Contacts of the helix formed by residues 292 - 296 (chain a) in PDB entry 4B2Q
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 a).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290a PRO 3.9 1.0 + - - -
291a PRO* 1.3 74.1 - - - +
293a ARG* 1.3 71.7 + - - -
294a GLU 3.1 0.9 + - - -
295a ALA* 2.7 16.6 + - - -
296a TYR 3.1 23.8 + - - +
297a PRO* 4.4 1.3 - - - +
298a GLY* 5.4 1.5 - - - +
270e ALA* 5.7 7.6 - - - -
276e PRO* 5.4 3.6 - - - -
267g LEU* 3.6 14.3 - - - +
270g ILE* 4.2 1.0 - - - +
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Residues in contact with ARG 293 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292a GLY* 1.3 68.0 - - - +
294a GLU* 1.3 84.2 + - + +
295a ALA 3.0 1.2 + - - -
296a TYR* 3.1 18.7 + - - +
337a SER* 3.1 26.9 + - - -
338a ALA* 3.9 3.0 + - - +
339a TYR* 3.4 57.0 - - + +
342a THR* 5.3 4.9 + - - +
263e GLN* 6.1 0.8 - - - +
279e VAL* 4.9 9.7 + - - +
280e GLY* 5.5 6.3 - - - -
259g ARG* 5.0 2.2 - - - +
263g ILE* 3.7 47.4 - - + +
266g GLU* 5.9 0.2 - - - -
267g LEU* 4.0 13.3 - - - +
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Residues in contact with GLU 294 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281a ARG* 3.3 9.6 + - - +
292a GLY 3.1 1.2 + - - -
293a ARG* 1.3 85.1 - - + +
295a ALA* 1.3 68.4 + - - +
296a TYR* 3.4 18.2 + - + -
338a ALA* 4.6 10.0 - - - +
339a TYR* 3.1 33.1 + - - +
340a ILE* 4.3 2.4 + - - +
278d ALA* 3.2 23.6 - - + +
266g GLU* 3.5 29.9 + - - +
267g LEU* 4.8 1.4 - - - +
270g ILE* 4.0 7.0 - - - +
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Residues in contact with ALA 295 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281a ARG* 2.8 28.2 - - - +
285a LEU* 3.8 15.3 - - + +
291a PRO* 4.5 1.8 - - - -
292a GLY 2.7 23.2 + - - +
294a GLU* 1.3 75.7 - - - +
296a TYR* 1.3 56.0 + - - +
297a PRO* 3.7 4.5 - - - +
276d PRO 4.6 0.2 - - - +
277d SER* 3.9 11.4 - - - -
278d ALA 3.4 23.6 - - - +
270g ILE* 3.4 18.5 - - + +
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Residues in contact with TYR 296 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274a SER 4.9 0.3 + - - -
277a ALA* 3.5 28.3 - - + +
278a VAL* 3.8 21.7 + - - +
280a TYR* 6.2 0.7 - + - -
281a ARG* 3.5 37.2 + - + -
292a GLY* 3.1 22.6 + - - -
293a ARG 3.1 13.6 + - - +
294a GLU* 3.7 26.5 - - + -
295a ALA* 1.3 76.6 - - - +
297a PRO* 1.3 69.9 - - + +
298a GLY* 4.7 0.2 - - - -
300a VAL* 4.1 13.1 - - + +
339a TYR* 4.0 22.8 + + + -
340a ILE* 3.5 37.3 - - + +
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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