Contacts of the helix formed by residues 138 - 149 (chain B) in PDB entry 4ZBW
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 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B ALA* 5.0 12.5 - - - +
117B LEU* 4.0 13.2 - - + -
136B ASP 3.6 3.0 + - - +
137B MET* 1.3 76.9 - - - +
139B LEU* 1.3 65.5 + - - +
140B LEU* 3.2 18.8 + - + +
141B ASP* 2.7 48.7 + - - +
142B ILE* 3.2 19.1 + - - +
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Residues in contact with LEU 139 (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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108B ILE* 3.8 5.2 - - + -
109B SER* 3.7 25.8 - - - +
112B VAL* 3.6 34.1 - - + -
117B LEU* 3.6 22.5 - - + +
120B PHE* 3.7 45.3 - - + -
138B ASN* 1.3 76.1 - - - +
140B LEU* 1.3 58.8 + - - +
142B ILE* 3.2 7.2 + - + +
143B PHE* 2.9 51.4 + - + -
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Residues in contact with LEU 140 (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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20B ALA* 4.5 6.3 - - + +
21B SER* 4.2 24.9 - - - +
24B PHE* 3.8 52.6 - - + -
106B TYR* 4.4 9.9 - - + -
109B SER* 3.6 31.0 - - - +
138B ASN* 3.2 16.1 + - - +
139B LEU* 1.3 77.7 - - - +
141B ASP* 1.3 60.1 + - - +
143B PHE* 3.1 10.4 + - + +
144B ILE* 2.9 34.8 + - + +
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Residues in contact with ASP 141 (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 ASP 4.7 1.7 - - - +
137B MET* 4.0 24.9 - - + +
138B ASN* 2.7 44.6 + - - +
140B LEU* 1.3 74.4 - - - +
142B ILE* 1.3 57.9 + - - +
144B ILE* 3.3 17.7 + - - +
145B GLU* 2.9 28.2 + - - +
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Residues in contact with ILE 142 (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 LEU* 3.9 13.7 - - + -
120B PHE* 3.8 20.2 - - + -
121B LYS* 3.6 40.2 - - + -
124B LEU* 3.7 28.5 - - + -
133B LEU* 4.3 13.5 - - + -
137B MET* 4.3 11.9 - - + -
138B ASN 3.2 13.7 + - - +
139B LEU* 3.2 12.3 + - + +
141B ASP* 1.3 76.4 - - - +
143B PHE* 1.3 59.9 + - + +
145B GLU* 3.2 7.3 + - - +
146B MET* 2.8 31.3 + - - +
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Residues in contact with PHE 143 (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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24B PHE* 4.2 10.5 - + + -
105B LEU* 3.3 47.8 - - + -
108B ILE* 3.9 14.1 - - + -
109B SER* 4.5 2.5 - - - -
120B PHE* 3.9 13.5 - + - -
139B LEU* 2.9 45.8 + - + -
140B LEU* 3.3 19.3 - - + +
142B ILE* 1.3 76.2 - - - +
144B ILE* 1.3 56.4 + - - +
146B MET* 3.2 9.8 + - - +
147B GLU* 2.9 35.2 + - - +
152B LEU* 3.9 21.0 - - + +
160B LEU* 3.7 23.8 - - + -
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Residues in contact with ILE 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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24B PHE* 4.2 26.2 - - + -
27B LEU* 4.8 7.2 - - + -
32B GLN* 3.9 44.0 - - + +
35B GLN* 5.8 1.1 - - - +
140B LEU* 2.9 20.1 + - + +
141B ASP* 3.6 20.9 - - - +
142B ILE 3.3 0.2 - - - -
143B PHE* 1.3 75.9 - - - +
145B GLU* 1.3 57.8 + - - +
147B GLU* 3.4 11.1 + - + +
148B LYS* 2.9 31.9 + - + +
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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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131B CYS* 3.6 13.4 - - + -
132B LYS* 3.1 46.2 + - - +
133B LEU* 4.3 4.0 - - + -
137B MET* 5.1 7.0 - - + +
141B ASP 2.9 14.3 + - - +
142B ILE* 3.2 11.4 + - - +
144B ILE* 1.3 78.8 - - - +
146B MET* 1.3 57.0 - - - +
148B LYS* 3.2 23.4 + - - +
149B ARG* 3.0 57.7 + - - +
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Residues in contact with MET 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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120B PHE* 4.1 12.3 - - + -
124B LEU* 3.9 24.7 - - + -
131B CYS* 4.0 10.5 - - - -
142B ILE* 2.8 34.3 + - - +
143B PHE* 3.2 17.0 + - - +
145B GLU* 1.3 72.3 - - - +
147B GLU* 1.3 64.1 + - - +
149B ARG 3.3 1.2 + - - -
150B VAL 3.1 3.8 + - - -
151B ILE* 3.0 41.0 + - + +
152B LEU* 3.8 27.1 - - + -
159B ILE* 4.2 24.7 - - + -
160B LEU* 4.5 18.2 - - + +
163B VAL* 6.0 0.4 - - + -
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Residues in contact with GLU 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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27B LEU* 4.8 2.6 - - - +
101B TYR* 2.3 33.4 + - - +
102B ARG* 3.0 42.3 + - - -
105B LEU* 4.1 3.1 - - - +
143B PHE 2.9 19.0 + - - +
144B ILE* 3.8 10.6 - - - +
146B MET* 1.3 73.8 - - - +
148B LYS* 1.3 60.8 + - - +
150B VAL* 2.9 23.0 + - - +
152B LEU* 3.3 27.7 - - + +
153B GLY* 4.8 0.7 - - - -
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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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144B ILE* 2.9 20.9 + - + +
145B GLU* 3.2 20.3 + - - +
147B GLU* 1.3 76.9 - - - +
149B ARG* 1.3 87.1 + - - +
150B VAL* 3.5 8.3 + - - +
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Residues in contact with ARG 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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130B LYS* 3.0 69.9 + - + +
131B CYS* 4.1 9.0 - - - -
132B LYS* 3.3 30.5 - - - +
145B GLU* 3.0 38.8 + - - +
146B MET 3.8 4.5 - - - +
147B GLU 3.1 0.2 - - - -
148B LYS* 1.3 117.3 - - - +
150B VAL* 1.3 72.8 + - - +
151B ILE* 3.2 7.2 + - + +
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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