Contacts of the strand formed by residues 302 - 307 (chain C) in PDB entry 5DFV
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 302 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C ILE* 3.7 30.5 - - + -
293C TYR* 3.1 23.3 - - + -
297C PHE* 3.0 17.0 + - + +
299C GLY 4.7 2.8 + - - -
301C LYS* 1.3 78.3 + - - +
303C THR* 1.3 62.8 + - - +
304C LEU* 4.3 7.4 - - + -
315C MET* 4.1 15.7 - - + -
316C GLN 3.3 5.4 - - - -
317C LEU* 4.0 4.6 - - + +
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Residues in contact with THR 303 (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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293C TYR* 3.4 4.7 - - - +
301C LYS 5.0 1.6 + - - -
302C ALA* 1.3 73.0 + - - +
304C LEU* 1.3 77.4 + - - +
305C THR* 4.1 14.5 + - + -
314C TYR 4.0 0.5 - - - +
315C MET* 3.5 1.9 - - - -
316C GLN* 2.7 57.6 + - + +
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Residues in contact with LEU 304 (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 TRP* 4.1 20.9 - - + +
213C ILE* 4.9 2.5 - - + -
214C GLY* 4.0 7.6 - - - +
251C ARG* 3.9 33.4 - - - +
252C ILE* 3.8 22.7 - - + +
289C GLY 4.9 1.7 - - - +
291C ALA* 4.3 4.5 - - + -
292C ILE 4.8 0.2 - - - +
293C TYR* 2.6 43.7 + - + +
302C ALA* 4.3 7.2 - - + -
303C THR* 1.3 83.5 - - - +
305C THR* 1.3 70.9 + - - +
314C TYR 3.7 4.5 - - - +
315C MET* 4.2 21.1 - - + -
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Residues in contact with THR 305 (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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119C LYS* 5.1 6.2 + - - +
252C ILE* 3.8 10.4 - - - +
289C GLY* 5.8 0.4 - - - -
303C THR* 4.1 15.4 + - + -
304C LEU* 1.3 84.7 - - - +
306C ALA* 1.3 62.6 + - - +
313C ALA* 3.7 2.9 - - - +
314C TYR* 3.0 52.8 + - - +
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Residues in contact with ALA 306 (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 PHE* 4.2 6.1 - - + -
252C ILE* 4.2 13.1 - - + +
253C TYR 4.8 0.7 - - - +
254C SER* 3.7 44.8 - - - +
289C GLY* 4.8 5.7 - - - -
305C THR* 1.3 77.8 - - - +
307C ASP* 1.3 60.8 + - - +
308C LYS* 4.0 4.3 + - - +
312C THR 3.8 4.9 - - - -
313C ALA* 4.6 1.3 - - + +
314C TYR* 5.3 0.9 - - - -
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Residues in contact with ASP 307 (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 PHE* 3.6 3.7 - - - -
306C ALA* 1.3 72.0 - - - +
308C LYS* 1.3 58.0 + - - +
309C SER* 2.6 26.8 + - - -
310C SER* 2.9 26.7 + - - +
311C SER* 2.9 23.4 + - - -
312C THR 2.9 22.3 + - - +
314C TYR* 4.2 14.3 + - + -
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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