Contacts of the helix formed by residues 139 - 150 (chain B) in PDB entry 2BV1
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 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B ILE* 1.3 76.4 - - - +
140B PHE* 1.3 59.7 + - - +
141B ARG* 3.2 16.1 + - - +
142B THR* 2.7 40.0 + - - +
143B ARG* 2.9 27.1 + - - +
164B VAL* 4.3 11.8 - - - +
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Residues in contact with PHE 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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138B ILE 3.9 0.4 + - - -
139B ASP* 1.3 74.6 - - - +
141B ARG* 1.3 67.8 + - + +
143B ARG* 3.7 25.0 - - - +
144B GLU* 3.0 59.3 + - + +
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Residues in contact with ARG 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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139B ASP* 3.2 9.6 + - - +
140B PHE* 1.3 81.9 - - + +
142B THR* 1.3 67.6 + - - +
144B GLU* 3.4 14.3 + - - +
145B SER* 3.0 27.5 + - - -
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Residues in contact with THR 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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138B ILE* 4.0 9.9 - - + -
139B ASP* 2.7 31.7 + - - +
141B ARG* 1.3 79.0 - - - +
143B ARG* 1.3 55.9 + - - +
145B SER* 3.6 6.3 + - - -
146B THR* 2.9 36.5 + - - +
160B GLU* 4.1 18.4 + - + +
161B ALA* 3.9 33.2 - - - +
164B VAL* 4.4 8.8 - - + +
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Residues in contact with ARG 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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124B TYR* 5.2 6.1 - - + +
128B VAL* 3.7 27.3 + - + +
129B HIS* 5.4 0.7 - - - +
130B SER* 3.9 20.9 + - - +
135B GLN* 3.5 25.0 + - - +
136B ILE 4.2 10.1 + - - -
137B ASN* 5.3 1.0 + - - +
138B ILE* 3.0 41.4 + - + +
139B ASP 2.9 13.2 + - - +
140B PHE* 3.7 31.5 - - - +
141B ARG 3.2 0.2 - - - -
142B THR* 1.3 76.2 - - - +
144B GLU* 1.3 59.3 + - - +
146B THR* 3.3 3.8 + - - -
147B ALA* 2.9 28.3 + - + +
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Residues in contact with GLU 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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140B PHE* 3.0 47.5 + - + +
141B ARG* 3.9 12.3 + - - +
143B ARG* 1.3 76.7 - - - +
145B SER* 1.3 61.2 + - - +
147B ALA* 3.4 8.6 + - - +
148B LYS* 3.3 39.9 + - + +
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Residues in contact with SER 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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141B ARG 3.0 16.3 + - - -
142B THR* 3.6 5.0 + - - -
144B GLU* 1.3 74.8 - - - +
146B THR* 1.3 66.9 + - - +
148B LYS* 3.4 16.2 + - - +
149B LYS* 3.4 31.2 + - - +
160B GLU* 3.3 23.4 + - - -
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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
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124B TYR* 4.7 0.9 - - + -
128B VAL* 4.2 17.9 - - + -
142B THR* 2.9 26.7 + - - +
143B ARG* 3.6 6.9 - - - -
145B SER* 1.3 75.5 + - - +
147B ALA* 1.3 63.8 + - - +
149B LYS* 3.1 23.5 + - - +
150B ILE* 3.3 15.4 + - + +
157B CYS 4.4 9.5 + - - +
158B PHE* 3.8 34.5 - - + -
160B GLU* 5.1 1.2 - - - +
161B ALA* 3.9 21.0 + - + +
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Residues in contact with ALA 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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124B TYR* 3.5 35.9 - - + +
143B ARG* 2.9 18.7 + - + +
144B GLU* 3.6 10.3 - - - +
145B SER 3.3 0.4 - - - -
146B THR* 1.3 76.2 - - - +
148B LYS* 1.3 60.2 + - + +
150B ILE* 3.5 17.9 + - - +
151B LYS* 4.5 2.9 + - - +
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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 GLU* 3.3 31.8 + - + +
145B SER* 3.5 17.9 - - - +
146B THR 3.1 0.2 - - - -
147B ALA* 1.3 80.2 - - + +
149B LYS* 1.3 61.2 + - + +
150B ILE 3.5 0.5 + - - -
151B LYS* 3.9 12.5 + - - +
152B ALA 4.9 1.2 + - - -
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Residues in contact with LYS 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 SER* 3.4 20.7 + - - +
146B THR* 3.1 11.8 + - - +
148B LYS* 1.3 73.6 - - + +
150B ILE* 1.3 63.6 + - - +
151B LYS 3.2 4.2 + - - -
152B ALA 3.3 5.6 + - - +
153B PRO* 3.1 26.8 - - + +
154B THR 6.0 0.2 - - - +
156B THR 4.3 5.8 + - - -
157B CYS* 3.3 44.4 + - + +
159B ASP* 5.9 0.2 - - - +
160B GLU* 4.2 33.2 + - - +
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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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117B PRO* 4.9 2.9 - - - +
120B ALA* 3.8 9.4 - - + +
121B GLU* 3.9 38.9 - - + +
124B TYR* 3.8 31.0 - - + -
146B THR 3.3 14.1 - - - +
147B ALA 3.6 11.0 - - - +
148B LYS 3.3 1.0 - - - -
149B LYS* 1.3 78.5 - - - +
151B LYS* 1.3 60.5 + - - +
152B ALA 3.2 1.3 + - - -
153B PRO* 3.5 16.9 - - - +
157B CYS* 3.7 12.1 - - - -
158B PHE* 3.6 33.9 - - + -
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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