Contacts of the helix formed by residues 143 - 160 (chain B) in PDB entry 3U9J
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 THR 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 PHE* 1.3 76.5 - - - +
144B TYR* 1.3 66.0 + - - +
145B GLU* 3.7 7.1 + - - +
146B GLU* 3.0 39.5 + - - +
147B LEU* 3.1 22.5 + - - +
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Residues in contact with TYR 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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5B PRO* 3.5 28.3 - - + +
7B GLU* 2.6 39.0 + - - +
8B VAL* 3.6 28.8 - - + +
139B MSE 5.1 11.7 - - + -
142B PHE 4.0 0.2 + - - -
143B THR* 1.3 73.9 - - - +
145B GLU* 1.3 66.3 + - + +
147B LEU* 3.2 8.1 + - - +
148B LYS* 3.0 36.1 + - + -
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Residues in contact with GLU 145 (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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143B THR* 3.3 6.1 + - - +
144B TYR* 1.3 82.8 - - + +
146B GLU* 1.3 62.6 + - - +
148B LYS* 3.1 44.9 + - - +
149B ASP* 3.0 30.4 + - - +
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Residues in contact with GLU 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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72B ARG* 2.8 44.7 + - - -
142B PHE* 3.5 10.5 - - + -
143B THR* 3.0 47.2 + - - +
145B GLU* 1.3 77.5 - - - +
147B LEU* 1.3 57.4 + - - +
149B ASP* 3.2 11.8 + - - +
150B ILE* 3.0 32.2 + - + +
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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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8B VAL* 3.9 23.3 - - + +
10B VAL* 4.4 5.2 - - + +
135B GLN* 4.5 0.4 - - - +
138B LEU* 3.7 43.1 - - + +
139B MSE 3.7 31.9 - - - +
142B PHE* 3.7 21.1 - - + +
143B THR 3.1 17.0 + - - +
144B TYR* 3.6 9.2 - - + +
146B GLU* 1.3 73.7 - - - +
148B LYS* 1.3 61.2 + - - +
150B ILE* 3.2 19.7 + - + +
151B LYS* 2.9 31.0 + - - +
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Residues in contact with LYS 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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7B GLU* 3.5 42.0 + - + +
8B VAL* 3.9 8.9 - - + +
144B TYR* 3.0 27.7 + - + +
145B GLU* 3.1 40.2 + - - +
147B LEU* 1.3 77.4 - - - +
149B ASP* 1.3 61.0 + - - +
151B LYS* 3.4 2.4 + - - +
152B LYS* 3.0 27.2 + - - +
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Residues in contact with ASP 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLU* 3.0 21.9 + - - +
146B GLU* 3.4 11.8 - - - +
147B LEU 3.2 0.2 - - - -
148B LYS* 1.3 78.6 - - - +
150B ILE* 1.3 64.0 + - + +
152B LYS* 3.3 14.2 + - - +
153B LYS* 3.1 34.2 + - - +
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Residues in contact with ILE 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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10B VAL* 3.9 17.9 - - + -
64B TYR* 3.8 21.8 - - + +
65B ILE* 4.2 8.3 - - + +
68B LEU* 4.3 15.0 - - + -
138B LEU* 5.2 4.5 - - + -
142B PHE* 4.0 27.6 - - + -
146B GLU* 3.0 18.7 + - + +
147B LEU* 3.2 26.4 + - + +
149B ASP* 1.3 75.6 - - + +
151B LYS* 1.3 58.4 + - - +
153B LYS* 3.1 13.2 + - + +
154B VAL* 2.8 34.5 + - + +
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Residues in contact with LYS 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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6B GLU* 2.6 48.6 + - - +
7B GLU* 3.5 18.1 - - - +
8B VAL* 4.8 0.2 - - - -
9B ASP* 3.3 24.8 + - - +
10B VAL* 4.0 16.4 - - + +
13B ALA* 5.6 6.7 - - - +
147B LEU 2.9 16.2 + - - +
