Contacts of the helix formed by residues 202 - 220 (chain C) in PDB entry 3CO6
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 ASP 202 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C ASP 3.6 12.5 + - - +
200C LYS 3.6 0.2 - - - -
201C GLY* 1.3 78.3 - - - +
203C SER* 1.3 62.6 + - - +
204C ASN* 2.8 31.9 + - - +
205C SER* 2.5 21.5 + - - -
206C SER* 2.7 30.5 + - - -
210C LYS* 5.6 0.4 - - - -
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Residues in contact with SER 203 (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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202C ASP* 1.3 75.7 - - - +
204C ASN* 1.3 59.1 + - - +
205C SER 2.9 7.8 + - - -
206C SER* 3.5 11.5 + - - -
207C ALA* 3.7 11.4 + - - +
210C LYS* 5.9 1.1 - - - +
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Residues in contact with ASN 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ASP* 2.8 14.3 + - - +
203C SER* 1.3 74.7 - - - +
205C SER* 1.3 67.3 + - - +
207C ALA* 6.1 0.2 - - - -
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Residues in contact with SER 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C ASP 5.2 0.2 - - - -
200C LYS* 3.9 23.9 - - - +
202C ASP* 2.5 37.6 + - - -
203C SER 2.9 2.2 + - - -
204C ASN* 1.3 74.0 + - - +
206C SER* 1.3 62.4 + - - +
207C ALA* 3.5 4.6 - - - +
208C GLY 4.8 2.2 + - - -
209C TRP* 3.8 11.8 + - - -
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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
----------------------------------------------------------
200C LYS 3.2 17.9 - - - -
201C GLY 4.0 2.0 - - - -
202C ASP 2.7 21.8 + - - -
203C SER* 3.7 4.3 + - - -
205C SER* 1.3 75.0 - - - +
207C ALA* 1.3 69.0 + - - +
208C GLY 3.1 3.3 + - - -
209C TRP* 3.2 23.7 + - - +
210C LYS* 3.0 50.0 + - - +
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Residues in contact with ALA 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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203C SER 3.7 10.8 + - - +
204C ASN* 6.1 0.2 - - - -
205C SER 3.5 3.9 - - - +
206C SER* 1.3 80.3 + - - +
208C GLY* 1.3 62.1 + - - +
210C LYS* 3.9 5.4 - - - +
211C ASN* 3.1 22.6 + - - +
214C ARG* 4.9 2.3 + - - -
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Residues in contact with GLY 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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18B T 5.5 1.4 - - - +
19B A 4.2 20.3 + - - -
205C SER 4.8 2.6 + - - -
206C SER 3.2 1.0 - - - -
207C ALA* 1.3 76.6 - - - +
209C TRP* 1.3 64.7 + - - +
211C ASN* 3.1 9.7 + - - +
212C SER* 3.0 22.8 + - - -
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Residues in contact with TRP 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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18B T 5.6 0.4 - - - -
165C TYR* 3.5 25.4 - - + +
187C TYR* 3.8 23.3 - + + -
190C MET* 3.9 26.5 - - + -
191C VAL* 3.7 27.4 - - + -
197C PHE* 3.6 26.2 - + + -
200C LYS* 2.8 37.2 + - + +
201C GLY* 4.7 0.4 - - - -
205C SER 3.8 7.0 - - - -
206C SER* 3.2 26.8 - - - +
208C GLY* 1.3 74.6 - - - +
210C LYS* 1.3 81.6 + - + +
212C SER* 3.2 6.3 + - - -
213C ILE* 2.9 38.1 + - + +
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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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187C TYR* 3.4 57.1 + - + +
201C GLY 4.3 9.2 + - - -
202C ASP 5.6 0.4 - - - -
203C SER* 5.9 1.0 - - - +
206C SER* 3.0 45.6 + - - +
207C ALA* 3.9 4.0 - - - +
209C TRP* 1.3 89.5 - - + +
211C ASN* 1.3 65.6 + - - +
213C ILE* 3.0 4.4 + - - +
214C ARG* 2.9 38.6 + - - +
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Residues in contact with ASN 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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4A T 4.9 1.6 - - - +
19B A 4.3 14.1 - - + +
20B A 2.9 51.7 + - - -
21B A 5.3 1.6 - - - +
207C ALA 3.1 14.5 + - - +
208C GLY* 3.1 12.7 + - - +
210C LYS* 1.3 77.2 - - - +
212C SER* 1.3 63.0 + - - +
214C ARG* 3.3 27.2 + - - +
215C HIS* 2.9 21.5 + - - +
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Residues in contact with SER 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B T 3.5 40.0 + - - +
