Contacts of the helix formed by residues 136 - 146 (chain A) in PDB entry 3BNF
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 PRO 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ALA* 3.0 32.7 - - - +
50A SER* 4.8 0.4 - - - +
135A SER* 1.4 82.0 - - - +
137A ASP* 1.3 59.8 + - - +
138A VAL 3.2 1.1 + - - -
139A PRO* 3.4 15.5 - - + +
140A ARG 3.6 6.2 + - - -
164A ASN* 3.2 13.5 - - + +
165A THR 3.0 28.7 - - - +
167A GLY* 3.9 8.1 - - - +
169A TYR* 3.6 26.0 - - + -
170A ASN* 2.9 27.3 - - - +
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Residues in contact with ASP 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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48A ALA* 3.6 9.4 - - - +
135A SER* 2.8 10.3 + - - +
136A PRO* 1.3 77.0 - - - +
138A VAL* 1.3 58.2 + - - +
140A ARG* 2.9 35.1 + - - +
141A ILE* 2.9 33.9 + - - +
161A GLU 3.1 20.4 - - - +
162A ILE* 3.7 10.1 - - + -
163A VAL* 3.1 3.7 + - - +
164A ASN* 2.8 47.8 + - - +
486A ARG* 4.9 2.6 - - - +
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Residues in contact with VAL 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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131A TRP* 3.2 33.7 - - + +
132A THR* 3.6 25.8 - - + +
135A SER* 3.1 16.8 + - - +
137A ASP* 1.3 74.0 - - - +
139A PRO* 1.4 76.9 - - + +
141A ILE* 3.0 3.1 + - - +
142A ILE* 2.8 45.0 + - + +
150A TYR* 3.7 24.4 - - + +
162A ILE* 4.3 4.9 - - + -
183A VAL* 4.9 3.6 - - + -
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Residues in contact with PRO 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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132A THR 5.4 0.2 - - - +
135A SER 3.5 7.4 - - - +
136A PRO 3.4 12.8 - - - +
138A VAL* 1.4 96.0 - - + +
140A ARG* 1.3 61.9 + - - +
142A ILE* 4.3 9.0 - - + -
143A GLU* 2.9 48.3 + - + +
169A TYR* 4.0 15.3 - - + +
170A ASN* 3.8 13.9 - - - +
182A LYS* 3.9 32.5 - - + +
183A VAL* 5.6 3.6 - - + -
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Residues in contact with ARG 140 (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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47A LYS* 5.4 11.0 - - - +
48A ALA* 3.9 16.1 - - + +
136A PRO 3.6 6.7 + - - +
137A ASP* 2.9 33.1 + - - +
139A PRO* 1.3 79.1 - - - +
141A ILE* 1.3 72.6 + - - +
143A GLU* 3.6 10.2 + - - +
144A GLN* 3.3 34.7 + - + +
161A GLU* 2.9 52.7 + - - -
169A TYR* 4.0 7.1 - - + -
486A ARG* 3.5 42.5 - - - +
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Residues in contact with ILE 141 (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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137A ASP 2.9 25.7 + - - +
138A VAL 3.9 2.0 - - - +
140A ARG* 1.3 88.0 - - - +
142A ILE* 1.3 61.7 + - - +
144A GLN* 4.4 9.2 - - - +
145A ASP* 2.8 43.5 + - + +
146A GLY 4.6 0.2 - - - +
150A TYR* 4.1 12.1 - - + -
158A TYR* 3.7 34.5 - - + +
161A GLU* 3.9 20.6 - - + +
162A ILE* 3.3 33.4 - - + -
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Residues in contact with ILE 142 (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 THR* 5.4 2.0 - - + -
138A VAL* 2.8 41.1 + - + +
139A PRO* 3.7 6.7 - - + +
141A ILE* 1.3 75.8 - - - +
143A GLU* 1.3 64.4 + - + +
146A GLY* 2.8 33.6 + - - -
147A GLU* 4.0 22.7 - - + +
150A TYR* 3.7 32.3 - - + -
151A PHE* 5.4 5.4 - - + -
182A LYS 5.0 3.8 - - - +
183A VAL* 4.8 13.0 - - + -
184A PRO* 4.9 20.2 - - + -
185A TYR* 6.3 0.4 - - + -
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Residues in contact with GLU 143 (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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47A LYS* 4.3 6.9 + - - -
139A PRO* 2.9 36.3 + - + +
140A ARG* 4.0 5.5 - - - +
142A ILE* 1.3 80.1 - - + +
144A GLN* 1.3 57.7 + - - +
146A GLY 4.9 0.2 - - - -
169A TYR* 2.5 33.8 + - - -
182A LYS* 4.8 12.2 + - - +
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Residues in contact with GLN 144 (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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140A ARG* 3.3 35.7 + - + +
141A ILE* 3.2 8.1 + - - +
142A ILE 3.1 0.6 - - - -
143A GLU* 1.3 78.6 - - - +
145A ASP* 1.3 87.6 + - - +
146A GLY 3.8 0.4 - - - -
161A GLU* 5.7 2.4 - - - +
486A ARG* 4.7 8.5 - - - +
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Residues in contact with ASP 145 (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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141A ILE* 2.8 32.7 + - + +
144A GLN* 1.3 111.0 - - - +
146A GLY* 1.3 58.3 + - - +
149A GLU* 3.4 34.6 - - + +
150A TYR 5.1 0.2 - - - +
158A TYR* 4.7 6.7 + - - +
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Residues in contact with GLY 146 (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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142A ILE* 2.8 22.8 + - - +
143A GLU 4.9 0.4 - - - -
144A GLN 3.8 0.6 - - - -
145A ASP* 1.3 74.8 - - - +
147A GLU* 1.3 66.4 + - - -
148A LEU 3.5 1.8 - - - -
149A GLU 4.2 1.1 - - - -
150A TYR* 3.1 22.9 + - - +
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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