Contacts of the helix formed by residues 200 - 220 (chain C) in PDB entry 1OY1
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 ASN 200 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C TYR* 3.5 10.7 + - - -
198C ALA* 3.5 2.8 - - - +
199C GLN* 1.3 83.9 - - - +
201C ILE* 1.3 64.1 + - - +
202C ALA* 2.8 16.1 + - - +
203C GLU* 2.7 54.7 + - - +
204C ALA* 3.2 16.6 + - - +
33D SER* 4.0 10.3 - - - +
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Residues in contact with ILE 201 (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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23C HIS* 3.6 33.4 - - + +
27C LEU* 3.7 17.5 - - + -
195C TYR* 3.1 15.2 + - - +
200C ASN* 1.3 75.4 - - - +
202C ALA* 1.3 60.2 + - - +
204C ALA* 3.3 1.2 + - - +
205C ALA* 2.9 27.7 + - - +
26D VAL* 3.8 33.7 - - + +
29D LEU* 3.6 16.6 - - + +
30D LEU* 3.7 15.5 - - + +
33D SER* 3.4 24.2 - - - -
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Residues in contact with ALA 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C ASN* 2.8 7.5 + - - +
201C ILE* 1.3 80.3 - - - +
203C GLU* 1.3 63.9 + - - +
205C ALA* 3.2 4.2 + - - +
206C SER* 3.0 21.3 + - - -
30D LEU* 4.2 10.5 - - - -
33D SER* 3.1 32.1 + - - +
34D ARG* 4.3 12.3 - - + +
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Residues in contact with GLU 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C VAL* 3.9 29.2 - - + +
179C ASP* 6.5 1.1 - - + -
197C LEU 4.0 2.4 - - - +
198C ALA* 3.6 6.6 - - + -
199C GLN* 2.9 41.3 + - - +
200C ASN* 2.7 36.8 + - - +
202C ALA* 1.3 72.5 - - - +
204C ALA* 1.3 63.8 + - - +
206C SER* 2.9 24.8 - - - -
207C GLY 3.4 3.3 + - - -
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Residues in contact with ALA 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 4.2 8.5 - - + -
178C VAL* 4.7 2.9 - - - -
193C PRO 5.9 0.4 - - - -
194C ALA* 5.0 7.2 - - - +
195C TYR* 3.7 32.3 - - + +
198C ALA* 3.9 16.0 - - + +
200C ASN 3.2 4.4 + - - +
201C ILE 3.6 7.4 - - - +
202C ALA 3.3 0.2 - - - -
203C GLU* 1.3 80.5 - - - +
205C ALA* 1.3 62.7 + - - +
207C GLY* 3.4 1.4 + - - -
208C ILE* 3.0 34.3 + - + +
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Residues in contact with ALA 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 3.8 19.5 - - + +
34C ARG* 6.0 0.4 - - - +
201C ILE 2.9 14.9 + - - +
202C ALA* 3.4 8.7 - - - +
204C ALA* 1.3 76.6 - - - +
206C SER* 1.3 65.9 + - - +
208C ILE* 3.2 3.5 + - - -
209C ASP* 2.8 38.8 + - - +
30D LEU* 3.7 23.3 - - + -
34D ARG* 5.6 4.7 - - - +
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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
----------------------------------------------------------
179C ASP* 3.0 31.0 + - - +
202C ALA 3.0 11.4 + - - -
203C GLU* 2.9 20.3 + - - -
205C ALA* 1.3 78.7 - - - +
207C GLY* 1.3 58.9 + - - -
209C ASP* 3.6 6.3 + - - +
210C LYS* 3.5 24.1 + - - +
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Residues in contact with GLY 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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178C VAL 3.6 20.2 + - - -
179C ASP 4.3 9.0 - - - -
180C ASP 4.7 0.7 - - - -
181C ILE* 3.8 2.8 - - - +
192C THR* 3.8 14.6 - - - -
203C GLU 3.4 2.8 + - - -
204C ALA 3.4 4.7 + - - -
205C ALA 3.3 0.2 - - - -
206C SER* 1.3 75.6 + - - +
208C ILE* 1.3 66.3 + - - +
209C ASP 3.1 1.6 - - - -
210C LYS* 3.0 6.6 + - - +
211C LEU* 2.9 22.2 + - - +
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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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24C GLU* 3.6 43.3 - - + +
27C LEU* 4.0 18.4 - - + +
28C THR* 3.6 33.0 - - - +
137C MSE 3.8 20.0 - - + -
192C THR* 4.5 4.2 - - + +
194C ALA* 4.8 7.9 - - + -
204C ALA* 3.0 20.6 + - + +
205C ALA* 3.9 4.9 - - - +
207C GLY* 1.3 75.0 - - - +
209C ASP* 1.3 64.4 + - - +
211C LEU* 3.2 7.5 + - - +
212C VAL* 2.9 27.4 + - + +
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Residues in contact with ASP 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 4.6 6.2 - - - +
31C ALA* 3.7 21.4 - - + +
34C ARG* 3.4 28.2 + - - -
205C ALA* 2.8 31.9 + - - +
206C SER* 3.8 6.2 - - - +
208C ILE* 1.3 80.6 - - - +
210C LYS* 1.3 63.8 + - + +
212C VAL* 3.3 1.7 + - - +
213C SER* 2.9 27.9 + - - +
34D ARG* 5.4 1.4 + - - -
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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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179C ASP* 2.7 35.1 + - - +
180C ASP* 3.8 23.6 + - - +
181C ILE* 3.6 18.6 - - + +
206C SER* 3.5 11.6 + - - +
