Contacts of the helix formed by residues 132 - 139 (chain B) in PDB entry 1BK6
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 VAL 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B VAL 5.2 1.1 - - - +
127B ILE* 4.4 21.1 - - + +
130B GLY 3.7 0.2 - - - -
131B VAL* 1.3 76.9 - - + +
133B PRO* 1.3 70.4 - - + +
135B LEU* 3.1 12.5 + - - +
136B VAL* 3.0 24.8 + - + +
155B LEU* 3.9 16.6 - - + -
158B ILE* 4.2 24.7 - - + -
168B VAL* 3.9 30.7 - - + +
169B VAL* 4.3 6.5 - - + -
172B ALA* 4.1 19.3 - - + -
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Residues in contact with PRO 133 (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 GLY* 4.1 16.6 - - - +
131B VAL 3.4 0.9 - - - -
132B VAL* 1.3 96.4 - - + +
134B ARG* 1.3 61.1 + - + +
136B VAL* 3.3 19.7 + - + +
137B GLU* 3.3 19.3 + - - +
172B ALA* 4.6 10.1 - - + +
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 2.9 38.4 + - + -
97B ASN* 3.4 32.2 + - - +
98B SER 3.4 7.3 + - - -
99B ASP* 5.4 0.8 + - - +
104B GLN* 2.7 34.3 - - - +
130B GLY 5.3 1.1 - - - +
131B VAL* 2.9 17.0 + - - +
133B PRO* 1.3 81.6 - - + +
135B LEU* 1.3 59.7 + - - +
137B GLU* 3.3 46.9 + - - +
138B PHE* 3.7 20.6 + - + -
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Residues in contact with LEU 135 (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 LEU* 3.9 31.0 - - + -
108B THR* 4.2 23.6 - - + +
111B PHE* 5.2 9.4 - - + -
115B LEU* 6.0 0.2 - - + -
126B VAL* 5.4 2.0 - - + -
131B VAL* 3.0 27.6 + - + +
132B VAL* 3.1 14.1 + - - +
134B ARG* 1.3 74.5 - - - +
136B VAL* 1.3 64.8 + - - +
137B GLU 3.2 0.7 - - - -
138B PHE* 3.4 14.4 + - + -
139B MET* 4.1 2.1 + - - +
151B ALA* 3.4 22.4 - - + +
154B ALA* 4.4 20.4 - - + -
155B LEU* 4.0 22.9 - - + +
158B ILE* 4.7 9.2 - - + -
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Residues in contact with VAL 136 (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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132B VAL* 3.0 20.4 + - + +
133B PRO* 3.4 8.5 - - + +
134B ARG 3.2 0.2 - - - -
135B LEU* 1.3 74.0 - - - +
137B GLU* 1.3 65.5 + - - +
139B MET* 3.5 10.2 + - + +
140B ARG* 5.3 1.8 - - - +
155B LEU* 4.1 19.3 - - + -
169B VAL 5.2 0.2 - - - +
172B ALA* 3.5 42.2 - - + +
173B ASP* 4.4 0.9 - - + -
174B ALA* 4.0 17.5 - - + +
177B LEU* 3.4 33.9 - - + +
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Residues in contact with GLU 137 (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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133B PRO 3.6 10.6 - - - +
134B ARG* 3.3 48.4 + - - +
135B LEU 3.2 0.6 - - - -
136B VAL* 1.3 75.8 - - - +
138B PHE* 1.3 62.1 + - + +
139B MET 2.8 11.4 + - - -
140B ARG* 3.0 63.8 + - - +
143B GLN* 3.7 6.3 + - - +
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Residues in contact with PHE 138 (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 LEU* 3.6 24.9 - - + -
104B GLN* 4.0 22.0 - - + -
108B THR* 3.3 27.1 - - - -
134B ARG* 3.7 48.9 - - - -
135B LEU* 3.4 10.3 + - + +
136B VAL 3.3 1.0 - - - -
137B GLU* 1.3 79.2 - - + +
139B MET* 1.3 56.3 + - - +
140B ARG 3.3 2.5 - - - -
143B GLN* 3.4 21.0 - - - +
147B LEU* 3.4 31.6 - - + -
148B GLN* 3.2 26.2 + - - +
151B ALA* 3.7 18.2 - - + -
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Residues in contact with MET 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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135B LEU 4.1 8.3 - - - +
136B VAL* 3.5 12.9 + - - +
137B GLU 2.8 2.2 + - - -
138B PHE* 1.3 79.3 - - - +
140B ARG* 1.3 65.4 + - - +
148B GLN* 4.0 22.9 - - - +
151B ALA* 4.2 3.8 - - + -
152B ALA* 3.8 15.9 - - - -
155B LEU* 3.7 18.6 - - + -
174B ALA* 4.1 12.3 - - + +
177B LEU* 4.0 25.1 - - + +
178B PHE* 3.3 42.2 - - + -
180B GLN* 3.7 11.6 + - - -
181B LEU* 4.0 25.4 - - + +
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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