Contacts of the helix formed by residues 143 - 157 (chain B) in PDB entry 4DBW
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 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142B VAL* 1.3 73.6 - - - +
144B LEU* 1.3 52.7 + - - +
145B CYS* 2.7 28.3 + - - +
146B THR* 2.6 60.6 + - + +
147B THR 3.4 1.2 + - - -
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Residues in contact with LEU 144 (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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90B HIS* 3.7 29.4 - - + +
116B ILE* 4.7 6.3 - - + +
119B PRO* 3.6 35.9 - - + +
121B SER* 3.8 10.1 - - - +
142B VAL* 3.1 11.3 + - + +
143B ASP* 1.3 70.6 + - - +
145B CYS* 1.3 55.6 + - - +
146B THR 3.3 0.2 - - - -
147B THR* 3.4 18.5 - - + +
148B TRP* 3.0 26.9 + - - +
168B PHE* 4.0 17.5 - - + -
172B GLN* 5.3 4.5 - - + +
175B MET* 6.2 7.0 - - + -
176B ILE* 3.9 14.6 - - + +
316B ASN* 4.1 12.1 - - - +
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Residues in contact with CYS 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASP* 2.7 25.7 + - - +
144B LEU* 1.3 73.1 - - - +
146B THR* 1.3 58.8 + - - +
148B TRP* 3.8 7.4 - - - +
149B GLU* 3.1 24.1 + - - +
175B MET* 3.6 34.5 - - - -
176B ILE* 4.2 7.2 - - - -
179B LYS* 4.2 31.6 - - + +
180B PRO* 6.0 1.1 - - - -
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Residues in contact with THR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PRO* 3.4 30.3 - - - +
142B VAL* 4.1 5.0 - - - +
143B ASP* 2.6 47.7 + - + +
145B CYS* 1.3 70.1 - - - +
147B THR* 1.3 64.9 + - - -
149B GLU* 3.2 7.6 + - - +
150B ALA* 3.2 21.7 + - - +
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Residues in contact with THR 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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85B LEU* 3.8 24.5 - - + -
90B HIS* 2.7 37.8 + - + +
92B PRO* 4.8 0.9 - - - -
95B VAL* 4.2 2.1 - - + +
116B ILE* 3.7 23.1 - - + -
142B VAL* 3.5 16.3 - - - +
143B ASP 3.4 0.6 + - - -
144B LEU* 3.4 16.6 - - + +
146B THR* 1.3 79.4 + - - +
148B TRP* 1.3 61.1 + - - +
150B ALA* 3.2 9.8 + - - +
151B MET* 3.0 23.6 + - + +
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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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116B ILE* 4.1 15.7 - - + -
144B LEU 3.0 17.5 + - - +
145B CYS* 3.8 5.4 - - - +
146B THR 3.2 0.2 - - - -
147B THR* 1.3 74.5 - - - +
149B GLU* 1.3 59.5 + - - +
151B MET* 3.0 13.3 + - + +
152B GLU* 2.8 52.5 + - - +
163B ILE* 3.4 41.1 - - + -
164B GLY 3.5 22.2 - - - -
165B VAL* 3.8 12.6 - - + -
176B ILE* 3.7 30.7 - - + -
179B LYS* 5.1 4.9 - - + -
182B LEU* 3.6 7.4 - - + +
184B TYR 2.6 30.1 + - - -
186B PRO* 3.5 30.7 - - + -
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Residues in contact with GLU 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 CYS 3.1 14.6 + - - +
146B THR* 3.2 10.6 + - - +
148B TRP* 1.3 76.0 - - - +
150B ALA* 1.3 58.3 + - - +
152B GLU* 3.2 20.7 + - + +
153B LYS* 3.0 55.4 + - + +
179B LYS* 4.1 18.4 + - - +
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Residues in contact with ALA 150 (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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92B PRO* 3.5 31.0 - - + +
95B VAL* 3.7 16.3 - - + +
96B ARG* 5.4 2.2 + - + +
146B THR 3.2 11.9 + - - +
147B THR 3.2 8.7 + - - +
