Contacts of the strand formed by residues 204 - 209 (chain C) in PDB entry 2D11
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 204 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C LYS 4.8 5.5 + - - +
85C PHE* 5.5 8.3 - - - -
202C GLY 5.2 1.3 - - - +
203C VAL* 1.3 72.5 - - - +
205C TYR* 1.3 61.4 + - - +
206C PHE* 3.6 26.9 - - + -
218C LEU 3.2 6.8 - - - +
219C GLY* 3.3 1.0 - - - -
220C VAL* 3.0 38.3 + - + +
283C LEU* 3.5 34.7 - - + +
287C ASN* 4.8 2.1 + - - -
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Residues in contact with TYR 205 (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 GLU 4.3 1.6 + - - -
200C MET* 3.4 45.2 - - + +
203C VAL* 3.5 33.9 + - + +
204C ASN* 1.3 71.9 - - - +
206C PHE* 1.3 72.5 + - - +
217C TRP* 3.9 35.6 - - + -
218C LEU 3.4 2.9 - - - -
228C TYR* 3.7 27.5 + + - -
233C LYS* 2.7 54.1 + - + +
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Residues in contact with PHE 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C ASN* 3.6 31.9 - - + -
205C TYR* 1.3 79.6 - - - +
207C GLU* 1.3 63.2 + - - +
208C ILE* 3.3 3.0 + - + -
217C TRP* 3.4 8.5 - - - -
218C LEU* 2.7 58.7 + - + +
220C VAL* 4.2 8.5 - - + -
276C ILE* 3.7 26.2 - - + -
279C ARG* 4.1 13.9 - - + -
280C ILE* 3.6 37.0 - - + -
283C LEU* 3.6 27.4 - - + -
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Residues in contact with GLU 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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206C PHE* 1.3 70.1 - - - +
208C ILE* 1.3 64.8 + - - +
215C GLU* 5.4 8.9 - - + +
216C LEU 3.6 5.4 - - - +
217C TRP* 3.4 38.1 - - + -
230C HIS* 4.4 15.4 + - + -
271C ALA* 4.2 2.3 - - - +
272C PRO* 3.5 26.9 - - + +
276C ILE* 6.0 1.4 - - - +
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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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206C PHE* 3.3 6.0 + - + +
207C GLU* 1.3 80.0 - - - +
209C LYS* 1.3 63.7 + - - +
214C THR 3.7 0.5 - - - +
215C GLU* 3.7 3.3 - - - -
216C LEU* 2.7 48.1 + - + +
217C TRP 4.6 0.4 - - - +
218C LEU* 3.6 34.8 - - + +
227C ILE* 4.1 22.0 - - + -
269C PHE* 3.6 48.0 - - + -
270C TYR 3.2 10.8 - - - +
271C ALA* 4.0 7.9 - - + -
272C PRO* 5.1 0.2 - - - -
280C ILE* 5.4 0.9 - - + -
334G PHE* 4.1 11.0 - - + -
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Residues in contact with LYS 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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208C ILE* 1.3 77.7 - - - +
210C ASN* 1.3 69.6 + - - +
213C GLY* 3.8 25.0 - - - +
214C THR 3.3 8.5 - - - +
215C GLU* 4.8 9.9 - - + -
216C LEU* 5.2 0.4 - - - -
269C PHE* 4.0 0.2 - - - +
270C TYR* 2.6 50.0 + - + +
272C PRO* 5.3 16.2 - - + -
334G PHE* 3.5 15.6 - - - -
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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