Contacts of the helix formed by residues 132 - 139 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ILE* 4.4 20.4 - - + +
130A GLY 3.7 0.2 - - - -
131A VAL* 1.3 77.8 - - + +
133A PRO* 1.3 69.3 - - + +
135A LEU* 3.1 12.2 + - - +
136A VAL* 3.0 25.7 + - + +
155A LEU* 4.0 16.6 - - + +
158A ILE* 4.1 24.7 - - + -
168A VAL* 3.9 40.6 - - + +
169A VAL* 4.3 6.1 - - + -
172A ALA* 4.2 11.4 - - + -
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Residues in contact with PRO 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLY* 4.1 16.8 - - - +
131A VAL 3.4 1.1 - - - -
132A VAL* 1.3 97.6 - - + +
134A ARG* 1.3 62.6 + - + +
136A VAL* 3.2 20.0 + - + +
137A GLU* 3.3 19.2 + - - +
172A ALA* 4.6 9.6 - - + -
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Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 2.9 37.2 + - + -
97A ASN* 3.5 33.1 + - - +
98A SER 3.4 8.3 + - - -
99A ASP* 5.4 0.8 + - - +
104A GLN* 2.8 32.1 - - - +
130A GLY 5.2 1.1 - - - +
131A VAL* 2.9 17.6 + - - +
133A PRO* 1.3 83.2 - - + +
135A LEU* 1.3 59.7 + - - +
137A GLU* 3.5 45.5 + - - +
138A PHE* 3.8 20.4 + - + -
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 3.9 30.3 - - + -
108A THR* 4.1 24.7 - - + +
111A PHE* 5.2 9.2 - - + -
115A LEU* 6.0 0.4 - - + -
126A VAL* 5.4 1.3 - - + -
131A VAL* 3.0 30.8 + - + +
132A VAL* 3.1 12.1 + - - +
134A ARG* 1.3 74.1 - - - +
136A VAL* 1.3 66.5 + - - +
137A GLU 3.2 0.6 + - - -
138A PHE* 3.4 13.5 + - + -
139A MET* 4.1 2.3 - - - +
151A ALA* 3.5 21.1 - - + +
154A ALA* 4.4 20.0 - - + -
155A LEU* 4.0 24.4 - - + +
158A ILE* 4.7 9.2 - - + -
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL* 3.0 21.0 + - + +
133A PRO* 3.2 9.8 + - + +
135A LEU* 1.3 76.7 - - - +
137A GLU* 1.3 63.2 + - - +
139A MET* 3.4 9.4 + - + +
140A ARG* 5.3 1.8 - - - +
155A LEU* 4.0 18.6 - - + -
169A VAL 5.2 0.2 - - - +
172A ALA* 3.6 39.9 - - + +
173A ASP* 4.3 1.1 - - + +
174A ALA* 4.1 19.3 - - + +
177A LEU* 3.4 33.1 - - + +
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PRO 3.3 11.8 + - - +
134A ARG* 3.5 46.8 + - - +
135A LEU 3.2 0.6 - - - -
136A VAL* 1.3 73.8 - - + +
138A PHE* 1.3 62.2 + - + +
139A MET 2.8 12.0 + - - -
140A ARG* 2.9 63.1 + - - +
143A GLN* 3.7 6.5 + - - +
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Residues in contact with PHE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 3.6 23.8 - - + -
104A GLN* 4.0 27.4 - - + -
108A THR* 3.3 27.1 - - - -
134A ARG* 3.8 42.4 - - - -
135A LEU* 3.4 16.6 + - + +
136A VAL 3.3 0.8 - - - -
137A GLU* 1.3 78.4 - - + +
139A MET* 1.3 57.5 + - - +
140A ARG 3.3 2.5 - - - -
143A GLN* 3.5 19.2 - - - +
147A LEU* 3.6 32.3 - - + +
148A GLN* 3.2 26.2 + - - +
151A ALA* 3.8 11.0 - - + -
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Residues in contact with MET 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU 4.1 8.7 - - - +
136A VAL* 3.4 14.1 + - + +
137A GLU 2.8 2.4 + - - -
138A PHE* 1.3 80.2 - - - +
140A ARG* 1.3 64.8 + - - +
148A GLN* 4.0 22.4 - - - +
151A ALA* 4.2 2.7 - - + -
152A ALA* 3.8 15.7 - - - -
155A LEU* 3.7 18.2 - - + -
174A ALA* 4.2 12.8 - - + -
177A LEU* 4.0 24.6 - - + +
178A PHE* 3.3 41.5 - - + -
180A GLN* 3.7 12.1 + - - -
181A LEU* 4.0 25.5 - - + +
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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