Contacts of the helix formed by residues 278 - 283 (chain A) in PDB entry 1RZR
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 ARG 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ILE* 5.7 11.0 - - + +
77A GLU* 5.3 9.9 - - - +
277A THR* 1.3 73.2 - - - +
279A LEU* 1.3 67.9 + - + +
280A SER 3.1 2.0 + - - -
281A THR* 3.1 22.8 + - - +
282A MSE 3.2 20.8 + - + +
72D ASN* 5.7 5.1 - - - +
73D ILE* 5.9 3.4 - - - +
222D THR* 4.0 24.7 - - - +
223D TYR* 4.9 1.8 - - - +
224D ASP* 5.6 1.6 + - - -
249D GLU* 3.5 35.1 + - - -
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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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73A ILE* 4.5 24.0 - - + -
248A ASP* 4.9 5.6 - - + +
249A GLU* 4.7 18.2 - - - +
252A LEU* 4.6 9.4 - - + -
277A THR* 3.1 16.4 - - + +
278A ARG* 1.3 79.6 - - + +
280A SER* 1.3 54.8 + - - +
282A MSE 2.6 54.7 + - + +
283A VAL* 2.8 18.0 + - + +
279D LEU* 4.7 12.3 - - + -
282D MSE 4.0 28.9 - - + -
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Residues in contact with SER 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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248A ASP* 3.1 12.8 + - - +
276A ASN* 4.0 0.7 + - - -
277A THR* 3.5 19.1 + - - -
278A ARG 3.1 0.4 - - - -
279A LEU* 1.3 78.6 - - - +
281A THR* 1.3 58.8 + - - +
283A VAL* 3.4 6.9 - - - +
286A GLN* 3.5 3.3 - - - -
287A LEU* 2.8 53.9 + - - +
289A SER* 3.1 23.4 + - - -
328A ARG* 3.7 15.3 - - - -
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Residues in contact with THR 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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277A THR 4.4 3.6 - - - +
278A ARG* 3.4 19.0 + - + +
280A SER* 1.3 80.2 - - - +
282A MSE 1.3 66.8 + - - +
283A VAL 3.1 7.7 + - - +
286A GLN* 3.6 25.5 + - - +
328A ARG* 4.3 15.7 - - - +
223D TYR* 2.8 34.2 + - - -
224D ASP* 5.1 2.6 + - - -
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Residues in contact with MSE 282 (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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252A LEU* 5.0 3.6 - - + -
278A ARG* 3.2 15.3 + - + +
279A LEU* 2.6 49.8 + - + +
281A THR* 1.3 75.9 + - - +
283A VAL* 1.3 59.0 + - + -
223D TYR* 3.9 24.5 + - + -
249D GLU* 3.1 38.6 - - + +
252D LEU* 4.2 24.8 - - + +
256D HIS* 3.6 17.0 + - - -
279D LEU* 3.4 30.7 - - + -
282D MSE 5.3 1.6 - - - +
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Residues in contact with VAL 283 (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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252A LEU* 3.2 42.2 - - + -
255A ILE* 3.8 22.7 - - + -
256A HIS* 4.1 12.6 - - + -
279A LEU* 2.9 18.4 - - + +
280A SER* 3.4 14.4 - - - +
281A THR 3.1 9.1 - - - +
282A MSE 1.3 80.5 - - - +
284A ARG* 1.3 72.7 + - - +
285A PRO* 4.1 9.0 - - + -
286A GLN* 3.2 11.3 + - - -
287A LEU* 4.1 13.5 - - + +
223D TYR* 4.6 0.3 + - - -
256D HIS* 4.6 0.2 - - - -
282D MSE 5.7 0.7 - - - -
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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