Contacts of the helix formed by residues 203 - 213 (chain C) in PDB entry 1D1T
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 VAL 203 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175C GLY* 3.8 20.9 - - - +
178C THR* 3.7 15.7 - - + -
179C GLY* 3.5 26.0 - - - +
202C GLY* 1.3 71.2 - - - -
204C GLY* 1.3 65.9 + - - +
206C SER* 3.0 4.3 + - - -
207C VAL* 2.9 20.1 + - - +
268C VAL* 3.6 20.0 - - + -
292C VAL* 3.8 5.8 - - + -
369C ARG* 4.2 1.1 - - - +
3377C NAD 2.7 57.3 + - + +
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Residues in contact with GLY 204 (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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197C VAL* 4.1 2.5 - - - -
199C GLY 3.2 27.6 - - - -
200C LEU* 4.7 0.2 - - - -
201C GLY 3.0 6.5 + - - +
203C VAL* 1.3 78.7 - - - +
205C LEU* 1.3 56.6 + - - +
207C VAL* 2.8 35.8 + - - +
208C ILE* 3.1 7.7 + - - +
268C VAL* 3.5 14.0 - - - +
3377C NAD 4.1 0.6 + - - -
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Residues in contact with LEU 205 (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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200C LEU* 3.1 32.5 - - + +
201C GLY 2.8 13.2 + - - +
204C GLY* 1.3 71.0 - - - -
206C SER* 1.3 59.2 + - - +
208C ILE* 3.6 9.3 - - + +
209C MET* 3.2 25.6 + - - +
228C LYS 4.7 0.4 - - - +
231C LYS* 4.1 21.3 - - + -
232C ALA* 3.8 36.6 - - + +
235C VAL* 3.3 18.3 - - + +
344C GLN* 5.4 1.1 - - + +
345C LEU* 3.9 17.9 - - + -
368C ILE* 3.9 35.2 - - + -
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Residues in contact with SER 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C GLY 3.9 0.9 - - - -
176C PHE* 3.3 41.0 - - - -
179C GLY* 3.6 5.6 - - - -
180C TYR* 3.3 11.4 + - - +
202C GLY 2.8 18.2 + - - -
203C VAL 3.0 10.3 + - - -
205C LEU* 1.3 77.7 - - - +
207C VAL* 1.3 64.7 + - - +
209C MET* 3.5 11.1 - - - +
210C GLY 3.1 15.6 + - - -
345C LEU* 3.7 13.9 - - - +
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Residues in contact with VAL 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C GLY* 3.0 21.3 - - - +
182C ALA* 4.2 2.5 - - + -
183C ALA* 4.1 2.9 - - + -
197C VAL* 3.2 31.2 - - + -
203C VAL 2.9 7.4 + - - +
204C GLY* 2.8 26.9 + - - +
206C SER* 1.3 73.7 - - - +
208C ILE* 1.3 57.1 + - - +
210C GLY* 2.8 4.2 + - - -
211C CYS* 2.8 35.3 + - - -
266C PHE* 3.4 45.3 - - + -
268C VAL* 4.4 8.1 - - + -
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Residues in contact with ILE 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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197C VAL* 3.9 19.1 - - + -
200C LEU* 3.6 31.2 - - + -
204C GLY 3.6 10.8 - - - +
205C LEU* 3.6 15.7 - - + +
207C VAL* 1.3 78.9 - - - +
209C MET* 1.3 64.0 + - - +
211C CYS* 3.1 6.4 + - - +
212C LYS* 2.9 22.9 + - - +
219C ILE* 3.9 12.6 - - + +
221C GLY* 5.1 1.8 - - - -
232C ALA* 4.3 15.0 - - + -
235C VAL* 3.6 14.8 - - + -
236C GLY* 3.7 30.3 - - - +
237C ALA* 3.8 7.6 - - + +
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Residues in contact with MET 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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176C PHE* 3.6 34.8 - - + -
180C TYR* 4.5 4.0 - - + -
205C LEU 3.2 16.8 + - - +
206C SER* 3.5 9.6 - - - +
208C ILE* 1.3 78.8 - - - +
210C GLY* 1.3 58.0 + - - +
212C LYS* 3.5 6.4 + - - +
213C SER* 2.9 30.8 + - - -
235C VAL* 3.3 22.2 - - + +
340C PHE* 4.0 17.9 - - + -
341C ASP* 4.0 25.4 - - + +
344C GLN* 6.0 2.2 - - - -
345C LEU* 4.5 13.2 - - - -
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Residues in contact with GLY 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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180C TYR* 3.6 27.1 - - - -
183C ALA* 3.7 14.4 - - - -
184C VAL* 4.0 6.0 - - - +
206C SER 3.1 6.8 + - - -
207C VAL 2.8 13.1 + - - -
209C MET* 1.3 73.5 - - - +
211C CYS* 1.3 62.9 + - - -
213C SER* 3.3 4.3 + - - -
214C ALA* 3.1 22.0 + - - +
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Residues in contact with CYS 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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183C ALA* 3.6 17.2 - - - +
189C VAL* 3.9 2.9 - - - -
195C CYS* 3.6 32.8 - - - -
197C VAL* 5.0 3.8 - - - -
207C VAL* 2.8 23.1 + - - -
208C ILE* 3.5 7.9 - - - +
210C GLY* 1.3 70.2 - - - +
212C LYS* 1.3 55.9 + - - +
214C ALA* 2.7 31.5 + - - +
216C ALA* 3.3 14.0 + - + +
219C ILE* 3.6 16.8 - - + -
266C PHE* 3.9 16.4 - - - -
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Residues in contact with LYS 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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208C ILE 2.9 15.7 + - - +
209C MET* 3.7 7.6 - - - +
211C CYS* 1.3 76.1 - - - +
213C SER* 1.3 58.6 + - - +
214C ALA 3.1 4.5 + - - -
215C GLY* 3.1 13.2 + - - -
216C ALA 4.1 16.3 + - - +
217C SER* 4.4 4.0 + - - +
219C ILE* 3.5 16.4 - - + +
235C VAL 4.6 4.0 - - - +
236C GLY* 3.4 32.9 + - - +
238C THR* 3.5 21.6 - - - +
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Residues in contact with SER 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C TYR* 4.2 23.0 + - - -
184C VAL* 5.5 2.5 - - - -
209C MET 2.9 17.9 + - - -
210C GLY 3.6 5.2 - - - -
211C CYS 3.2 0.2 - - - -
212C LYS* 1.3 75.3 - - - +
214C ALA* 1.3 57.7 + - - +
215C GLY 3.4 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