Contacts of the helix formed by residues 145 - 162 (chain B) in PDB entry 4D10
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 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ALA 5.1 2.8 - - - +
143B LYS* 3.2 19.3 + - - +
144B ASN* 1.3 74.8 - - - +
146B ARG* 1.3 76.5 + - + +
147B LEU* 3.3 6.2 - - - +
148B TRP* 4.2 0.9 - - - +
149B PHE* 3.3 24.0 + - - +
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Residues in contact with ARG 146 (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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105B ARG* 6.0 3.8 - - - +
106B ASN* 3.6 19.2 + - - -
109B GLU* 3.3 36.2 + - - +
145B ASP* 1.3 87.5 + - + +
147B LEU* 1.3 74.0 + - - +
149B PHE* 4.2 7.4 - - - -
150B LYS* 3.0 60.2 + - + +
151B THR* 5.0 0.2 + - - -
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Residues in contact with LEU 147 (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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99B ILE* 6.0 2.0 - - + -
105B ARG* 4.1 26.9 - - + +
108B SER* 5.3 1.6 - - - +
109B GLU* 3.5 49.8 - - + +
139B LEU* 4.1 26.4 - - + +
143B LYS 4.8 2.7 - - - +
144B ASN* 4.0 26.5 - - + +
145B ASP 3.3 16.3 - - - +
146B ARG* 1.3 93.7 - - - +
148B TRP* 1.3 55.2 + - - +
151B THR* 2.7 28.6 + - - -
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Residues in contact with TRP 148 (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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136B LEU* 3.3 53.0 - - + +
139B LEU* 3.5 28.5 - - + -
140B LYS* 4.7 5.6 - - + -
141B ASP 5.5 2.5 - - - -
144B ASN* 3.7 25.0 - - + +
145B ASP 3.7 1.7 + - - +
146B ARG 3.3 0.2 - - - -
147B LEU* 1.3 79.2 - - - +
149B PHE* 1.3 62.8 + - + +
151B THR 3.6 0.9 + - - -
152B ASN* 3.0 48.9 + - + +
174B GLN* 3.4 41.8 + - - +
175B LEU* 5.5 3.1 - - + -
178B SER* 5.8 8.5 - - - -
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Residues in contact with PHE 149 (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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145B ASP 3.3 16.8 + - - +
146B ARG* 3.4 6.3 + - - +
148B TRP* 1.3 85.0 - - + +
150B LYS* 1.3 72.9 + - + +
152B ASN* 3.1 3.5 + - - +
153B THR* 2.8 48.6 + - + -
175B LEU* 3.6 21.4 - - + +
178B SER* 4.5 13.7 - - - -
193B GLN* 3.5 37.9 - - + -
196B GLU* 3.4 25.8 - - + -
197B ILE* 3.7 29.8 - - + -
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Residues in contact with LYS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ASN* 5.9 5.8 - - - +
146B ARG* 3.0 43.2 + - + +
149B PHE* 1.3 90.4 - - + +
151B THR* 1.3 57.6 + - - +
153B THR* 3.7 4.5 - - - -
154B LYS* 3.0 45.3 + - + +
196B GLU* 6.0 0.2 - - - +
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Residues in contact with THR 151 (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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112B ILE* 5.9 1.0 - - - +
113B ASN* 5.5 2.3 + - - -
116B LEU* 4.7 7.7 - - + +
132B TYR* 3.5 35.9 - - + +
135B THR* 4.4 17.4 - - + +
136B LEU* 3.8 22.2 - - + -
139B LEU* 4.9 2.3 - - - +
146B ARG 5.0 0.2 + - - -
147B LEU 2.7 25.9 + - - -
148B TRP 3.9 2.0 - - - -
149B PHE 3.3 0.6 - - - -
150B LYS* 1.3 79.7 - - - +
152B ASN* 1.3 57.3 + - - +
154B LYS* 5.6 0.2 - - - -
155B LEU* 2.9 29.6 + - - +
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Residues in contact with ASN 152 (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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136B LEU* 3.4 28.0 - - + +
148B TRP* 3.0 32.0 + - - +
149B PHE 3.6 3.1 - - - +
151B THR* 1.3 74.7 - - - +
153B THR* 1.3 56.2 + - - +
155B LEU* 3.7 7.1 - - - +
156B GLY* 2.8 27.0 + - - -
171B ILE* 3.4 48.9 + - - +
174B GLN* 3.6 20.3 + - - +
175B LEU* 3.8 14.5 - - + +
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Residues in contact with THR 153 (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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149B PHE* 2.8 44.6 + - + -
150B LYS* 3.7 8.1 - - - -
152B ASN* 1.3 74.8 - - - +
154B LYS* 1.3 60.6 + - + +
156B GLY* 3.1 3.7 + - - -
157B LYS* 2.9 47.7 + - - +
