Contacts of the helix formed by residues 203 - 216 (chain C) in PDB entry 3OLJ
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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133C PHE* 3.7 44.6 - - + -
136C ALA* 5.0 4.5 - - + -
196C ALA* 4.0 19.3 - - + +
197C ILE* 4.2 13.7 - - + +
200C MET* 3.1 32.0 + - + +
201C PRO 3.1 0.6 - - - -
202C CYS* 1.3 78.1 - - - +
204C LYS* 1.3 67.0 + - - +
205C LYS 3.5 0.7 - - - -
206C LYS* 3.4 8.1 + - - +
207C ALA* 3.0 34.0 + - + -
303C PHE* 4.9 1.1 - - + -
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Residues in contact with LYS 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ILE 5.4 8.3 - - - +
200C MET 3.8 3.6 + - - +
201C PRO* 3.1 22.5 + - + +
203C VAL* 1.3 80.6 - - - +
205C LYS* 1.3 57.1 + - - +
207C ALA* 3.8 3.3 - - - +
208C ASP* 2.8 62.9 + - - +
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Residues in contact with LYS 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C PRO 4.6 1.6 + - - -
202C CYS 4.9 3.5 + - - +
203C VAL 3.5 0.4 - - - -
204C LYS* 1.3 77.5 - - - +
206C LYS* 1.3 62.4 + - - +
208C ASP* 4.0 5.2 - - - +
209C TRP* 3.1 24.9 + - - +
212C ARG* 4.8 3.1 + - - +
299C ILE* 4.1 34.7 - - + +
302C GLU* 4.1 34.3 + - + +
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Residues in contact with LYS 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C PHE* 3.1 29.0 - - + -
202C CYS 5.2 1.0 + - - -
203C VAL* 3.4 7.7 + - - +
204C LYS 3.3 0.2 - - - -
205C LYS* 1.3 76.4 - - + +
207C ALA* 1.3 66.1 + - - +
209C TRP* 3.3 2.6 + - - +
210C ALA* 3.1 22.5 + - - +
235C PHE* 3.0 58.3 + - + -
299C ILE* 3.5 21.3 - - + -
300C GLU* 2.7 26.4 + - - +
303C PHE* 3.2 46.7 - - + -
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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
----------------------------------------------------------
133C PHE* 5.8 0.6 - - - -
137C SER* 6.2 0.2 - - - -
140C ILE* 3.8 25.3 - - + +
197C ILE* 4.2 15.3 - - + -
203C VAL* 3.0 32.8 + - + +
204C LYS* 3.8 4.5 - - - +
206C LYS* 1.3 76.6 - - - +
208C ASP* 1.3 57.6 + - - +
210C ALA 3.4 0.2 + - - -
211C LEU* 3.0 40.7 + - + +
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Residues in contact with ASP 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LYS* 2.8 60.7 + - - +
205C LYS* 4.0 5.1 - - - +
207C ALA* 1.3 74.7 - - - +
209C TRP* 1.3 58.2 + - - +
211C LEU* 3.4 11.4 + - - +
212C ARG* 2.9 54.4 + - - +
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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
----------------------------------------------------------
205C LYS 3.1 18.5 + - - +
206C LYS 3.5 4.3 - - - +
207C ALA 3.3 0.2 - - - -
208C ASP* 1.3 78.6 - - - +
210C ALA* 1.3 67.1 + - - +
212C ARG* 3.5 29.2 + - - +
213C TRP* 2.9 56.2 + + - +
227C ALA* 3.6 24.5 - - + -
230C ALA* 4.2 10.3 - - + -
231C VAL* 4.0 6.7 - - + -
235C PHE* 3.5 28.7 - + + -
292C ILE* 3.7 39.3 - - + -
295C ASN* 2.9 28.1 - - - +
296C ALA* 4.2 6.5 - - + -
299C ILE* 3.5 21.8 - - + -
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Residues in contact with ALA 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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140C ILE* 3.7 24.5 - - + -
206C LYS 3.1 12.9 + - - +
207C ALA 3.9 1.8 - - - +
209C TRP* 1.3 85.4 - - - +
211C LEU* 1.3 64.1 + - - +
213C TRP* 3.0 21.5 + - - +
214C ILE 3.5 4.2 + - - -
228C PHE* 3.6 12.2 - - + -
231C VAL* 3.8 28.7 - - + -
235C PHE* 5.0 0.4 - - + -
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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
----------------------------------------------------------
140C ILE* 3.9 29.2 - - + -
143C GLU* 3.8 22.4 - - - +
197C ILE* 5.1 13.5 - - + -
207C ALA* 3.0 29.8 + - + +
208C ASP* 3.8 11.9 - - - +
210C ALA* 1.3 73.4 - - - +
212C ARG* 1.3 65.4 - - - +
214C ILE* 3.1 20.5 + - + +
215C GLY* 3.1 10.7 + - - -
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Residues in contact with ARG 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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205C LYS* 4.8 3.6 + - - +
208C ASP* 2.9 39.5 + - - +
209C TRP* 3.6 36.8 - - - +
210C ALA 3.3 0.2 - - - -
211C LEU* 1.3 75.3 - - - +
213C TRP* 1.3 59.7 + - + +
215C GLY* 3.3 3.1 + - - +
216C ASP* 2.9 30.8 + - - +
299C ILE* 5.7 0.8 - - - +
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Residues in contact with TRP 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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144C ASN* 4.8 1.4 - - - +
148C ARG* 3.6 12.3 + - - -
209C TRP* 2.9 61.2 + + - +
210C ALA* 3.0 10.7 + - - +
212C ARG* 1.3 78.8 - - + +
214C ILE* 1.3 62.1 + - - +
216C ASP* 3.9 12.8 + - - +
219C ALA* 3.9 22.0 - - + -
223C GLU* 4.3 12.3 - - + -
224C ARG* 3.9 30.4 + - + +
227C ALA* 3.4 25.6 - - + -
228C PHE* 3.9 15.3 - + + -
231C VAL* 5.9 0.2 - - + -
288C ARG* 3.6 26.5 - - - -
292C ILE* 3.8 29.8 - - + -
295C ASN* 6.2 0.2 - - - -
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Residues in contact with ILE 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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140C ILE* 3.5 39.3 - - + +
143C GLU* 3.9 21.8 - - + +
144C ASN* 3.7 23.6 - - + +
147C GLU* 4.1 18.6 - - - +
148C ARG* 2.9 43.2 + - + +
210C ALA 3.8 4.7 - - - +
211C LEU* 3.1 12.0 + - + +
213C TRP* 1.3 77.7 - - - +
215C GLY* 1.3 57.0 + - - +
228C PHE* 3.6 17.7 - - + -
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Residues in contact with GLY 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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211C LEU 3.1 12.3 + - - -
212C ARG* 3.7 3.4 - - - -
214C ILE* 1.3 76.5 - - - +
216C ASP* 1.3 57.3 + - - +
217C LYS* 3.0 25.3 + - - +
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Residues in contact with ASP 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ARG* 2.9 24.8 + - - -
212C ARG 2.9 16.5 + - - +
213C TRP* 4.1 19.3 - - + +
214C ILE 3.3 1.8 - - - -
215C GLY* 1.3 71.9 - - - +
217C LYS* 1.3 61.0 + - - +
218C GLU* 2.8 35.3 + - - +
219C ALA* 2.8 31.2 + - + +
224C ARG* 4.2 2.8 - - - -
288C ARG* 5.7 1.2 + - - -
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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