Contacts of the strand formed by residues 206 - 215 (chain C) in PDB entry 1AUT
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 THR 206 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C CYS* 3.7 24.7 - - - -
202C SER* 3.1 2.6 - - - -
203C PHE 2.7 37.2 + - - +
204C HIS 3.7 3.8 + - - -
205C GLY* 1.3 77.6 - - - +
207C TRP* 1.3 65.5 + - - +
208C PHE* 3.9 10.9 + - + -
107L HIS* 3.0 28.1 + - - +
124L TYR* 3.5 21.3 - - + +
141L CYS 3.7 2.5 - - - +
142L GLY 3.7 3.1 - - - +
143L ARG* 2.9 20.2 + - - +
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Residues in contact with TRP 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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29C TRP* 4.0 11.2 - + + -
121C ILE* 3.1 26.4 - - + +
122C CYS* 3.2 16.3 + - - +
137C LEU* 4.2 23.1 - - + -
200C VAL* 3.5 34.5 - - + -
201C ALA* 3.6 17.9 - - - -
202C SER* 3.6 33.1 - - - -
205C GLY 4.1 9.6 + - - -
206C THR* 1.3 72.2 - - - +
208C PHE* 1.3 61.0 + - - +
142L GLY* 2.8 39.7 + - - +
144L PRO* 3.9 20.1 - - + +
146L LYS* 5.3 10.8 - - - +
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Residues in contact with PHE 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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121C ILE* 4.0 3.6 - - - -
122C CYS* 3.3 27.6 - - + -
123C LEU 4.0 2.9 - - - -
124C PRO* 3.9 14.8 - - + -
128C LEU* 3.6 19.1 - - + -
129C LEU* 3.7 20.6 - - - -
200C VAL* 3.5 6.1 - - - +
201C ALA 3.0 30.5 + - - +
203C PHE* 3.3 38.1 - + + -
206C THR* 3.9 17.0 - - - -
207C TRP* 1.3 74.1 - - - +
209C LEU* 1.3 62.7 + - - +
210C VAL* 3.6 1.8 + - - +
107L HIS* 3.7 30.5 - + + -
108L TYR* 4.0 20.4 - + - -
121L ALA* 4.3 4.9 - - + -
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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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45C VAL* 4.3 13.5 - - + -
47C ILE* 3.9 17.5 - - + -
53C LEU* 3.9 15.7 - - + -
121C ILE* 3.7 12.5 - - + +
122C CYS 2.9 17.0 + - - +
123C LEU* 3.6 26.5 - - + -
124C PRO* 3.2 24.1 - - - +
198C PRO* 3.9 23.6 - - + -
199C MET 4.2 3.8 - - - +
200C VAL* 4.9 0.9 - - + -
208C PHE* 1.3 72.4 - - - +
210C VAL* 1.3 61.0 + - - +
211C GLY 3.6 22.0 - - - +
212C LEU* 4.4 1.3 - - + -
231C VAL* 4.2 19.8 - - + +
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Residues in contact with VAL 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LEU* 3.8 44.4 - - - +
130C ASN* 3.7 15.3 - - - +
136C THR* 4.8 2.9 - - + -
162C VAL* 4.9 0.7 - - + -
181C LEU* 3.6 21.1 - - + +
199C MET* 2.9 38.9 + - + +
200C VAL 4.6 0.2 - - - -
201C ALA* 4.0 15.7 - - + -
208C PHE 4.1 3.4 - - - +
209C LEU* 1.3 76.8 - - - +
211C GLY* 1.3 59.9 + - - +
229C THR 3.6 0.7 - - - +
231C VAL* 3.3 23.4 + - - +
232C SER 4.7 1.4 + - - -
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Residues in contact with GLY 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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181C LEU* 5.0 1.1 - - - -
199C MET* 2.9 37.6 + - - +
209C LEU* 3.6 4.7 - - - +
210C VAL* 1.3 82.9 - - - +
212C LEU* 1.3 72.3 + - - +
228C TYR* 4.7 3.1 - - - -
229C THR 2.9 16.2 - - - -
231C VAL* 3.9 4.0 - - - +
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Residues in contact with LEU 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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45C VAL* 3.7 25.1 - - + -
53C LEU* 4.4 3.8 - - + -
54C THR 3.7 31.6 - - - +
55C ALA* 4.4 0.9 - - - +
102C ASP 4.5 4.7 - - - +
103C ILE* 4.0 27.6 - - + -
196C GLY* 3.7 22.2 - - - +
197C GLY 3.1 8.3 - - - +
209C LEU* 4.4 7.0 - - + -
211C GLY* 1.3 82.9 - - - +
213C VAL* 1.3 66.3 + - - +
214C SER* 3.0 1.7 + - - -
228C TYR* 3.2 6.6 - - - +
229C THR* 2.9 35.5 + - - +
231C VAL* 4.2 11.2 - - + -
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Residues in contact with VAL 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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1C 0G6 4.0 13.5 - - + -
55C ALA* 4.0 5.4 - - - +
138C VAL* 3.5 32.1 - - + -
139C THR 5.0 0.7 - - - +
190C ALA* 3.5 27.4 - - + -
194C ASP* 3.3 22.4 - - + +
195C SER* 3.4 22.7 - - - +
196C GLY* 2.8 23.6 + - - -
197C GLY* 2.9 18.0 + - - +
212C LEU* 1.3 70.0 - - - +
214C SER* 1.3 59.8 + - - +
227C VAL 5.2 0.7 - - - +
228C TYR* 3.8 13.6 - - + -
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Residues in contact with SER 214 (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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1C 0G6 2.8 24.8 + - - -
55C ALA* 5.8 0.2 - - - -
57C HIS* 3.2 11.4 + - - -
99C THR 4.2 0.5 + - - -
102C ASP* 2.7 34.6 + - - +
180C MET* 6.0 1.2 - - - +
195C SER* 3.6 0.2 + - - -
212C LEU 3.0 4.4 + - - -
213C VAL* 1.3 76.2 - - - +
215C TRP* 1.3 76.9 + - - +
227C VAL* 3.0 15.4 + - - -
228C TYR* 4.0 6.1 - - - -
229C THR* 3.6 16.9 + - - -
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Residues in contact with TRP 215 (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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1C 0G6 3.2 65.8 + + + +
98C THR 4.8 0.7 - - - -
99C THR* 3.7 14.7 + - + -
172C MET* 4.0 8.3 - - + -
174C ASN* 3.5 41.7 - - + -
175C MET 3.5 21.8 - - - -
176C VAL* 4.2 6.5 - - + -
180C MET* 3.3 32.2 - - + +
214C SER* 1.3 95.0 - - - +
216C GLY* 1.3 69.9 + - - +
217C GLU* 3.8 8.1 - - - -
226C GLY* 3.8 1.0 - - - -
227C VAL* 2.7 69.3 + - + +
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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