207C GLY 3.0 8.3 + - - +
209C ASP* 1.3 78.4 - - + +
211C LEU* 1.3 64.4 + - - +
213C SER* 3.4 5.8 + - - -
214C ARG* 3.0 25.3 + - - +
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Residues in contact with LEU 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ILE* 3.8 35.2 - - + -
135C GLY* 4.2 5.2 - - - -
136C PHE 3.7 18.4 - - - +
137C MSE 4.4 11.7 - - + -
181C ILE* 3.6 6.6 - - - +
190C VAL* 3.9 16.4 - - + +
191C THR* 3.8 6.5 - - - -
192C THR* 3.5 37.0 - - - +
207C GLY 2.9 12.7 + - - +
208C ILE* 3.4 10.8 - - - +
210C LYS* 1.3 76.5 - - - +
212C VAL* 1.3 63.0 + - + +
214C ARG* 3.2 3.8 + - - +
215C VAL* 2.9 35.9 + - + +
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Residues in contact with VAL 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C THR* 4.2 23.6 - - + +
31C ALA* 3.8 32.5 - - + +
32C ILE* 3.9 21.5 - - + +
35C SER* 4.6 1.3 - - - +
93C ILE* 5.0 4.3 - - + -
208C ILE* 2.9 24.6 + - + +
209C ASP 3.9 1.1 - - - +
211C LEU* 1.3 84.6 - - + +
213C SER* 1.3 58.3 + - - +
215C VAL* 3.2 4.8 + - - +
216C LEU* 2.9 49.1 + - + +
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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
----------------------------------------------------------
35C SER* 4.5 9.1 + - - -
209C ASP* 2.9 18.5 + - - +
210C LYS* 3.8 7.0 - - - -
212C VAL* 1.3 77.7 - - - +
214C ARG* 1.3 59.0 + - - +
216C LEU* 3.4 7.7 + - - +
217C VAL* 2.9 36.3 + - - +
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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
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181C ILE* 4.5 14.4 - - + +
183C VAL* 3.9 21.0 - - + +
185C GLU* 3.3 27.3 + - - -
190C VAL* 3.8 24.5 - - + -
210C LYS 3.0 16.9 + - - +
211C LEU 3.7 4.0 - - - +
213C SER* 1.3 75.1 - - - +
215C VAL* 1.3 64.9 + - - +
217C VAL* 4.3 13.4 - - - +
218C LEU* 2.9 47.8 + - + +
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Residues in contact with VAL 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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7C ILE* 5.1 2.2 - - + -
91C ALA* 3.5 29.4 - - + -
92C LEU 4.9 0.2 - - - +
93C ILE* 3.6 33.4 - - + -
133C PRO* 3.7 17.6 - - + +
134C LEU 4.3 3.1 - - - +
135C GLY* 4.1 9.0 - - - -
190C VAL* 4.1 17.3 - - + -
211C LEU* 2.9 28.3 + - + +
212C VAL* 3.7 3.8 - - + +
214C ARG* 1.3 76.8 - - - +
216C LEU* 1.3 60.1 + - + +
218C LEU* 3.4 1.5 + - - -
219C ALA* 2.8 26.7 + - - +
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Residues in contact with LEU 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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5C LYS* 5.4 4.8 - - + +
7C ILE* 3.4 38.8 - - + -
31C ALA 4.8 0.4 - - - +
32C ILE* 4.9 0.9 - - - +
35C SER* 3.2 37.7 - - - +
37C ALA* 3.9 15.3 - - + -
212C VAL* 2.9 32.7 + - + +
213C SER* 3.6 6.1 - - - +
215C VAL* 1.3 76.0 - - + +
217C VAL* 1.3 66.6 + - + +
219C ALA* 3.0 21.6 + - + +
220C GLU* 3.6 8.7 + - - +
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Residues in contact with VAL 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C SER* 2.9 29.6 + - - +
214C ARG* 3.3 17.9 + - - +
216C LEU* 1.3 76.6 - - + +
218C LEU* 1.3 68.0 + - + +
220C GLU* 2.9 26.4 + - - +
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Residues in contact with LEU 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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131C GLY 5.1 0.5 - - - +
133C PRO* 3.4 22.6 - - + +
183C VAL* 4.4 8.1 - - + -
185C GLU* 4.8 12.6 - - - +
188C LYS* 3.9 56.8 + - + +
190C VAL* 4.0 24.5 - - + -
214C ARG* 2.9 32.2 + - + +
215C VAL 3.7 0.2 - - - +
217C VAL* 1.3 81.4 - - + +
219C ALA* 1.3 62.6 + - - +
220C GLU 3.1 9.1 + - - +
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Residues in contact with ALA 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LYS* 3.2 28.4 + - + +
7C ILE* 5.4 0.4 - - + -
90C ASP* 4.3 20.0 - - + +
91C ALA* 4.9 4.0 - - + -
133C PRO* 3.7 12.7 - - + +
215C VAL 2.8 14.0 + - - +
216C LEU* 3.0 21.8 - - + +
217C VAL 3.0 0.8 - - - -
218C LEU* 1.3 77.7 - - - +
220C GLU* 1.3 57.2 + - - +
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Residues in contact with GLU 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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5C LYS* 3.2 26.8 + - - +
188C LYS* 5.6 1.4 + - - -
216C LEU 4.3 6.5 - - - +
217C VAL* 2.9 19.0 + - - +
218C LEU* 3.6 7.3 - - - +
219C ALA* 1.3 82.2 - - - +
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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