Contacts of the strand formed by residues 190 - 196 (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 TYR 190 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150C ARG* 3.3 3.5 - - - -
151C GLY 3.0 25.3 + - - -
152C PHE* 2.8 39.7 + - + +
153C PHE* 3.7 32.6 - + - -
154C PRO* 4.2 0.7 - - + -
155C ASP* 3.6 53.5 + - + -
178C ALA* 4.0 12.8 - - + -
179C TYR 3.4 17.5 - - - -
180C LYS* 4.0 16.8 - - + -
181C GLU* 3.4 2.8 - - - +
189C SER* 1.3 75.0 + - - +
191C CYS* 1.3 59.9 - - - +
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Residues in contact with CYS 191 (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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148C LEU* 3.3 26.2 - - - -
149C ALA 3.3 6.7 - - - -
150C ARG* 5.0 1.1 - - - -
152C PHE* 4.0 1.3 - - - -
175C ASP* 5.5 2.0 - - - -
178C ALA* 3.1 8.5 - - - +
179C TYR* 2.7 40.9 + - + +
181C GLU* 3.7 21.8 - - + +
190C TYR* 1.3 74.4 - - - +
192C LEU* 1.3 67.4 + - - +
193C SER* 4.9 2.2 - - - -
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Residues in contact with LEU 192 (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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147C CYS 4.1 0.2 - - - +
148C LEU* 3.5 3.0 - - - -
149C ALA* 2.8 43.8 + - + +
152C PHE* 4.1 10.3 - - + -
157C VAL* 3.6 31.4 - - + +
158C GLU* 5.6 0.2 - - - -
159C LEU* 4.4 27.2 - - + +
174C THR* 4.9 4.3 - - + -
175C ASP* 3.6 37.2 - - + +
177C GLN* 4.0 1.6 - - - -
178C ALA* 3.7 23.6 - - + +
191C CYS* 1.3 80.1 - - - +
193C SER* 1.3 63.5 + - - +
214C VAL* 6.2 0.9 - - + -
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Residues in contact with SER 193 (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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146C VAL* 5.2 5.4 - - - -
147C CYS 3.2 12.1 - - - -
148C LEU* 4.1 13.5 - - - -
159C LEU* 4.4 2.5 - - - -
174C THR* 3.6 4.5 - - - +
175C ASP* 2.9 53.6 + - - +
191C CYS* 4.9 2.1 - - - -
192C LEU* 1.3 76.3 - - - +
194C SER* 1.3 64.5 + - - +
195C ARG* 3.4 12.5 + - - -
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Residues in contact with SER 194 (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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146C VAL* 3.4 1.6 - - - +
147C CYS* 2.9 31.4 + - - +
159C LEU* 3.5 27.2 - - - +
161C TRP* 2.7 30.3 + - - -
172C VAL* 4.0 1.4 - - - +
173C SER 3.4 8.5 + - - -
174C THR* 3.2 19.5 + - - -
193C SER* 1.3 77.4 - - - +
195C ARG* 1.3 70.6 + - - +
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Residues in contact with ARG 195 (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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207B LYS* 4.3 13.2 - - - +
143C ALA* 3.5 25.1 - - + -
145C LEU 3.2 4.3 - - - +
146C VAL* 3.6 24.9 - - + -
161C TRP* 4.0 3.7 + - - +
171C GLY 3.0 4.8 - - - +
172C VAL* 3.4 2.8 - - - -
173C SER* 2.7 77.6 + - - +
174C THR 3.5 2.6 + - - -
175C ASP* 2.8 39.6 + - - +
193C SER* 3.4 17.0 + - - -
194C SER* 1.3 82.8 + - - +
196C LEU* 1.3 60.0 + - - +
197C ARG 4.1 0.4 - - - -
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Residues in contact with LEU 196 (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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144C THR* 3.3 5.6 - - - -
145C LEU* 2.7 39.9 + - + +
161C TRP* 3.7 41.0 - - + -
163C VAL* 3.8 26.2 - - + -
168C VAL* 4.2 7.6 - - + -
170C SER 3.8 22.0 - - - +
171C GLY 3.4 6.3 - - - +
172C VAL* 4.2 12.6 - - + -
195C ARG* 1.3 72.3 - - - +
197C ARG* 1.3 61.6 + - - +
198C VAL* 3.5 14.9 + - + -
210C PHE* 4.1 14.4 - - + -
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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