175B LEU* 3.7 9.8 - - - +
196B GLU* 4.9 16.4 - - + +
200B LEU* 3.7 27.0 - - + +
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Residues in contact with LYS 154 (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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117B ASP* 4.5 14.5 + - - -
132B TYR* 3.3 32.8 + - + +
150B LYS* 3.0 30.5 + - + +
153B THR* 1.3 72.9 - - + +
155B LEU* 1.3 60.8 + - - +
157B LYS* 3.3 26.3 + - + +
158B LEU* 3.0 33.7 + - + +
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Residues in contact with LEU 155 (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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129B GLN* 3.8 18.8 - - + +
132B TYR* 3.7 27.4 - - + -
133B GLU* 3.8 14.4 - - + +
136B LEU* 3.8 20.6 - - + -
151B THR 2.9 18.6 + - - +
152B ASN* 3.7 9.2 - - - +
154B LYS* 1.3 75.2 - - - +
156B GLY* 1.3 57.9 + - - +
158B LEU* 3.2 7.8 + - + +
159B TYR* 2.8 59.2 + - + +
171B ILE* 4.0 22.0 - - + -
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Residues in contact with GLY 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 ASN 2.8 18.7 + - - -
153B THR* 3.1 5.8 + - - -
155B LEU* 1.3 74.0 - - - +
157B LYS* 1.3 51.0 + - - +
159B TYR* 3.4 1.5 + - - -
160B LEU* 2.8 37.1 + - - +
168B LEU* 3.4 26.7 - - - +
171B ILE* 4.4 8.9 - - - +
175B LEU* 6.0 0.7 - - - -
200B LEU* 4.6 5.2 - - - -
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Residues in contact with LYS 157 (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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153B THR* 2.9 37.2 + - - +
154B LYS* 3.5 26.4 - - + +
155B LEU 3.3 0.2 - - - -
156B GLY* 1.3 71.7 - - - +
158B LEU* 1.3 61.6 + - + +
160B LEU* 3.2 13.1 + - + +
161B GLU* 3.0 32.9 + - + +
196B GLU* 6.3 1.6 - - - +
200B LEU* 3.9 17.3 - - + -
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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
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125B MET* 3.4 38.2 - - + +
128B LEU* 4.3 12.8 - - + -
129B GLN* 4.1 28.9 - - + +
132B TYR* 3.7 35.4 - - + -
154B LYS* 3.0 20.0 + - + +
155B LEU* 3.2 11.2 + - - +
157B LYS* 1.3 76.0 - - + +
159B TYR* 1.3 56.7 + - - +
161B GLU* 3.3 8.1 + - + +
162B ARG* 2.9 27.5 + - - +
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Residues in contact with TYR 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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129B GLN* 3.8 18.1 + - - -
133B GLU* 3.0 34.2 + - - +
155B LEU* 2.8 49.4 + - + +
156B GLY* 3.6 5.2 - - - +
158B LEU* 1.3 69.8 - - - +
160B LEU* 1.3 63.0 + - - +
162B ARG* 3.5 6.5 + - + +
163B GLU 3.4 2.6 + - - -
164B GLU* 3.2 59.5 + - + +
167B LYS* 3.7 40.5 + - + +
168B LEU* 4.0 15.5 - - + -
171B ILE* 3.9 15.9 - - + -
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Residues in contact with LEU 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 GLY 2.8 19.7 + - - +
157B LYS* 3.2 13.4 + - + +
159B TYR* 1.3 76.8 - - - +
161B GLU* 1.3 63.6 + - + +
163B GLU* 3.5 13.2 + - - +
164B GLU 4.9 0.4 - - - -
165B TYR* 5.0 12.2 + - + -
168B LEU* 3.8 24.0 - - + +
200B LEU* 3.8 29.2 - - + +
203B GLN* 3.8 36.1 - - + +
204B MET* 3.8 19.3 - - + +
207B ALA* 6.1 0.4 - - + -
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Residues in contact with GLU 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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125B MET* 4.5 11.0 - - + +
157B LYS* 3.0 19.4 + - + +
158B LEU* 3.3 14.3 + - + +
160B LEU* 1.3 76.3 - - + +
162B ARG* 1.3 61.3 + - - +
163B GLU* 3.3 6.3 + - - +
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Residues in contact with ARG 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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125B MET* 3.8 26.7 - - - -
129B GLN* 3.9 16.7 - - - +
158B LEU 2.9 16.6 + - - +
159B TYR* 3.7 10.8 - - + +
160B LEU 3.3 0.8 - - - -
161B GLU* 1.3 75.5 - - - +
163B GLU* 1.3 67.0 + - - +
164B GLU* 4.3 16.2 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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