Contacts of the helix formed by residues 273 - 281 (chain A) in PDB entry 3GUU
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 CYS 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ALA* 3.8 5.6 - - - -
100A ASP* 4.2 1.6 - - - -
101A CYS* 2.0 54.3 - - - -
114A PRO* 3.5 31.9 - - + +
115A ASN* 3.4 17.7 - - + +
271A GLY 4.0 3.6 - - - -
272A PHE* 1.3 73.6 - - - +
274A LEU* 1.3 68.0 + - - +
275A PRO 3.3 1.8 - - - -
276A GLN* 2.8 17.0 + - - +
277A VAL* 2.9 22.7 + - - +
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TYR* 3.5 30.3 - - + +
94A GLU 3.7 6.1 - - - +
95A ASP* 3.9 29.2 - - + +
96A ALA* 4.0 3.8 - - - +
115A ASN* 3.2 14.2 - - - +
118A THR* 3.8 13.0 - - + -
233A PHE* 4.1 7.9 - - + -
273A CYS* 1.3 76.9 - - - +
275A PRO* 1.4 64.0 - - + +
277A VAL* 3.2 4.3 + - - +
278A VAL* 2.9 31.8 + - + +
430A ALA* 3.4 41.3 - - + +
431A PHE* 4.6 5.4 - - + +
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Residues in contact with PRO 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PRO 4.1 12.8 - - - +
115A ASN* 3.5 11.0 - - - +
117A VAL* 3.9 21.3 - - + -
273A CYS 3.5 2.9 - - - -
274A LEU* 1.4 98.0 - - + +
276A GLN* 1.3 70.6 + - - +
278A VAL* 3.5 5.0 + - + +
279A LEU* 3.0 40.9 + - + +
430A ALA 4.8 4.9 - - - +
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Residues in contact with GLN 276 (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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114A PRO* 4.6 7.2 + - - +
271A GLY 3.4 16.7 + - - +
272A PHE* 3.7 31.4 - - + -
273A CYS* 2.8 36.1 + - - +
275A PRO* 1.3 88.5 - - - +
277A VAL* 1.3 67.4 + - - +
279A LEU* 4.4 4.0 - - - +
280A THR* 2.6 34.0 + - - +
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASP 4.0 13.2 - - - +
96A ALA* 4.6 7.2 - - + -
232A GLY* 3.3 39.4 - - - +
233A PHE* 3.7 20.6 - - + +
236A ALA* 4.5 2.2 - - + -
267A ILE* 4.0 17.7 - - + -
272A PHE* 3.6 20.2 - - + +
273A CYS 2.9 19.1 + - - +
274A LEU* 3.2 10.3 + - - +
276A GLN* 1.3 78.8 - - - +
278A VAL* 1.3 62.6 + - - +
281A TYR* 3.6 20.1 + - - -
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PRO 4.4 6.3 - - - +
230A PHE* 4.3 16.6 - - + +
232A GLY* 5.8 0.4 - - - +
233A PHE* 3.7 29.6 - - + -
274A LEU* 2.9 28.8 + - + +
275A PRO* 3.7 7.0 - - + +
277A VAL* 1.3 77.6 - - - +
279A LEU* 1.4 72.4 + - + +
281A TYR 4.8 0.3 - - - -
282A PRO* 3.8 18.4 - - - +
430A ALA 4.2 1.8 - - - +
431A PHE* 3.9 30.3 - - - +
432A GLY* 5.0 2.9 - - - +
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Residues in contact with LEU 279 (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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275A PRO* 3.0 26.8 + - + +
276A GLN* 3.4 3.6 + - - +
278A VAL* 1.4 84.2 - - + +
280A THR* 1.3 64.6 + - - +
281A TYR 3.5 0.2 - - - -
282A PRO* 3.5 11.5 - - - +
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Residues in contact with THR 280 (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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266A GLN* 3.9 23.6 - - - +
272A PHE* 3.4 16.8 - - + -
276A GLN* 2.6 26.8 + - - +
279A LEU* 1.3 80.7 - - - +
281A TYR* 1.3 81.2 + - + +
282A PRO* 3.4 4.7 - - - +
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Residues in contact with TYR 281 (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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229A PRO 4.9 0.2 - - - -
231A ALA* 3.8 8.0 - - - +
232A GLY* 3.5 28.0 - - - +
235A LEU* 3.7 14.8 - - + -
263A THR* 3.5 24.1 + - + -
266A GLN* 2.7 30.5 + - - +
267A ILE* 3.7 19.9 - - + +
272A PHE* 3.6 30.8 - + - -
277A VAL* 3.6 17.9 + - - +
278A VAL 4.8 1.3 - - - -
280A THR* 1.3 87.4 - - + +
282A PRO* 1.4 68.5 - - - +
283A PHE 3.2 0.9 + - - -
284A LEU* 3.2 38.9 + - + +
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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