + - - -
182B ILE* 5.5 1.8 - - - +
186B LYS* 5.3 7.3 - - - +
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TRP* 4.7 3.4 - - + -
161B ILE* 3.1 17.1 + - + +
162B ILE* 3.7 6.5 - - - +
164B GLN* 1.3 82.2 - - + +
166B ARG* 1.3 67.8 + - - +
167B ASP* 3.2 3.1 - - - -
168B GLN* 2.8 42.9 + - - +
169B ALA 4.1 1.2 + - - -
175B ALA* 3.9 25.1 - - + +
178B MET* 3.9 18.2 - - + +
179B ALA 4.3 3.6 - - - +
182B ILE* 3.2 33.4 - - + -
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Residues in contact with ARG 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLU* 2.7 42.1 + - - +
162B ILE* 2.7 28.0 + - + +
163B GLY* 3.7 12.5 + - - +
164B GLN 3.5 2.8 - - - -
165B VAL* 1.3 76.4 - - - +
167B ASP* 1.3 58.3 - - - +
168B GLN 3.2 1.7 + - - -
169B ALA* 2.9 40.2 + - - +
170B GLU 3.3 20.2 + - - -
171B HIS 4.0 4.4 + - - -
172B LEU* 3.4 20.0 - - - +
175B ALA* 3.8 17.9 - - - +
403B GOL 4.2 2.8 + - - -
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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) + - + + + + + -
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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