Contacts of the helix formed by residues 204 - 215 (chain C) in PDB entry 2ODE
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 GLN 204 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C GLY* 3.4 12.2 - - - +
43C GLU* 5.0 2.2 - - - +
178C ARG* 4.0 3.0 - - - +
180C LYS* 3.8 15.6 - - + +
181C THR 4.3 1.0 - - - +
202C GLY 3.7 0.6 - - - -
203C GLY* 1.3 86.7 + - - +
205C ARG* 1.3 66.2 + - - +
206C SER* 4.3 6.5 - - - +
207C GLU* 2.9 15.9 + - + +
208C ARG* 3.5 4.5 - - - +
235C ALA* 6.1 3.8 - - + +
236C GLU* 3.3 26.9 + - + +
2002C ALF 2.7 32.8 - - - -
122D ASN* 3.0 43.9 + - - +
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Residues in contact with ARG 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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114B ASP* 5.3 0.6 + - - -
116B GLN* 3.7 40.9 - - - +
203C GLY 3.7 1.0 + - - -
204C GLN* 1.3 70.9 - - - +
206C SER* 1.3 62.6 + - - +
207C GLU 3.1 0.9 + - - -
208C ARG* 3.2 30.2 + - - +
209C LYS* 4.5 3.3 + - - -
234C LEU* 3.6 16.2 - - - +
236C GLU* 3.0 31.8 + - + +
237C ASP* 3.1 31.9 + - - +
240C MET* 3.7 11.5 - - - +
245C GLU* 2.9 42.0 + - - +
248C LYS* 5.4 2.6 - - - +
115D VAL* 6.3 3.4 - - - -
120D GLU* 4.9 1.1 - - - +
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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
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204C GLN* 3.2 2.9 - - - +
205C ARG* 1.3 78.3 - - - +
207C GLU* 1.3 61.8 + - - +
208C ARG 3.7 0.2 + - - -
209C LYS* 3.1 25.5 + - - +
210C LYS* 4.7 4.2 - - - -
236C GLU* 5.8 0.4 - - - +
120D GLU* 3.3 53.9 + - - +
121D VAL 4.0 4.3 - - - -
122D ASN* 3.3 32.4 + - - +
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Residues in contact with GLU 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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182C THR* 2.8 25.9 + - - -
183C GLY* 2.9 25.3 + - - +
202C GLY* 3.4 30.6 - - - +
204C GLN 2.9 10.8 + - - +
206C SER* 1.3 79.6 - - - +
208C ARG* 1.3 58.5 + - - +
209C LYS 3.4 0.7 - - - -
210C LYS* 2.9 52.6 + - - +
211C TRP* 3.6 5.6 - - - -
81D GLU* 4.5 1.8 - - - +
122D ASN* 3.0 38.7 + - - +
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Residues in contact with ARG 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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41C ALA* 4.0 11.7 - - - +
42C GLY 4.8 0.2 - - - +
203C GLY 2.9 23.6 + - - -
204C GLN 3.5 9.2 + - - +
205C ARG* 3.2 30.6 + - - +
207C GLU* 1.3 73.3 - - - +
209C LYS* 1.3 60.5 + - - +
210C LYS 3.0 6.6 + - - -
211C TRP* 3.1 45.5 + - + +
212C ILE 4.6 0.9 + - - -
234C LEU* 5.2 0.8 - - - +
236C GLU* 4.0 5.3 + - - -
245C GLU* 2.8 42.2 + - - +
249C LEU* 3.8 35.8 - - + +
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Residues in contact with LYS 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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205C ARG 4.5 3.8 + - - -
206C SER* 3.1 30.3 + - - +
208C ARG* 1.3 76.3 - - - +
210C LYS* 1.3 71.2 + - + +
211C TRP 3.4 0.2 - - - -
212C ILE* 3.7 17.3 - - - +
213C HIS* 4.9 1.4 + - - -
115D VAL 5.4 0.8 + - - -
117D ALA 4.1 8.0 + - - -
118D PRO* 3.9 23.8 - - - +
