Contacts of the strand formed by residues 206 - 212 (chain C) in PDB entry 4F9P
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 GLU 206 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C CYS 4.2 2.2 - - - -
160C ARG* 4.9 4.3 - - + +
202C GLY* 3.6 4.3 - - - -
203C SER 3.4 22.1 + - - +
205C THR* 1.3 80.7 + - - +
207C PHE* 1.3 69.8 + - - +
208C THR* 5.4 0.9 - - - +
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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
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140C LEU* 6.3 0.2 - - + -
157C LEU 3.7 0.2 - - - +
158C SER* 3.4 5.5 - - - -
159C CYS* 3.0 38.7 + - + +
161C ALA* 5.2 0.9 - - + -
165C ILE* 3.7 19.7 - - + -
166C SER 3.0 24.7 - - - -
167C ASN* 4.5 3.6 - - - -
169C LEU* 3.2 42.2 - - + -
171C TRP* 4.1 7.6 - - + +
187C ALA* 3.7 9.0 - - + -
201C SER 3.6 4.0 - - - +
202C GLY* 3.1 30.5 - - - -
203C SER* 3.4 8.3 - - - -
204C GLY 2.9 24.2 - - - -
205C THR 3.2 24.5 - - - -
206C GLU* 1.3 72.8 - - - +
208C THR* 1.3 66.3 + - - +
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Residues in contact with THR 208 (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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156C SER* 3.9 25.1 - - - -
157C LEU 3.1 11.2 - - - +
158C SER* 5.2 3.9 - - - -
171C TRP* 4.3 4.9 + - - +
200C GLY* 3.2 4.0 - - - -
201C SER* 3.0 41.2 + - - -
206C GLU* 5.4 1.0 - - - +
207C PHE* 1.3 78.5 + - - +
209C LEU* 1.3 65.2 + - - +
210C SER* 3.8 5.5 + - - +
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Residues in contact with LEU 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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155C VAL* 3.8 1.0 - - - +
156C SER* 3.2 3.5 - - - -
157C LEU* 2.7 47.2 + - + +
171C TRP* 3.9 38.1 - - + -
184C ILE* 6.5 0.9 - - + -
199C SER 3.7 4.9 - - - +
200C GLY* 4.4 2.2 - - - -
208C THR* 1.3 73.2 - - - +
210C SER* 1.3 59.4 + - - +
211C ILE 4.1 0.2 + - - -
222C TYR* 6.2 3.6 - - + -
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Residues in contact with SER 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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155C VAL 3.6 6.7 - - - -
156C SER* 4.5 9.9 - - - +
197C ARG 3.1 0.9 - - - +
198C PHE* 3.7 1.1 - - - -
199C SER* 2.6 58.0 + - - +
200C GLY* 5.5 0.7 - - - -
208C THR* 3.8 6.0 + - - -
209C LEU* 1.3 73.0 - - - +
211C ILE* 1.3 61.6 + - - +
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Residues in contact with ILE 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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154C SER* 3.6 6.5 - - - -
155C VAL* 3.1 38.4 + - + +
197C ARG* 3.6 9.0 - - - -
198C PHE* 4.2 25.1 - - + -
209C LEU 4.1 0.8 + - - -
210C SER* 1.3 77.1 - - - +
212C ASN* 1.3 60.9 + - - +
214C VAL* 5.6 9.2 - - + -
218C ASP* 5.7 1.3 - - - +
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Residues in contact with ASN 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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152C GLY 5.4 0.2 - - - +
154C SER* 3.8 14.7 + - - -
197C ARG* 3.2 40.8 + - + +
211C ILE* 1.3 75.6 - - - +
213C SER* 1.3 96.4 + - - +
214C VAL* 3.7 0.7 - - - -
192D PHE* 5.8 6.0 - - + -
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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