Contacts of the helix formed by residues 115 - 128 (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 LEU 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B THR* 3.8 15.9 - - + -
112B GLU* 3.0 37.6 + - + +
114B ASP* 1.3 88.2 - - + +
116B LEU* 1.3 58.4 + - - +
117B PRO* 3.4 2.2 - - - -
118B CYS* 3.4 13.3 + - + +
119B LYS* 2.9 31.2 + - + +
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Residues in contact with LEU 116 (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 TYR* 3.5 44.8 - - + +
111B THR* 3.4 25.6 - - - +
112B GLU 3.5 4.7 + - - +
113B SER* 3.3 25.3 + - - +
115B LEU* 1.3 73.9 - - - +
117B PRO* 1.3 73.9 - - + +
119B LYS* 4.5 0.2 - - - -
120B ALA* 2.8 27.7 + - - +
153B PRO* 4.0 13.2 - - - +
154B THR 4.1 3.4 - - - -
155B PRO* 3.9 37.2 - - + -
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Residues in contact with PRO 117 (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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113B SER 3.6 7.0 - - - +
114B ASP 3.4 17.3 - - - +
115B LEU 3.5 0.7 - - - -
116B LEU* 1.3 93.5 - - + +
118B CYS* 1.3 55.6 + - - +
120B ALA* 3.7 1.7 - - - +
121B GLU* 3.0 43.3 + - - +
150B ILE 4.9 1.9 - - - +
153B PRO* 3.7 24.9 - - + +
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Residues in contact with CYS 118 (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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114B ASP 5.5 0.4 - - - +
115B LEU* 3.4 17.2 + - + +
116B LEU 3.2 0.4 - - - -
117B PRO* 1.3 77.6 - - - +
119B LYS* 1.3 67.2 + - - +
121B GLU* 3.3 10.5 + - - +
122B GLU* 3.0 26.1 + - - +
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Residues in contact with LYS 119 (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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104B ALA 6.0 0.2 - - - +
107B ASP* 6.5 1.1 - - + -
108B TYR* 3.7 21.1 - - + -
111B THR* 4.5 18.4 - - + +
115B LEU* 2.9 23.4 + - + +
116B LEU* 4.1 0.4 - - - +
118B CYS* 1.3 73.1 - - + +
120B ALA* 1.3 58.3 + - - +
122B GLU* 3.0 39.8 + - - +
123B ILE* 2.8 45.7 + - + +
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Residues in contact with ALA 120 (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 TYR* 3.7 8.8 - - + +
116B LEU 2.8 22.8 + - - +
117B PRO 3.7 3.1 - - - +
119B LYS* 1.3 72.4 - - - +
121B GLU* 1.3 54.8 - - - +
124B TYR* 2.9 31.9 + - - +
150B ILE* 3.8 13.9 - - + +
153B PRO* 3.8 25.8 - - + -
158B PHE* 3.6 22.2 - - + -
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Residues in contact with GLU 121 (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* 3.0 26.5 + - - +
118B CYS* 3.7 8.3 - - - +
120B ALA* 1.3 76.6 - - - +
122B GLU* 1.3 58.7 + - - +
124B TYR* 3.8 3.2 - - - +
125B LYS* 3.0 32.7 + - - +
150B ILE* 3.9 24.5 - - + +
151B LYS* 5.9 1.2 - - - -
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Residues in contact with GLU 122 (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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118B CYS* 3.0 15.8 + - - +
119B LYS* 3.0 46.3 + - - +
121B GLU* 1.3 73.9 - - - +
123B ILE* 1.3 62.3 + - + +
125B LYS* 4.0 2.8 - - - +
126B ALA* 2.8 38.0 + - + +
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Residues in contact with ILE 123 (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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101B PHE* 3.7 32.3 - - + -
104B ALA* 3.8 25.1 - - + +
105B CYS* 4.8 0.9 - - - +
108B TYR* 3.6 33.7 - - + -
119B LYS* 2.8 33.1 + - + +
122B GLU* 1.3 76.6 - - + +
124B TYR* 1.3 58.3 + - - +
126B ALA* 4.5 0.4 - - - -
127B PHE* 2.8 41.0 + - + +
128B VAL* 3.7 0.6 + - + +
158B PHE* 3.7 28.9 - - + -
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Residues in contact with TYR 124 (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 ALA 2.9 18.6 + - - +
121B GLU* 3.8 4.5 - - - +
123B ILE* 1.3 77.3 - - - +
125B LYS* 1.3 60.6 + - + +
128B VAL* 2.8 47.1 + - + -
129B HIS* 2.8 70.8 + + + -
130B SER 5.3 0.2 + - - -
143B ARG* 4.8 4.7 - - + +
146B THR* 4.7 1.6 - - + -
147B ALA* 3.5 35.0 - - + +
150B ILE* 3.8 32.3 - - + -
158B PHE* 4.2 0.6 - - - -
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Residues in contact with LYS 125 (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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121B GLU 3.0 19.0 + - - +
122B GLU* 4.1 3.4 - - - +
124B TYR* 1.3 80.8 - - + +
126B ALA* 1.3 57.1 + - - +
129B HIS* 4.1 11.2 - - + +
132B ALA* 3.3 23.6 - - - +
133B ALA 4.9 0.3 + - - -
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Residues in contact with ALA 126 (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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122B GLU* 2.8 24.7 + - + +
125B LYS* 1.3 77.8 - - - +
127B PHE* 1.3 79.5 + - + +
132B ALA* 3.4 8.7 - - - +
133B ALA 4.3 1.1 + - - +
134B LYS* 3.3 26.3 + - + +
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Residues in contact with PHE 127 (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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97B GLU* 3.8 8.7 - - - -
100B GLU* 4.0 21.5 - - + -
101B PHE* 3.7 59.9 - + + -
104B ALA* 4.3 13.9 - - + -
123B ILE* 2.8 28.5 + - + +
126B ALA* 1.3 91.5 - - + +
128B VAL* 1.3 59.2 + - + +
129B HIS 3.7 0.7 - - - -
132B ALA* 3.9 4.3 - - - -
134B LYS* 3.6 28.9 - - + -
135B GLN* 3.1 5.9 - - - -
136B ILE* 2.7 35.8 + - + +
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Residues in contact with VAL 128 (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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101B PHE* 4.2 23.1 - - + -
123B ILE 4.1 3.6 - - - +
124B TYR* 2.8 47.5 + - + +
127B PHE* 1.3 74.8 - - - +
129B HIS* 1.3 68.9 + - - +
130B SER 3.6 0.3 + - - -
135B GLN* 3.4 13.7 + - - +
136B ILE* 4.2 12.3 - - + +
138B ILE* 4.2 11.1 - - + +
143B ARG* 3.7 24.0 + - + -
146B THR* 4.2 15.5 - - + -
158B PHE* 4.3 11.4 - - + -
161B ALA* 5.4 0.9 - - + -
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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