Contacts of the helix formed by residues 277 - 282 (chain I) in PDB entry 1SXG
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 THR 277 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I ILE* 4.3 10.5 - - + -
74I PHE* 4.3 22.9 - - + +
77I GLU* 3.1 14.8 - - - +
248I ASP* 2.7 29.9 + - + +
275I ASP* 3.4 26.0 - - + +
276I ASN* 1.3 81.6 - - - +
278I ARG* 1.3 64.7 + - - +
279I LEU* 3.0 25.3 + - + +
280I SER* 3.3 13.5 + - - -
281I THR* 4.8 0.5 + - - +
294I MET* 4.1 2.9 - - + -
328I ARG* 5.5 0.2 + - - -
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Residues in contact with ARG 278 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B SER* 3.6 33.4 + - - +
73B ILE* 3.0 33.1 - - - +
223B TYR* 5.6 1.2 - - - +
249B GLU* 2.9 22.0 + - - +
73I ILE* 3.8 26.7 - - + +
77I GLU* 2.8 34.1 + - - +
277I THR* 1.3 73.3 - - - +
279I LEU* 1.3 66.7 + - + +
280I SER 3.1 2.1 + - - -
281I THR* 3.3 21.4 + - - -
282I MET* 3.4 25.9 - - - +
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Residues in contact with LEU 279 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU* 4.2 24.7 - - + -
282B MET* 4.5 8.3 - - + -
73I ILE* 3.8 37.9 - - + -
248I ASP* 4.4 2.0 - - + -
249I GLU* 3.8 38.8 - - + +
252I LEU* 4.0 17.1 - - + +
277I THR* 3.0 15.1 + - + +
278I ARG* 1.3 80.8 - - - +
280I SER* 1.3 56.3 + - - +
281I THR 3.2 0.4 - - - -
282I MET* 2.9 37.2 + - + +
283I VAL* 3.3 13.7 - - - +
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Residues in contact with SER 280 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248I ASP* 2.7 28.7 + - - -
276I ASN* 3.6 10.7 - - - -
277I THR* 3.3 12.0 + - - -
278I ARG 3.1 0.8 - - - -
279I LEU* 1.3 78.5 - - - +
281I THR* 1.3 58.1 + - - +
282I MET 3.2 0.8 + - - -
283I VAL* 3.7 0.7 - - - +
286I GLN* 3.5 6.6 - - - +
287I LEU* 2.9 41.2 + - - +
289I SER* 3.6 6.2 - - - -
328I ARG* 3.2 26.0 - - - -
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Residues in contact with THR 281 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B TYR* 3.1 25.9 + - - -
224B ASP* 5.3 2.4 + - - -
278I ARG* 3.3 14.0 + - - +
279I LEU 3.2 0.6 - - - -
280I SER* 1.3 78.9 - - - +
282I MET* 1.3 59.1 + - - +
283I VAL 3.4 5.4 - - - -
284I ARG* 3.3 11.6 + - - -
286I GLN* 3.4 21.8 - - - +
328I ARG* 3.8 25.8 - - - +
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Residues in contact with MET 282 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B TYR* 3.7 47.6 - - + -
249B GLU* 3.1 26.0 - - + +
252B LEU* 4.1 17.8 - - + +
256B HIS* 3.3 15.4 - - - -
279B LEU* 4.1 15.7 - - + -
282B MET 5.1 2.9 - - - +
283B VAL* 5.4 0.2 - - - +
252I LEU* 4.3 5.9 - - + +
278I ARG* 3.4 38.8 - - - +
279I LEU* 2.9 27.9 + - + +
281I THR* 1.3 79.0 - - - +
283I VAL* 1.3 63.7 + - - +
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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
------------------------------------------------------------
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