Contacts of the helix formed by residues 267 - 275 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A THR 5.8 0.7 - - - +
137A GLN* 3.8 9.2 - - - +
163A GLU* 3.6 7.2 - - - +
256A ILE 5.1 1.5 + - - +
261A TYR* 4.0 33.2 - - + -
265A PHE* 4.0 8.9 + - + -
266A ILE* 1.3 78.7 - - - +
268A LEU* 1.3 67.2 + - - +
269A ARG* 3.4 23.8 - - - +
270A VAL* 2.9 27.5 + - - +
271A TRP* 3.8 2.1 + - - -
286A PHE* 4.1 12.2 - - + -
400A UDP 4.3 18.2 + - - +
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Residues in contact with LEU 268 (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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137A GLN* 4.5 1.4 - - - +
163A GLU* 3.5 36.1 - - + +
165A TYR* 3.6 33.0 - - + +
166A LYS* 3.6 23.6 - - + -
240A MET* 4.1 10.3 - - + -
267A THR* 1.3 73.0 - - - +
269A ARG* 1.3 63.6 + - - +
271A TRP* 2.9 6.9 + - + +
272A GLU* 2.9 48.3 + - + +
400A UDP 4.1 14.9 + - - +
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Residues in contact with ARG 269 (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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186A TYR* 3.2 37.0 + - - +
187A GLY 2.8 34.1 + - - +
188A GLY* 4.0 1.6 - - - -
195A ARG* 4.1 1.0 - - - +
247A ASN* 6.2 0.7 - - - +
254A LEU 4.1 8.7 + - - -
255A ILE* 3.7 21.3 - - + +
256A ILE 4.0 13.7 - - - -
267A THR* 3.2 15.9 - - - +
268A LEU* 1.3 78.4 - - - +
270A VAL* 1.3 58.8 + - + +
272A GLU* 3.5 13.0 - - - +
273A THR* 2.7 40.0 + - - +
400A UDP 2.8 55.6 + - - +
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Residues in contact with VAL 270 (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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255A ILE* 4.0 27.8 - - + -
266A ILE* 4.0 18.2 - - + -
267A THR* 2.9 34.1 + - - +
269A ARG* 1.3 77.6 - - - +
271A TRP* 1.3 63.1 + - + +
274A MET* 2.9 52.5 + - + +
280A MET* 3.9 6.0 - - - +
286A PHE* 4.1 10.3 - - + -
292A ILE* 4.1 19.3 - - + -
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Residues in contact with TRP 271 (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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163A GLU* 2.9 52.2 + - + +
164A GLN* 3.6 27.5 - - + +
166A LYS* 4.3 11.4 + - + -
167A ILE* 3.6 38.9 - - + +
266A ILE* 3.6 19.6 - - + +
267A THR 3.9 4.7 - - - -
268A LEU 2.9 6.7 + - - +
270A VAL* 1.3 75.3 - - + +
272A GLU* 1.3 59.6 + - - +
273A THR 3.1 1.8 - - - -
274A MET* 3.8 35.2 - - + +
275A ALA* 3.0 33.6 + - - +
330A ILE* 6.1 0.7 - - + -
331A LEU* 4.1 7.2 - - + +
334A THR* 3.8 27.6 - - + -
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Residues in contact with GLU 272 (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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166A LYS* 3.8 16.2 - - - +
240A MET* 4.2 9.4 - - - +
243A VAL* 3.6 21.3 - - + +
244A SER* 3.1 24.9 + - - +
247A ASN* 3.4 16.7 + - - +
268A LEU* 2.9 36.9 + - + +
269A ARG* 3.5 9.3 - - - +
271A TRP* 1.3 76.3 - - - +
273A THR* 1.3 59.5 + - - +
276A SER* 3.4 11.8 + - - -
400A UDP 2.5 50.2 + - - -
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Residues in contact with THR 273 (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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247A ASN* 3.8 12.2 + - - +
253A ALA* 3.4 33.2 - - + +
254A LEU 4.9 1.2 + - - -
255A ILE* 3.6 14.3 - - + +
269A ARG* 2.7 28.6 + - - +
270A VAL 3.9 1.1 - - - -
272A GLU* 1.3 74.7 - - - +
274A MET* 1.3 65.1 + - - +
275A ALA 3.2 1.6 - - - -
276A SER* 2.7 23.5 + - - +
278A ALA 3.6 2.9 - - - +
280A MET* 3.7 28.7 - - + -
327A GLN* 3.4 7.3 + - - -
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Residues in contact with MET 274 (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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270A VAL* 2.9 32.9 + - + +
271A TRP* 3.8 20.4 - - + +
273A THR* 1.3 76.5 - - - +
275A ALA* 1.3 57.8 + - - +
280A MET* 3.7 20.1 - - + -
292A ILE* 3.6 37.0 - - + +
293A ILE* 4.6 1.1 - - + -
327A GLN* 3.1 42.6 + - + +
328A HIS* 3.1 16.1 + - - -
330A ILE* 4.4 7.0 - - + -
331A LEU* 3.5 37.8 - - + +
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Residues in contact with ALA 275 (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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166A LYS* 5.3 1.6 - - - +
172A PHE* 3.8 26.2 - - + -
173A GLN 4.9 1.6 - - - +
174A LEU* 3.7 9.2 - - + -
175A SER* 2.9 28.1 + - - -
244A SER* 4.9 6.3 - - - +
271A TRP 3.0 17.8 + - - +
272A GLU* 4.3 3.1 - - - +
274A MET* 1.3 73.8 - - - +
276A SER* 1.3 62.7 + - - +
328A HIS* 3.8 4.4 - - - -
331A LEU* 3.4 19.0 - - + +
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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