Contacts of the strand formed by residues 279 - 283 (chain B) in PDB entry 1SXQ
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 VAL 279 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ILE 2.9 14.9 + - - +
252B ALA* 3.1 6.2 - - - +
253B ALA 3.0 22.2 + - - -
273B THR* 4.8 0.2 - - - -
278B ALA* 1.3 69.6 - - - +
280B MET* 1.3 71.7 + - - +
281B LEU* 4.2 3.4 - - + -
298B PHE* 4.3 0.7 - - + -
313B LEU* 4.0 21.3 - - + -
320B ARG* 3.8 39.5 - - + +
323B MET* 3.9 35.4 - - + -
324B LEU* 3.7 13.2 - - + +
327B GLN* 3.5 9.0 - - - +
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Residues in contact with MET 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ALA 3.7 4.9 - - - -
255B ILE* 3.5 29.2 - - + -
270B VAL* 3.7 25.8 - - - +
273B THR* 3.7 12.8 - - + -
274B MET* 3.7 29.8 - - + +
278B ALA 3.3 1.6 + - - -
279B VAL* 1.3 71.5 - - - +
281B LEU* 1.3 63.3 + - - +
282B ILE* 3.8 15.5 - - + -
292B ILE* 4.1 7.2 - - + -
293B ILE* 3.4 33.2 - - + -
298B PHE* 3.2 25.5 - - + +
327B GLN* 2.9 15.8 + - + +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ALA* 3.7 27.6 - - + -
253B ALA 3.1 12.2 + - - +
254B LEU* 3.6 9.6 - - - +
255B ILE 3.0 23.3 + - - -
279B VAL* 4.1 12.8 - - + +
280B MET* 1.3 81.5 - - - +
282B ILE* 1.3 61.2 + - - +
297B ARG 3.9 13.7 - - - +
298B PHE* 3.4 6.1 - - - +
300B VAL* 4.8 8.1 - - + -
306B LEU* 3.5 33.4 - - + -
309B ARG* 3.8 30.7 - - + -
310B VAL* 4.0 9.9 - - + -
313B LEU* 4.3 4.0 - - + -
323B MET* 4.6 0.7 - - + -
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Residues in contact with ILE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B ILE* 3.8 13.9 - - + -
280B MET* 3.8 25.6 - - + -
281B LEU* 1.3 75.6 - - - +
283B ASP* 1.3 77.4 - - - +
284B GLU 3.2 0.3 + - - -
286B PHE* 3.9 24.2 - - + -
287B ASP* 4.5 2.9 - - + -
292B ILE* 3.9 26.5 - - + -
293B ILE* 5.2 1.3 - - + +
298B PHE* 2.7 17.0 + - + +
299B TYR* 3.2 45.6 - - + +
300B VAL* 2.9 29.0 + - - -
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Residues in contact with ASP 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B LYS* 2.8 40.9 + - - +
202B PHE* 3.7 15.9 - - + -
254B LEU* 5.0 1.0 - - + +
255B ILE 3.0 19.4 + - - +
256B ILE* 3.9 14.6 - - + +
257B GLY 5.5 0.9 + - - -
262B ASN* 5.5 0.5 - - - +
281B LEU 4.1 0.6 + - - -
282B ILE* 1.3 74.4 - - - +
284B GLU* 1.3 69.9 + - - +
285B GLU* 3.1 16.7 + - - +
286B PHE* 2.9 27.8 + - + +
287B ASP 3.7 0.7 + - - -
300B VAL* 3.4 14.6 - - - +
301B ASN* 4.3 4.5 - - - +
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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