Contacts of the helix formed by residues 292 - 296 (chain U) in PDB entry 3FKS
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 GLY 292 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290U PRO 3.6 3.0 + - - -
291U PRO* 1.3 76.8 - - - +
293U ARG* 1.3 62.8 + - - -
294U GLU 3.9 1.0 + - - -
295U ALA* 4.0 4.7 + - - -
296U TYR 2.7 17.0 + - - -
297U PRO 4.4 5.1 - - - -
298U GLY* 5.1 1.1 - - - -
339U TYR* 6.0 0.2 - - - -
270V ALA* 4.7 14.8 - - - -
276V PRO* 4.5 13.6 - - - +
280V GLY* 5.7 4.3 - - - -
269Y ASP* 4.4 13.0 - - - +
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Residues in contact with ARG 293 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292U GLY* 1.3 69.4 - - - -
294U GLU* 1.3 78.3 + - + +
295U ALA 2.9 2.0 - - - -
296U TYR* 2.8 31.3 + - - +
337U SER 5.0 3.4 + - - -
338U ALA 4.7 3.4 + - - -
339U TYR* 3.5 64.4 + - + +
342U THR* 5.9 2.2 - - - -
279V VAL* 3.0 41.1 + - - +
280V GLY* 4.6 18.0 + - - +
281V TYR* 4.0 13.1 - - - -
319V ASP* 5.5 1.4 + - - -
266Y GLU* 5.1 9.0 - - - +
269Y ASP* 4.3 9.9 - - - +
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Residues in contact with GLU 294 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281U ARG* 3.8 9.5 + - - -
292U GLY 3.9 0.4 + - - -
293U ARG* 1.3 85.1 - - + +
295U ALA* 1.3 64.9 + - - +
296U TYR* 3.0 32.3 + - + -
338U ALA* 4.6 6.9 - - - +
339U TYR* 3.5 32.0 + - - +
340U ILE* 5.0 1.0 + - - +
278X ALA* 3.9 17.7 - - + +
266Y GLU* 6.1 0.4 - - - +
269Y ASP* 3.6 19.4 + - - +
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Residues in contact with ALA 295 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281U ARG* 3.6 12.6 - - - +
284U SER* 6.0 0.2 - - - -
285U LEU* 4.0 13.3 - - + +
291U PRO* 3.7 26.7 - - + +
292U GLY 4.0 3.4 + - - -
293U ARG 2.9 2.2 + - - -
294U GLU* 1.3 78.7 - - - +
296U TYR* 1.3 64.9 + - - +
297U PRO* 3.5 2.3 - - - +
276X PRO 4.4 3.8 - - - +
277X SER* 3.5 40.8 - - - +
269Y ASP* 4.7 6.3 - - + +
272Y THR* 6.1 1.1 - - + -
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Residues in contact with TYR 296 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274U SER* 4.6 1.6 + - - -
277U ALA* 3.6 29.1 - - + +
278U VAL* 3.9 15.2 - - - +
281U ARG* 3.7 33.7 + - + -
292U GLY* 2.7 32.7 + - - -
293U ARG 2.8 15.5 + - - +
294U GLU* 3.0 27.7 + - + -
295U ALA* 1.3 76.2 - - - +
297U PRO* 1.3 64.4 - - + +
300U VAL* 3.9 12.8 - - + -
339U TYR* 3.4 26.0 - + + -
340U ILE* 3.5 36.0 - - + +
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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
------------------------------------------------------------
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