Contacts of the helix formed by residues 155 - 161 (chain C) in PDB entry 3LBF
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 155 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C TRP* 3.7 43.3 - - + +
151C PRO* 3.9 3.4 - - + -
153C GLU 3.3 6.9 - - - +
154C ILE* 1.3 87.3 - - + +
156C THR* 1.3 66.6 + - - +
157C ALA 3.2 0.4 - - - -
158C LEU* 3.1 38.1 + - + +
159C MET* 3.7 3.3 + - - +
170C LEU* 3.8 17.5 - - + -
202C LEU* 4.0 17.7 - - + -
153D GLU* 4.0 8.5 - - + -
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Residues in contact with THR 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C TRP 5.1 0.2 + - - -
154C ILE 3.3 2.8 + - - -
155C PRO* 1.3 72.3 - - - +
157C ALA* 1.3 63.7 + - - +
159C MET* 3.0 27.9 + - + +
160C THR* 3.0 24.8 + - - +
152D PRO 2.6 29.1 + - - +
153D GLU* 3.6 13.5 + - - +
172D VAL* 4.1 12.8 - - + +
173D GLY* 5.9 3.4 - - - -
180D LYS* 6.2 3.8 - - - +
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Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C TRP 3.3 23.1 + - - +
134C GLN* 3.7 31.4 - - - +
135C GLY 4.2 0.2 - - - +
156C THR* 1.3 78.4 - - - +
158C LEU* 1.3 58.3 + - - +
160C THR* 3.5 7.7 + - - -
161C GLN* 3.0 41.6 + - - +
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LEU* 4.1 6.3 - - + -
82C ILE* 4.2 5.2 - - + -
132C GLY 3.8 12.8 - - - +
133C TRP 4.8 0.7 - - - +
135C GLY* 3.6 29.6 - - - -
145C ILE* 3.4 41.5 - - + +
147C VAL* 3.8 29.2 - - + -
155C PRO* 3.1 41.7 + - + +
156C THR 3.1 1.2 - - - -
157C ALA* 1.3 77.1 - - - +
159C MET* 1.3 64.2 + - - +
161C GLN* 4.1 0.7 - - - +
162C LEU* 3.9 5.2 + - - +
168C LEU* 3.9 22.8 - - + +
170C LEU* 5.0 0.2 - - + -
202C LEU* 5.2 1.6 - - + -
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Residues in contact with MET 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ILE* 4.0 41.7 - - + +
155C PRO 3.7 0.6 + - - -
156C THR* 3.0 22.1 + - + +
158C LEU* 1.3 79.2 - - - +
160C THR* 1.3 65.0 + - - +
162C LEU* 3.0 24.0 + - - +
168C LEU* 4.1 1.1 - - + -
182C VAL* 4.0 25.8 - - + -
184C ARG* 3.5 1.2 + - - -
189C PHE* 3.3 47.1 - - + -
191C ILE* 5.5 0.7 - - - -
154D ILE* 5.1 11.0 - - + +
191D ILE* 4.4 18.2 - - + -
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Residues in contact with THR 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C PRO* 5.4 1.0 - - - +
156C THR* 3.0 27.6 + - - +
157C ALA* 3.8 8.2 - - - -
159C MET* 1.3 76.7 - - - +
161C GLN* 1.3 60.8 + - + +
162C LEU 3.2 5.0 + - - +
184C ARG* 3.2 17.7 + - - +
189C PHE* 4.5 3.1 - - - -
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Residues in contact with GLN 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LEU* 4.1 1.2 - - - +
134C GLN 3.0 25.1 + - - -
135C GLY* 3.6 4.8 - - - -
136C TRP 2.9 25.5 + - - -
137C GLN* 3.4 30.5 - - + +
140C ALA* 3.7 16.8 - - + -
141C PRO* 3.1 7.4 - - - +
142C PHE* 2.9 42.3 + - + -
145C ILE* 4.2 9.4 - - + -
157C ALA* 3.0 27.2 + - - +
158C LEU* 4.1 0.4 - - - +
159C MET 3.2 0.4 - - - -
160C THR* 1.3 79.0 - - + +
162C LEU* 1.3 58.3 + - - +
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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