Contacts of the strand formed by residues 209 - 216 (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 VAL 209 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C LEU* 4.1 0.9 - - - -
204C ALA* 4.6 13.2 - - + -
205C ARG* 3.5 1.6 + - - -
206C THR* 2.8 35.8 + - + +
208C THR* 1.3 92.5 - - - +
210C ASN* 1.3 82.0 + - - +
211C ALA* 4.5 1.1 - - + +
224C PHE* 3.6 27.6 - - + -
225C LEU 3.3 5.2 - - - +
226C SER* 3.7 11.2 - - - +
231C PHE* 3.8 23.1 - - + -
309C LEU* 5.1 2.5 - - + -
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Residues in contact with ASN 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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178C LEU* 4.0 13.6 - - - +
179C ALA* 3.3 33.5 - - - +
202C VAL* 5.5 2.9 - - + +
204C ALA 3.2 9.2 - - - +
205C ARG* 3.7 26.0 - - - +
206C THR 3.7 6.6 - - - +
209C VAL* 1.3 93.2 - - - +
211C ALA* 1.3 62.6 + - - +
223C TRP* 3.4 19.6 - - + -
225C LEU* 2.8 41.5 + - + +
292C LEU* 6.0 0.8 - - - +
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Residues in contact with ALA 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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202C VAL* 3.5 5.9 - - - +
203C HIS* 2.8 23.6 + - - -
204C ALA* 3.1 13.0 + - + -
209C VAL* 4.7 0.2 - - + -
210C ASN* 1.3 77.1 - - - +
212C GLY* 1.3 59.4 + - - +
223C TRP* 3.3 22.2 - - - +
224C PHE* 4.0 17.9 - - + -
306C HIS* 5.1 1.1 - - + -
309C LEU* 3.9 29.8 - - + -
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Residues in contact with GLY 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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201C GLU 3.3 14.4 - - - -
203C HIS* 3.6 19.9 + - - -
211C ALA* 1.3 75.8 - - - +
213C TYR* 1.3 61.8 + - - +
222C ARG* 3.8 3.3 - - - +
223C TRP* 3.0 42.6 + - - +
304C ASN 4.4 1.0 - - - +
306C HIS* 4.9 2.4 - - - +
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Residues in contact with TYR 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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199C HIS* 4.2 8.3 - + - -
200C VAL* 3.6 1.7 - - - -
201C GLU* 2.8 51.4 + - - +
203C HIS* 3.6 19.9 - - + +
212C GLY* 1.3 74.6 - - - +
214C LEU* 1.3 70.5 + - - +
215C GLU* 2.6 46.3 + - + +
220C ARG* 2.9 45.0 + - + +
221C VAL 3.3 17.7 - - - -
222C ARG* 3.8 6.3 - - + -
223C TRP* 3.3 1.2 - - - +
304C ASN* 3.2 42.0 + - + +
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Residues in contact with LEU 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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187C PHE* 4.0 15.7 - - + -
190C LEU* 3.9 29.4 - - + -
197C ALA* 4.8 0.7 - - + -
199C HIS 3.3 3.1 - - - -
200C VAL* 3.9 32.3 - - + -
213C TYR* 1.3 86.0 - - - +
215C GLU* 1.3 66.0 + - - +
216C LEU* 3.4 25.1 - - + -
220C ARG* 3.5 2.3 - - - -
221C VAL* 2.8 40.0 + - + +
223C TRP* 3.7 22.7 - - + +
288C VAL* 4.3 13.2 - - + -
292C LEU* 5.5 0.2 - - + -
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Residues in contact with GLU 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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197C ALA* 3.6 0.9 - - - -
198C LEU* 2.7 35.4 + - + +
199C HIS* 2.9 37.9 + - + +
213C TYR* 2.6 39.7 + - + +
214C LEU* 1.3 74.2 - - - +
216C LEU* 1.3 58.0 + - - +
219C ALA 3.8 4.0 - - - +
220C ARG* 4.2 8.0 - - + +
304C ASN* 5.2 0.7 + - - -
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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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190C LEU* 3.4 38.4 - - + +
191C ALA* 4.1 1.6 - - + +
194C PHE* 3.7 18.4 - - + +
195C GLY 3.3 22.9 - - - +
196C ARG 3.2 9.0 - - - +
197C ALA* 3.8 17.0 - - + +
198C LEU* 4.7 4.3 - - - +
214C LEU* 3.4 35.9 - - + -
215C GLU* 1.3 77.7 - - - +
217C GLU* 1.3 69.1 + - - +
218C GLY 3.0 2.2 + - - +
219C ALA 2.8 22.2 + - - +
221C VAL* 4.7 5.2 - - + -
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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
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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