Contacts of the helix formed by residues 267 - 275 (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 THR 267 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B THR 5.7 1.1 - - - +
137B GLN* 3.8 8.3 - - - +
163B GLU* 3.6 9.2 - - - +
256B ILE 5.1 1.4 + - - +
261B TYR* 4.0 33.4 - - + -
265B PHE* 3.9 12.0 + - + +
266B ILE* 1.3 79.0 - - - +
268B LEU* 1.3 67.9 + - - +
269B ARG* 3.4 23.0 - - - +
270B VAL* 3.0 26.9 + - - +
271B TRP* 3.8 1.7 + - - -
286B PHE* 4.1 10.2 - - + -
400B UDP 4.3 17.3 + - - +
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Residues in contact with LEU 268 (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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22B GLU* 3.9 17.3 - - - +
137B GLN* 4.5 1.7 - - - +
163B GLU* 3.5 35.1 - - + +
165B TYR* 3.5 39.3 - - + +
166B LYS* 4.2 9.9 - - + -
240B MET* 3.7 19.3 - - + -
267B THR* 1.3 73.5 - - - +
269B ARG* 1.3 58.5 + - - +
271B TRP* 3.0 9.2 + - - +
272B GLU* 2.9 33.2 + - - +
400B UDP 3.9 26.8 + - - +
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Residues in contact with ARG 269 (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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186B TYR* 3.3 36.4 + - - +
187B GLY 2.8 35.5 + - - +
188B GLY* 4.0 1.8 - - - -
195B ARG* 4.0 1.0 - - - +
247B ASN* 6.2 0.2 - - - +
254B LEU 4.0 8.9 + - - -
255B ILE* 3.7 21.3 - - + +
256B ILE 4.0 14.6 - - - -
267B THR* 3.4 14.1 - - - +
268B LEU* 1.3 76.2 - - - +
270B VAL* 1.3 62.6 + - - +
272B GLU* 3.5 13.0 + - - +
273B THR* 2.7 40.0 + - - +
400B UDP 2.8 55.1 + - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ILE* 3.9 27.4 - - + -
266B ILE* 3.9 17.5 - - + -
267B THR* 3.0 34.5 + - - +
269B ARG* 1.3 77.1 - - - +
271B TRP* 1.3 62.7 + - + +
274B MET* 2.8 51.8 + - + +
280B MET* 3.7 6.3 - - - +
286B PHE* 4.1 10.5 - - + -
292B ILE* 4.0 21.1 - - + -
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Residues in contact with TRP 271 (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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163B GLU* 3.0 53.6 + - + +
164B GLN* 3.6 29.6 - - + +
166B LYS* 3.9 11.0 - - + -
167B ILE* 3.7 35.9 - - + -
266B ILE* 3.7 16.3 - - + +
267B THR 3.9 4.3 - - - -
268B LEU 3.0 6.5 + - - +
270B VAL* 1.3 75.3 - - + +
272B GLU* 1.3 60.4 + - - +
273B THR 3.1 2.0 - - - -
274B MET* 3.8 36.9 - - + +
275B ALA* 2.8 35.0 + - - +
292B ILE* 6.4 0.2 - - + -
330B ILE* 5.8 1.3 - - + -
331B LEU* 4.1 6.8 - - + +
334B THR* 4.1 26.2 - - + -
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Residues in contact with GLU 272 (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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166B LYS* 4.0 26.2 + - + +
240B MET* 4.2 13.2 - - - +
243B VAL* 3.6 19.0 - - + +
244B SER* 3.1 26.5 + - - +
247B ASN* 3.4 18.3 + - - +
268B LEU* 2.9 23.9 + - + +
269B ARG* 3.5 9.6 - - - +
271B TRP* 1.3 75.7 - - - +
273B THR* 1.3 58.9 + - - +
276B SER* 3.5 11.8 + - - -
400B UDP 2.5 52.8 + - - -
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Residues in contact with THR 273 (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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247B ASN* 3.8 12.7 + - - +
253B ALA* 3.4 32.9 - - + +
254B LEU 4.8 1.4 + - - -
255B ILE* 3.5 14.1 - - + +
269B ARG* 2.7 27.7 + - - +
270B VAL 3.9 1.1 - - - -
272B GLU* 1.3 74.5 - - - +
274B MET* 1.3 66.2 + - - +
275B ALA 3.1 1.3 - - - -
276B SER* 2.7 24.6 + - - +
278B ALA 4.3 3.4 - - - +
280B MET* 3.7 30.1 - - + -
327B GLN* 3.4 6.2 + - - -
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Residues in contact with MET 274 (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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270B VAL* 2.8 30.7 + - + +
271B TRP* 3.8 25.8 - - + +
273B THR* 1.3 73.4 - - - +
275B ALA* 1.3 58.6 + - - +
280B MET* 3.7 20.6 - - + -
292B ILE* 3.6 36.3 - - + +
293B ILE* 4.6 2.2 - - + -
327B GLN* 3.1 42.8 + - + +
328B HIS* 3.1 16.6 + - - -
330B ILE* 4.4 5.8 - - + -
331B LEU* 3.4 37.2 - - + +
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Residues in contact with ALA 275 (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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166B LYS* 5.2 1.3 - - - -
172B PHE* 3.7 26.5 - - + -
173B GLN 4.9 1.8 - - - +
174B LEU* 3.6 9.4 - - - -
175B SER* 2.9 27.8 + - - -
244B SER* 4.6 7.4 - - - +
271B TRP 2.8 18.5 + - - +
272B GLU* 4.2 3.4 - - - +
274B MET* 1.3 75.5 - - - +
276B SER* 1.3 61.0 + - - +
328B HIS* 3.8 3.6 - - - -
331B LEU* 3.5 18.4 - - + +
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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