Contacts of the strand formed by residues 219 - 226 (chain C) in PDB entry 3O9Z
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 ALA 219 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C ALA* 4.5 5.0 - - - +
150C LYS* 3.1 20.4 - - + +
152C VAL* 4.0 10.3 - - + -
194C PHE* 3.5 32.4 - - + +
215C GLU* 3.7 0.7 - - - -
216C LEU* 2.8 34.0 + - - +
217C GLU 4.0 0.2 + - - -
218C GLY* 1.3 80.5 - - - +
220C ARG* 1.3 61.8 + - - +
221C VAL* 4.2 4.8 + - + +
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Residues in contact with ARG 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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149C ALA* 5.3 1.2 - - + +
150C LYS 3.0 10.8 + - - +
151C ASP* 2.9 43.2 + - - +
152C VAL* 2.8 26.9 + - - +
213C TYR* 2.9 35.6 + - + +
214C LEU 3.5 5.2 - - - +
215C GLU* 4.2 7.6 - - + +
219C ALA* 1.3 70.7 - - - +
221C VAL* 1.3 65.9 + - - +
222C ARG* 4.1 13.1 - - - +
303C GLU* 2.9 36.7 + - - +
304C ASN* 2.8 27.5 + - - -
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Residues in contact with VAL 221 (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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152C VAL* 3.4 24.9 - - + -
154C LEU* 4.1 6.3 - - + -
190C LEU* 3.7 36.3 - - + -
194C PHE* 5.0 2.2 - - + -
213C TYR* 3.3 10.8 - - - -
214C LEU* 2.8 53.7 + - + +
216C LEU* 4.7 6.7 - - + -
219C ALA* 4.3 14.4 - - + +
220C ARG* 1.3 83.8 - - - +
222C ARG* 1.3 72.6 + - - +
223C TRP* 3.9 4.9 + - + -
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Residues in contact with ARG 222 (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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151C ASP* 3.4 21.0 + - - -
152C VAL 3.0 8.7 + - - +
153C VAL* 3.3 32.4 - - + +
154C LEU 2.8 25.8 + - - +
212C GLY 3.8 4.5 - - - -
213C TYR* 3.8 10.5 - - + -
220C ARG* 4.1 13.1 - - - +
221C VAL* 1.3 72.5 - - - +
223C TRP* 1.3 59.3 + - - +
303C GLU 3.5 19.5 + - - -
304C ASN 3.5 18.8 - - - +
305C ARG 3.4 22.7 + - - -
306C HIS* 3.6 20.5 - - + +
307C PRO* 4.2 12.9 - - - +
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Residues in contact with TRP 223 (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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154C LEU* 3.2 15.0 - - + +
179C ALA* 5.0 0.7 - - + -
186C PHE* 3.6 36.1 - + + -
187C PHE* 3.9 20.8 - + - -
201C GLU 4.2 7.0 - - - -
202C VAL* 4.7 4.3 - - + -
210C ASN* 3.4 39.3 - - + -
211C ALA* 3.3 17.8 - - - +
212C GLY* 3.0 57.8 + - - +
213C TYR 3.3 5.9 + - - +
214C LEU* 3.7 34.6 - - + +
221C VAL* 4.0 8.3 - - + -
222C ARG* 1.3 75.2 - - - +
224C PHE* 1.3 63.3 + - - +
225C LEU* 4.3 3.4 - - + -
292C LEU* 4.1 19.7 - - + -
306C HIS* 3.5 7.6 - - - +
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Residues in contact with PHE 224 (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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154C LEU* 3.1 5.4 + - - +
155C THR* 3.6 8.0 - - + -
156C TYR* 2.9 27.9 + - - +
157C VAL* 4.2 4.0 - - + -
186C PHE* 5.1 0.7 - - - -
209C VAL* 3.6 26.9 - - + -
210C ASN 3.7 3.6 - - - -
211C ALA* 4.0 14.1 - - + -
223C TRP* 1.3 77.8 - - - +
225C LEU* 1.3 63.2 + - - +
226C SER* 3.7 20.0 - - - -
231C PHE* 3.6 43.5 - + + -
306C HIS* 3.5 24.9 - + + +
308C PHE* 3.7 35.2 - + + -
309C LEU* 4.1 14.6 - - + -
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Residues in contact with LEU 225 (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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156C TYR* 3.2 18.6 - - + +
178C LEU* 3.6 37.2 - - + +
179C ALA* 3.7 17.9 - - + +
182C ILE* 3.6 30.1 - - + -
183C GLY* 3.9 10.1 - - - -
186C PHE* 3.8 20.0 - - + -
209C VAL* 3.3 5.4 - - - +
210C ASN* 2.8 46.2 + - + +
223C TRP* 4.4 1.3 - - + -
224C PHE* 1.3 76.2 - - - +
226C SER* 1.3 69.1 + - - +
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Residues in contact with SER 226 (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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156C TYR 2.9 8.4 + - - +
157C VAL* 3.2 7.2 - - - +
158C THR* 2.9 26.7 + - - +
178C LEU* 5.0 0.7 - - - -
208C THR 2.7 19.5 + - - -
209C VAL* 3.7 3.8 - - - +
224C PHE* 3.7 22.8 - - - -
225C LEU* 1.3 80.1 - - - +
227C ILE* 1.3 61.6 + - - +
228C ASP* 2.9 26.3 + - - +
231C PHE* 3.5 11.1 - - - -
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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