149B GLU* 1.3 72.9 - - - +
151B MET* 1.3 66.1 + - - +
153B LYS* 3.2 17.8 + - + +
154B CYS* 3.2 24.6 + - - -
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Residues in contact with MET 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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85B LEU* 4.3 11.0 - - - -
95B VAL* 3.9 15.9 - - + -
114B TYR* 3.2 58.8 - - + +
115B LEU 3.9 0.4 - - - -
116B ILE* 3.8 23.6 - - + +
147B THR* 3.0 21.2 + - + +
148B TRP* 3.0 26.4 + - + +
150B ALA* 1.3 74.8 - - - +
152B GLU* 1.3 63.7 + - - +
154B CYS* 3.0 16.3 + - - +
155B LYS 3.2 9.2 + - - -
163B ILE* 3.7 21.0 - - + +
164B GLY 3.9 6.1 - - - +
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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
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148B TRP* 2.8 43.7 + - - +
149B GLU* 3.2 18.1 + - + +
151B MET* 1.3 75.5 - - - +
153B LYS* 1.3 63.3 + - + +
155B LYS* 3.2 5.2 + - - +
156B ASP* 3.0 28.4 + - - +
163B ILE* 3.8 9.9 - - + -
179B LYS* 3.3 18.2 + - - -
181B GLY 4.9 0.2 - - - +
182B LEU* 3.4 3.3 - - - +
183B LYS* 2.9 22.3 + - + +
184B TYR* 2.8 43.0 + - + -
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Residues in contact with LYS 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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96B ARG* 5.0 4.7 + - + +
149B GLU* 3.0 46.5 + - + +
150B ALA* 3.4 16.5 - - + +
151B MET 3.2 0.2 - - - -
152B GLU* 1.3 78.1 - - + +
154B CYS* 1.3 56.3 + - - +
156B ASP* 3.1 12.6 + - - +
157B ALA* 2.8 30.1 + - - +
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Residues in contact with CYS 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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95B VAL* 4.2 10.8 - - - -
96B ARG* 3.9 34.1 - - - +
99B LEU* 3.6 32.5 - - + -
114B TYR* 5.2 3.1 - - + -
150B ALA 3.2 19.1 + - - -
151B MET* 3.0 11.1 + - - +
153B LYS* 1.3 77.2 - - - +
155B LYS* 1.3 61.6 + - - +
157B ALA* 3.2 6.7 + - - +
158B GLY 3.1 4.0 + - - -
159B LEU* 3.0 28.4 + - - +
160B ALA* 3.6 6.2 + - + -
163B ILE* 5.4 0.7 - - + -
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Residues in contact with LYS 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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12B ASP* 3.3 28.4 + - - +
14B HIS* 4.0 7.1 + - - -
151B MET 3.2 7.1 + - - +
152B GLU 3.2 10.2 + - - +
154B CYS* 1.3 77.4 - - - +
156B ASP* 1.3 59.7 + - - +
158B GLY* 3.0 19.1 + - - -
160B ALA* 3.3 23.5 - - - +
161B LYS* 2.7 26.1 + - - +
162B SER* 4.7 1.3 - - - -
163B ILE* 4.2 21.5 - - + -
184B TYR* 3.4 48.2 - - + +
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Residues in contact with ASP 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 18.6 + - - +
153B LYS* 3.5 13.2 - - - +
155B LYS* 1.3 78.3 - - - +
157B ALA* 1.3 61.1 + - - +
158B GLY* 3.2 0.7 + - - -
183B LYS* 2.7 34.3 + - - +
184B TYR* 2.6 28.6 + - - -
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Residues in contact with ALA 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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96B ARG* 3.5 35.6 + - - +
153B LYS 2.8 15.2 + - - +
154B CYS* 3.6 6.7 - - - +
155B LYS 3.2 0.4 - - - -
156B ASP* 1.3 76.5 - - - +
158B GLY* 1.3 60.5 + - - +
159B LEU* 3.3 11.3 + - + +
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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