19B A 5.8 0.8 + - - -
165C TYR* 3.8 30.2 + - - -
208C GLY 3.0 12.4 + - - -
209C TRP* 3.4 11.0 - - - -
211C ASN* 1.3 78.6 - - - +
213C ILE* 1.3 57.6 + - - +
215C HIS* 3.4 2.3 - - - +
216C ASN* 2.8 36.9 + - - -
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Residues in contact with ILE 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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165C TYR* 3.8 24.0 - - + +
169C ILE* 3.8 25.3 - - + +
183C LEU* 4.1 9.4 - - + -
186C ILE* 4.1 17.3 - - + -
187C TYR* 4.1 6.3 - - + -
190C MET* 4.0 21.8 - - + -
209C TRP* 2.9 36.6 + - + +
210C LYS 3.0 7.4 + - - +
212C SER* 1.3 73.0 - - - +
214C ARG* 1.3 67.6 + - - +
216C ASN* 3.2 2.6 + - - +
217C LEU* 2.9 39.6 + - + +
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Residues in contact with ARG 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A T 3.5 31.5 + - - +
3A G 3.5 28.9 + - + +
4A T 3.5 22.0 + - + +
21B A 6.2 0.2 - - - +
183C LEU* 3.8 21.5 - - + -
187C TYR* 3.0 32.3 + - - +
207C ALA 4.9 2.2 + - - -
210C LYS* 2.9 26.5 + - - +
211C ASN* 3.4 36.5 + - - +
213C ILE* 1.3 75.3 - - - +
215C HIS* 1.3 62.2 + - - +
217C LEU* 3.2 9.6 + - - +
218C SER* 3.1 20.4 + - - -
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Residues in contact with HIS 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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4A T 3.9 4.4 - - - +
5A T 2.9 33.2 + + + +
6A T 2.9 27.2 + + + -
7A A 3.9 5.1 + - - -
17B G 5.0 4.0 + + - -
18B T 3.1 38.4 + - + +
19B A 3.4 4.7 + - - +
211C ASN* 2.9 21.9 + - - +
212C SER* 3.4 5.6 - - - +
214C ARG* 1.3 77.4 - - - +
216C ASN* 1.3 66.9 + - - +
218C SER 3.4 0.9 + - - -
219C LEU* 2.9 59.5 + - + +
220C HIS* 5.7 0.2 - - - -
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Residues in contact with ASN 216 (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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16B G 5.8 1.8 - - - +
17B G 4.5 6.7 + - - -
18B T 4.4 5.1 - - - +
165C TYR* 3.5 27.7 - - - +
166C ALA* 3.9 11.6 + - - +
169C ILE* 3.6 20.9 - - + -
212C SER 2.8 28.5 + - - +
213C ILE 3.2 0.4 + - - +
215C HIS* 1.3 85.6 - - - +
217C LEU* 1.3 67.9 + - - +
219C LEU* 4.6 0.2 - - - -
220C HIS* 3.0 54.2 + - + -
223C PHE* 3.6 6.4 - - + -
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Residues in contact with LEU 217 (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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2C CA 2.8 19.4 - - - -
169C ILE* 3.7 29.6 - - + -
183C LEU* 3.6 31.2 - - + -
186C ILE* 4.2 6.3 - - + -
213C ILE* 2.9 25.1 + - + +
214C ARG* 3.2 8.3 + - - +
216C ASN* 1.3 78.2 - - - +
218C SER* 1.3 57.9 + - - +
220C HIS 3.7 4.2 - - - +
223C PHE* 3.8 15.2 - - + +
237C TRP* 3.7 62.8 - - + +
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Residues in contact with SER 218 (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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3A G 3.2 18.0 - - - +
4A T 2.5 42.5 + - - -
5A T 3.7 26.3 + - - -
2C CA 3.2 11.7 - - - -
214C ARG 3.1 12.8 + - - -
217C LEU* 1.3 75.7 - - - +
219C LEU* 1.3 63.7 + - - +
237C TRP* 4.4 1.3 - - - -
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Residues in contact with LEU 219 (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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5A T 4.1 6.0 - - + +
6A T 4.4 20.4 - - + -
215C HIS* 2.9 46.2 + - + +
216C ASN 4.2 1.3 - - - +
218C SER* 1.3 76.8 - - - +
220C HIS* 1.3 85.2 + - + +
221C SER* 3.7 2.3 + - - -
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Residues in contact with HIS 220 (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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16B G 4.8 13.7 - - + +
2C CA 2.8 18.1 - - - -
166C ALA* 4.3 15.3 - - + +
215C HIS* 5.7 0.2 - - - -
216C ASN* 3.0 54.4 + - + +
217C LEU 3.7 3.3 - - - +
219C LEU* 1.3 99.4 - - + +
221C SER* 1.3 64.6 + - - +
222C LYS* 3.1 13.3 + - + +
223C PHE* 3.2 17.3 + + + +
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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
------------------------------------------------------------
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