119D ARG* 5.8 0.2 - - - -
120D GLU* 3.8 27.8 + - - +
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Residues in contact with LYS 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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182C THR* 3.6 9.5 + - - -
183C GLY* 3.6 10.0 - - - +
184C ILE* 3.3 18.7 - - + +
206C SER 4.7 4.0 - - - -
207C GLU* 2.9 49.5 + - - +
209C LYS* 1.3 85.2 - - + +
211C TRP* 1.3 65.8 + - + +
212C ILE 3.2 2.9 - - - -
213C HIS* 3.2 30.4 + - + -
78D PHE* 2.8 34.2 + - + +
79D SER* 3.8 0.6 - - - +
81D GLU* 2.8 34.7 + - - -
120D GLU 5.7 0.4 - - - -
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Residues in contact with TRP 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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39C LEU* 3.9 24.0 - - + -
40C GLY 3.7 31.6 - - - -
184C ILE* 4.6 4.9 - - + -
201C VAL* 3.4 26.2 - - + +
202C GLY 2.9 29.4 + - - -
203C GLY* 4.1 1.6 - - - -
207C GLU 3.6 13.2 + - - -
208C ARG* 3.1 31.8 + - + +
210C LYS* 1.3 80.9 - - + +
212C ILE* 1.3 58.2 + - - +
214C CYS* 2.9 26.4 + - - -
215C PHE* 3.1 28.1 - + + -
223C PHE* 5.0 0.2 - + - -
249C LEU* 4.0 26.5 - - + -
253C ILE* 3.9 30.5 - - + -
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Residues in contact with ILE 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 ARG 4.6 0.8 + - - -
209C LYS 3.7 18.6 + - - +
210C LYS 4.4 1.1 - - - +
211C TRP* 1.3 78.2 - - - +
213C HIS* 1.3 75.0 + - + +
214C CYS 3.2 1.2 + - - -
215C PHE* 3.2 34.8 + - + +
216C GLU 4.8 0.7 + - - -
258C TRP* 3.5 36.5 - - + +
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Residues in contact with HIS 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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35C LYS* 5.0 1.7 + - - -
184C ILE* 4.0 7.2 - - + -
209C LYS 5.2 1.2 + - - -
210C LYS* 3.2 32.2 + - + +
211C TRP 3.1 1.2 + - - -
212C ILE* 1.3 87.2 - - + +
214C CYS* 1.3 56.8 + - - +
215C PHE 3.5 0.4 + - - -
216C GLU* 5.1 3.1 + - - +
78D PHE* 3.6 49.8 - + + -
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Residues in contact with CYS 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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35C LYS* 3.0 28.9 + - - +
37C LEU* 3.6 30.5 - - + +
39C LEU* 5.1 0.9 - - - -
184C ILE* 4.4 13.2 - - + -
199C PHE* 4.3 20.4 - - + -
201C VAL* 4.3 22.7 - - - -
211C TRP* 2.9 19.8 + - - -
213C HIS* 1.3 78.2 - - - +
215C PHE* 1.3 60.5 + - - +
216C GLU 3.4 2.9 - - - -
218C VAL* 3.4 7.1 - - - +
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Residues in contact with PHE 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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37C LEU* 3.8 15.9 - - + -
39C LEU* 4.4 6.1 - - + -
211C TRP* 3.1 45.1 - + + -
212C ILE* 3.2 38.0 + - + +
213C HIS 3.5 0.6 - - - -
214C CYS* 1.3 75.5 - - - +
216C GLU* 1.3 61.6 + - - +
217C GLY 3.7 1.2 + - - -
218C VAL* 3.5 13.7 + - - +
253C ILE* 3.8 22.2 - - + -
256C ASN* 3.9 16.2 - - - -
258C TRP* 3.3 36.8 - + + +
259C PHE* 3.6 31.5 - + - -
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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