148B LYS 3.7 4.7 - - - +
150B ILE* 1.3 77.1 - - - +
152B LYS* 1.3 63.6 + - - +
154B VAL* 3.1 4.1 + - + -
155B ILE* 2.8 49.1 + - + +
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Residues in contact with LYS 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 LYS 3.0 13.8 + - - +
149B ASP* 3.4 17.3 - - - +
151B LYS* 1.3 77.2 - - - +
153B LYS* 1.3 64.4 + - + +
155B ILE* 3.6 5.6 + - - +
156B ALA* 3.1 23.6 + - + +
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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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64B TYR* 3.9 30.5 - - + +
149B ASP* 3.1 21.7 + - - +
150B ILE* 3.1 14.3 + - + +
152B LYS* 1.3 78.4 - - + +
154B VAL* 1.3 63.3 + - + +
156B ALA* 3.2 5.1 + - - -
157B GLN* 3.1 34.3 + - - +
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Residues in contact with VAL 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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10B VAL* 3.8 21.8 - - + +
14B PRO* 4.3 5.6 - - + -
60B ILE* 4.4 9.6 - - + -
64B TYR* 4.1 12.3 - - + -
65B ILE* 3.7 33.7 - - + -
150B ILE* 2.8 25.7 + - + +
151B LYS* 3.6 7.9 - - + +
153B LYS* 1.3 75.7 - - - +
155B ILE* 1.3 64.7 + - + +
157B GLN* 3.3 3.2 + - - +
158B HIS* 2.8 51.7 + - + +
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Residues in contact with ILE 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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13B ALA* 4.2 25.1 - - + -
14B PRO* 4.5 13.5 - - + -
151B LYS* 2.8 46.8 + - + +
152B LYS* 3.9 5.8 - - - +
154B VAL* 1.3 74.5 - - + +
156B ALA* 1.3 58.6 + - - +
158B HIS* 3.2 3.3 + - + -
159B CYS* 2.9 50.5 + - + +
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Residues in contact with ALA 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 LYS* 3.1 20.1 + - + +
153B LYS* 3.2 7.6 + - - +
155B ILE* 1.3 78.2 - - - +
157B GLN* 1.3 72.2 + - - +
159B CYS* 5.3 1.1 - - - -
160B SER* 3.3 29.9 + - - +
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Residues in contact with GLN 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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56B MSE 4.1 11.1 - - - +
60B ILE* 3.5 30.1 - - + +
64B TYR* 3.3 49.4 + - + -
153B LYS* 3.1 27.5 + - - +
154B VAL 3.9 2.5 - - - +
155B ILE 3.3 0.2 - - - -
156B ALA* 1.3 87.4 - - - +
158B HIS* 1.3 61.0 + - - +
160B SER* 3.9 11.0 + - - -
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Residues in contact with HIS 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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14B PRO* 3.7 19.7 - - + +
18B MSE 3.8 23.6 - - + -
53B GLU* 5.1 4.2 - - - +
56B MSE 4.0 19.0 - - + +
57B HIS* 2.8 31.4 + + - -
60B ILE* 3.6 38.7 - - + +
61B GLU* 5.3 2.5 - - + -
154B VAL* 2.8 40.7 + - + +
155B ILE* 3.2 5.8 + - + +
157B GLN* 1.3 78.8 - - - +
159B CYS* 1.3 68.5 + - - +
160B SER 3.6 1.0 + - - -
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Residues in contact with CYS 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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155B ILE* 2.9 38.1 + - + +
156B ALA* 4.0 2.2 - - - -
158B HIS* 1.3 89.0 - - - +
160B SER* 1.3 61.2 + - - +
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Residues in contact with SER 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 ALA 3.3 17.1 + - - -
157B GLN* 3.9 10.4 + - - -
158B HIS 3.6 2.0 - - - -
159B CYS* 1.3 81.2 - - - +
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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