Contacts of the strand formed by residues 279 - 285 (chain C) in PDB entry 4OE5
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 LEU 279 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203C PHE* 3.7 32.7 - - + +
205C ALA* 4.3 1.6 - - + +
273C VAL* 3.5 29.4 - - + +
274C THR* 4.2 8.5 - - - -
276C SER 3.1 9.0 + - - +
277C GLU 3.4 1.1 - - - +
278C HIS* 1.3 78.7 - - - +
280C CYS* 1.3 59.5 + - - +
281C GLY 3.3 26.5 - - - +
282C ILE* 4.1 14.4 - - + -
298C VAL* 3.9 27.8 - - + -
305C PHE* 4.0 11.4 - - + +
307C THR* 4.0 9.4 + - - +
309C PRO* 3.6 25.6 - - + +
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Residues in contact with CYS 280 (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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200C LEU* 3.5 40.4 - - + +
201C GLU 3.5 18.6 - - - +
202C GLY* 3.5 21.5 - - - -
203C PHE 2.8 24.5 + - - -
204C VAL* 3.9 8.1 - - - -
228C ASN* 4.5 1.1 - - - -
278C HIS 3.2 0.8 + - - -
279C LEU* 1.3 74.2 - - - +
281C GLY* 1.3 57.7 + - - +
307C THR* 3.8 11.9 - - + -
308C PHE 4.2 0.9 - - - +
309C PRO* 3.3 12.6 - - - +
310C ARG* 3.0 18.0 + - - +
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Residues in contact with GLY 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C LEU* 5.3 1.1 - - - -
203C PHE 3.5 3.8 + - - -
204C VAL* 3.3 14.3 - - - -
205C ALA 2.8 30.3 + - - -
279C LEU* 3.3 12.5 - - - +
280C CYS* 1.3 81.3 - - - +
282C ILE* 1.3 59.4 + - - -
309C PRO* 4.5 2.0 - - - -
310C ARG* 3.1 15.3 - - - -
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Residues in contact with ILE 282 (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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204C VAL* 4.8 0.7 - - - -
205C ALA* 3.4 8.5 - - + +
207C ILE* 3.9 22.2 - - + -
273C VAL* 5.0 3.1 - - + -
274C THR* 4.1 17.3 - - + -
279C LEU* 4.1 13.2 - - + -
281C GLY* 1.3 79.7 - - - +
283C ASN* 1.3 62.3 + - - +
284C PHE* 4.0 17.7 - - + -
291C PHE* 5.3 0.7 - - + -
294C LEU* 4.3 18.4 - - + -
298C VAL* 3.9 19.5 - - + -
309C PRO* 5.6 0.9 - - + +
310C ARG 2.9 7.7 + - - +
311C LEU* 3.5 28.9 - - + -
312C ALA* 2.9 29.7 + - - +
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Residues in contact with ASN 283 (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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204C VAL* 4.4 10.7 - - + +
205C ALA 2.9 9.4 + - - +
206C ALA* 3.5 1.8 - - - -
207C ILE* 2.9 25.8 + - - +
218C ASN* 4.0 5.1 + - - +
219C LEU* 2.9 53.5 + - - +
222C ALA* 5.2 2.0 - - - +
223C PRO* 3.8 12.8 - - + +
281C GLY 4.2 0.2 - - - -
282C ILE* 1.3 72.5 - - - +
284C PHE* 1.3 60.8 + - - +
312C ALA* 3.5 20.9 - - - +
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Residues in contact with PHE 284 (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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207C ILE* 3.5 29.4 - - + -
209C PRO* 5.1 7.0 - - + -
219C LEU* 4.3 3.3 - - - +
282C ILE* 4.0 14.4 - - + -
283C ASN* 1.3 75.4 + - - +
285C THR* 1.3 71.4 + - - +
286C GLY* 3.3 37.0 - - - -
287C SER 3.6 10.1 - - - -
290C THR* 3.6 36.6 - - + -
291C PHE* 3.7 28.5 - + + -
294C LEU* 3.7 12.8 - - + -
312C ALA 2.8 16.0 + - - +
313C GLY* 3.4 4.5 - - - -
314C GLU* 2.9 23.7 + - - +
315C CYS* 4.4 2.7 - - - -
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Residues in contact with THR 285 (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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207C ILE 3.2 11.5 + - - +
209C PRO* 3.0 23.0 - - - +
212C PHE* 3.8 33.0 - - + -
219C LEU* 3.6 23.6 - - - +
284C PHE* 1.3 84.7 + - - +
286C GLY* 1.3 62.9 + - - +
314C GLU* 3.2 42.1 + - + +
348C CYS* 4.6 7.9 - - - -
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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