Contacts of the strand formed by residues 145 - 152 (chain C) in PDB entry 1SBB
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 145 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C LEU* 4.4 10.1 - - + -
130C PHE 3.9 8.5 - - - +
131C GLU* 4.2 3.1 - - - +
144C THR* 1.3 98.6 - - + +
146C VAL* 1.3 61.2 + - - +
161C TRP* 3.9 24.0 - - + -
195C ARG* 3.2 5.7 - - - +
196C LEU* 2.7 44.1 + - + +
198C VAL* 4.0 11.4 - - + -
203C TRP* 3.8 28.0 - - + -
210C PHE* 3.5 42.2 - - + -
241C ALA* 5.4 0.2 - - + -
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Residues in contact with VAL 146 (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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129C LEU* 3.5 6.2 - - - +
130C PHE* 2.7 55.5 + - + +
132C PRO* 3.6 30.5 - - + -
143C ALA* 5.0 1.8 - - + +
144C THR 3.9 1.3 - - - +
145C LEU* 1.3 82.2 - - - +
147C CYS* 1.3 69.2 + - - +
148C LEU* 5.5 1.6 - - + -
161C TRP* 4.4 2.2 - - - -
193C SER* 5.2 5.4 - - - -
194C SER 3.4 9.9 - - - +
195C ARG* 3.6 20.2 - - + -
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Residues in contact with CYS 147 (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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127C VAL* 3.3 24.2 - - - -
128C SER 3.4 8.5 - - - +
129C LEU* 4.6 0.9 - - + -
146C VAL* 1.3 77.5 - - - +
148C LEU* 1.3 61.3 + - - +
159C LEU* 4.3 11.4 - - + -
161C TRP* 3.7 15.8 - - + -
192C LEU 4.6 0.2 - - - -
193C SER* 3.2 7.6 - - - -
194C SER* 2.9 31.9 + - - +
212C CYS* 2.0 50.3 - - + -
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Residues in contact with LEU 148 (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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126C LYS 3.1 11.8 - - - +
127C VAL* 4.4 1.1 - - - -
128C SER* 3.3 24.1 + - - -
130C PHE* 3.9 26.0 - - + -
146C VAL* 5.5 1.6 - - + -
147C CYS* 1.3 78.3 - - - +
149C ALA* 1.3 62.1 + - - +
150C ARG* 4.3 17.7 - - + +
191C CYS* 3.3 33.9 - - - -
192C LEU 3.5 13.2 - - - +
193C SER* 4.1 9.6 - - - -
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Residues in contact with ALA 149 (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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125C PRO* 4.4 1.6 - - + -
126C LYS 3.1 7.0 - - - +
127C VAL* 4.2 16.4 - - + +
147C CYS* 4.3 0.8 - - - -
148C LEU* 1.3 72.9 - - - +
150C ARG* 1.3 60.8 + - - +
152C PHE* 3.5 18.1 - - + -
159C LEU* 5.0 3.6 - - + +
191C CYS* 3.3 2.3 - - - -
192C LEU* 2.8 44.8 + - + +
214C VAL* 4.2 20.9 - - + -
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Residues in contact with ARG 150 (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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125C PRO* 3.6 0.3 - - - +
126C LYS* 2.7 80.3 + - + +
148C LEU* 4.3 21.8 - - + +
149C ALA* 1.3 77.7 - - - +
151C GLY* 1.3 83.7 + - - +
152C PHE* 3.2 5.1 + - - -
181C GLU* 2.7 46.3 + - - +
189C SER* 4.6 0.2 + - - -
190C TYR 3.3 7.0 - - - -
191C CYS* 4.4 4.5 - - + -
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Residues in contact with GLY 151 (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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123C THR* 2.9 18.9 + - - -
124C PRO 3.4 7.9 - - - +
150C ARG* 1.3 96.9 - - - +
152C PHE* 1.3 58.8 + - - +
181C GLU* 3.5 2.0 + - - -
187C TYR 5.5 0.2 - - - +
189C SER* 3.1 21.4 + - - -
190C TYR 3.0 6.5 + - - -
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Residues in contact with PHE 152 (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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123C THR 3.4 6.7 - - - +
124C PRO 3.7 0.4 - - - -
125C PRO* 3.4 42.0 - - + -
149C ALA* 3.5 25.6 - - + -
150C ARG* 3.2 6.0 - - - -
151C GLY* 1.3 79.6 - - - +
153C PHE* 1.3 64.5 + - - +
154C PRO 3.4 13.7 - - - -
155C ASP* 3.8 12.8 - - + -
157C VAL* 3.6 37.7 - - + -
178C ALA* 4.0 12.1 - - + -
189C SER* 3.6 1.2 - - - -
190C TYR* 2.8 65.0 + - + +
191C CYS 4.0 1.1 - - - -
192C LEU* 4.1 4.0 - - + -
216C PHE* 4.2 2.0 - - + -
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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