Contacts of the strand formed by residues 206 - 213 (chain C) in PDB entry 3SBW
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 ILE 206 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C SER* 3.6 3.3 - - - -
170C SER* 3.1 41.4 + - - +
204C ASN 3.7 13.2 - - - +
205C GLU* 1.3 76.3 - - - +
207C PHE* 1.3 66.3 + - - +
208C TYR* 3.6 26.5 - - + +
223C GLU* 3.6 38.8 - - + +
224C LEU 3.6 3.1 - - - -
225C VAL* 4.6 9.2 - - + -
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Residues in contact with PHE 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C LEU* 3.8 26.2 - - + -
167C TRP* 4.8 7.4 - - + -
168C THR 3.5 5.4 - - - +
169C SER* 4.3 4.7 - - - -
175C LEU* 3.9 29.2 - - + -
197C LEU* 4.2 2.7 - - + -
199C ILE* 3.9 21.5 - - + -
201C THR* 3.5 32.5 - - - -
205C GLU* 3.5 29.2 - - + -
206C ILE* 1.3 77.4 - - - +
208C TYR* 1.3 64.9 + - - +
223C GLU* 3.3 6.2 - - - +
224C LEU* 2.8 43.2 + - + +
226C ILE* 3.6 21.3 - - + -
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Residues in contact with TYR 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ILE 3.7 0.9 - - - +
167C TRP* 3.5 12.1 - - - -
168C THR* 2.8 46.3 + - - +
169C SER 4.3 10.5 - - - -
170C SER* 4.9 3.6 - - - -
172C HIS* 4.0 30.7 + + - -
206C ILE* 3.6 27.8 - - + +
207C PHE* 1.3 76.1 - - - +
209C CYS* 1.3 58.1 + - - +
210C THR* 4.8 1.8 - - - +
221C THR* 3.6 25.4 - - + -
222C ALA 3.2 8.5 - - - +
223C GLU* 3.8 28.1 + - + -
224C LEU* 4.8 0.2 - - - -
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Residues in contact with CYS 209 (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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137C ILE* 4.2 0.4 - - - -
155C CYS* 2.1 54.3 - - + -
165C VAL* 4.2 6.3 - - + -
166C ILE 3.6 3.6 - - - -
167C TRP* 3.9 18.6 - - + -
208C TYR* 1.3 73.5 - - - +
210C THR* 1.3 62.1 + - - +
211C PHE* 4.2 9.3 + - - -
220C HIS 3.7 1.6 - - - +
221C THR* 3.3 1.6 - - - -
222C ALA* 2.9 50.5 + - - -
224C LEU* 4.1 2.7 - - - +
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Residues in contact with THR 210 (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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165C VAL* 3.2 5.1 - - - +
166C ILE* 2.9 53.4 + - + +
168C THR* 4.9 4.0 + - - +
208C TYR* 4.8 4.5 - - - +
209C CYS* 1.3 73.5 + - - +
211C PHE* 1.3 65.2 + - - +
212C ARG* 3.5 3.0 + - - +
219C ASN* 3.8 33.2 - - + +
220C HIS 3.5 4.9 - - - +
221C THR* 2.7 27.8 + - - +
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Residues in contact with PHE 211 (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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134C TYR* 3.7 39.8 - + + +
137C ILE* 3.9 31.4 - - + -
155C CYS* 3.9 26.2 - - + -
156C GLN 4.0 1.1 - - - -
157C ALA* 3.8 23.1 - - + -
163C ALA* 4.3 4.5 - - + -
164C GLU 3.4 4.7 - - - -
165C VAL* 3.5 26.2 - - + -
193C VAL* 3.7 24.9 - - + -
209C CYS* 4.2 6.5 - - - -
210C THR* 1.3 74.1 - - - +
212C ARG* 1.3 60.4 + - - +
213C ARG* 3.8 1.8 + - - +
218C GLU 3.2 6.9 - - - +
219C ASN* 3.5 0.3 - - - -
220C HIS* 2.9 39.9 + - + +
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Residues in contact with ARG 212 (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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162C LYS 4.4 0.5 - - - +
163C ALA* 3.3 2.2 - - - -
164C GLU* 2.7 49.7 + - + +
166C ILE* 3.8 27.0 - - + +
210C THR* 3.5 1.4 + - - +
211C PHE* 1.3 71.8 - - - +
213C ARG* 1.3 67.2 + - - +
214C LEU* 5.1 8.6 - - + +
217C GLU* 4.5 17.5 + - + +
218C GLU 3.6 2.2 - - - -
219C ASN* 3.2 29.1 + - - +
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Residues in contact with ARG 213 (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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131C ASN* 3.9 13.2 + - - +
132C ALA 3.0 32.3 + - - +
133C PRO* 3.7 0.8 - - - +
134C TYR* 3.7 15.0 - - + -
160C TYR 3.3 10.9 + - - -
161C PRO* 3.4 37.2 - - + +
162C LYS 4.0 8.1 - - - +
163C ALA* 4.0 10.5 - - + -
211C PHE 3.8 0.8 + - - +
212C ARG* 1.3 75.5 - - - +
214C LEU* 1.3 88.6 + - - +
216C PRO* 3.4 33.9 + - - +
217C GLU* 3.4 5.4 - - - +
218C GLU* 3.1 65.0 + - + +
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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