Contacts of the strand formed by residues 268 - 274 (chain A) in PDB entry 1T43
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 GLU 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A HIS* 4.1 7.2 - - + +
239A GLY 4.1 1.4 - - - +
240A TRP* 3.5 37.5 + - - +
243A GLY* 4.1 14.1 - - - -
244A GLU 4.7 1.9 + - - -
247A ARG* 5.1 7.8 + - - -
260A THR* 2.8 45.0 + - + +
261A CYS 3.6 7.6 - - - +
262A ARG* 3.5 27.3 - - - +
263A ASP* 4.4 0.2 - - - +
267A ASN* 1.3 87.8 - - + +
269A ARG* 1.3 60.9 + - - +
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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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94A ASP* 3.2 47.0 - - - +
186A TYR* 3.4 22.2 + - - -
237A GLU* 3.2 28.4 + - + -
238A HIS* 3.1 33.6 + - - -
239A GLY* 4.0 2.6 - - - -
240A TRP* 3.8 26.1 - - - +
261A CYS 3.3 4.6 + - - -
263A ASP* 3.1 36.4 + - + -
266A ASP* 4.5 10.5 + - - -
267A ASN 3.3 1.0 + - - -
268A GLU* 1.3 75.5 + - - +
270A VAL* 1.3 68.7 - - + +
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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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97A CYS* 3.0 41.5 - - + -
98A LEU* 3.5 28.0 - - + +
101A GLN* 5.6 3.4 - - + +
235A LEU* 4.5 2.7 - - + -
236A LEU 3.0 26.9 - - - +
237A GLU* 4.6 1.1 - - + -
238A HIS* 3.4 2.7 + - - -
259A GLU 3.8 0.4 - - - +
260A THR* 3.4 2.1 - - - +
261A CYS* 3.0 30.2 + - - +
269A ARG* 1.3 86.9 - - + +
271A THR* 1.3 68.9 + - - +
272A LEU* 4.1 16.8 - - + -
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Residues in contact with THR 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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236A LEU* 3.0 27.3 + - - +
238A HIS* 2.7 25.7 + - - -
243A GLY 4.6 0.9 + - - -
246A VAL* 3.7 16.2 - - + +
247A ARG* 4.2 4.9 - - - -
250A PHE* 3.3 30.1 - - + -
258A VAL* 3.6 17.3 - - + -
259A GLU 3.1 11.9 - - - +
260A THR* 3.5 20.2 + - - +
270A VAL* 1.3 76.0 + - - +
272A LEU* 1.3 65.6 + - - +
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Residues in contact with LEU 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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101A GLN* 5.0 7.0 - - + -
105A ARG* 3.0 48.0 - - - +
233A PHE* 4.0 6.3 - - + -
234A LEU 3.3 5.4 - - - -
235A LEU* 3.2 28.0 - - + -
250A PHE* 4.2 3.4 - - - -
257A ASP 3.9 0.2 - - - +
258A VAL* 3.1 10.3 - - - +
259A GLU* 2.7 47.7 + - - +
261A CYS* 3.1 35.4 - - - -
270A VAL* 4.1 12.6 - - + -
271A THR* 1.3 78.0 - - - +
273A GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 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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225A ARG* 3.2 22.1 + - - -
233A PHE* 3.9 8.5 - - - -
234A LEU* 3.4 23.6 + - - +
250A PHE* 4.2 1.6 - - - -
256A HIS 4.6 0.4 - - - -
257A ASP 3.4 17.7 - - - -
258A VAL* 4.2 2.9 - - - -
259A GLU* 5.7 0.2 - - - -
272A LEU* 1.3 78.8 - - - +
274A ARG* 1.3 60.6 + - - +
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Residues in contact with ARG 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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105A ARG* 5.4 1.4 - - - +
108A GLU* 4.8 7.7 + - - -
109A GLN* 4.3 11.7 - - - +
225A ARG* 3.5 7.7 + - - +
231A GLY* 2.9 25.2 + - - +
232A GLY 2.6 24.0 - - - +
233A PHE* 3.4 36.7 - - + -
234A LEU 5.2 0.2 - - - +
255A TYR* 3.4 7.1 + - - +
256A HIS* 2.7 73.3 + - + +
257A ASP* 4.6 10.5 + - - +
273A GLY* 1.3 71.5 - - - -
275A TYR* 1.3 54.8 + - - +
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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