Contacts of the strand formed by residues 270 - 276 (chain A) in PDB entry 1T4S
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 LEU 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LYS* 5.1 1.7 + - - -
45A TYR* 6.1 1.3 - - - +
93A ILE* 3.2 29.4 - - + +
227A ILE* 3.9 7.6 - - - +
229A LEU* 4.0 18.8 - - + +
264A ILE* 4.1 24.0 + - + +
265A TYR* 5.6 0.9 - - - +
267A THR* 4.4 1.6 + - - -
268A GLY* 3.4 5.2 - - - +
269A LEU* 1.3 75.2 - - - +
271A SER* 1.3 58.2 + - - +
272A GLY 3.4 26.9 - - - +
273A LEU* 4.7 4.0 - - + -
303A CYS* 3.5 42.0 - - + +
304A PHE* 3.8 26.0 - - + -
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Residues in contact with SER 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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6A LYS* 5.9 1.6 - - - +
88A GLN* 3.1 26.3 + - - -
93A ILE* 2.9 26.3 - - - +
94A SER 3.3 0.9 + - - -
111A HIS* 2.7 31.2 + - - -
115A HIS* 4.1 7.4 + - - -
226A PRO* 3.8 21.9 - - - +
227A ILE 2.9 13.6 + - - -
269A LEU 3.2 1.9 + - - -
270A LEU* 1.3 74.1 - - - +
272A GLY* 1.3 55.6 + - - +
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Residues in contact with GLY 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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93A ILE* 5.1 0.2 - - - -
94A SER* 3.5 13.9 - - - -
111A HIS* 3.1 22.5 - - - -
227A ILE 3.2 1.4 + - - -
228A HIS* 3.4 12.4 - - - -
229A LEU 2.9 22.7 + - - -
270A LEU* 3.4 9.6 - - - +
271A SER* 1.3 76.5 - - - +
273A LEU* 1.3 60.4 + - - -
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Residues in contact with LEU 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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93A ILE* 5.7 0.2 - - + -
94A SER* 2.9 12.5 + - - +
95A VAL* 3.5 14.5 - - + -
96A VAL* 2.8 27.4 + - - +
107A SER* 4.7 0.2 + - - -
228A HIS* 4.2 1.8 + - - -
229A LEU* 3.2 25.6 - - + +
231A PHE* 4.7 1.1 - - + -
270A LEU* 4.7 5.8 - - + -
272A GLY* 1.3 74.2 - - - +
274A ASP* 1.3 101.8 + - - +
275A ILE* 3.4 24.0 - - + -
300A THR* 4.5 5.2 - - + -
303A CYS* 4.0 24.2 - - + -
304A PHE* 3.9 28.7 - - + -
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Residues in contact with ASP 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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96A VAL* 3.6 8.7 - - - +
104A ALA* 4.3 7.9 - - - +
107A SER* 2.6 32.2 + - - -
228A HIS* 2.9 24.5 + - - -
229A LEU 2.7 8.7 + - - -
230A SER* 2.9 27.0 + - - +
231A PHE* 2.9 25.3 + - - +
273A LEU* 1.3 92.8 - - - +
275A ILE* 1.3 60.1 + - - +
276A MET* 3.7 20.6 - - + -
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Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.9 26.6 - - + +
95A VAL* 4.8 2.0 - - + -
96A VAL 3.0 13.2 + - - +
97A LEU* 4.0 12.2 - - + -
98A GLY* 3.3 23.2 + - - +
231A PHE* 3.8 13.5 - - + +
233A VAL* 5.8 2.7 - - + -
273A LEU* 3.4 32.3 - - + -
274A ASP* 1.3 74.1 - - - +
276A MET* 1.3 59.7 + - - +
278A VAL* 4.7 7.9 - - + +
296A ALA* 4.2 23.3 - - + +
299A LEU* 5.2 5.4 - - + -
300A THR* 3.5 28.0 - - - +
303A CYS* 5.8 0.7 - - - -
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Residues in contact with MET 276 (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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96A VAL* 4.2 9.2 - - + +
98A GLY* 4.1 17.5 - - - -
99A GLY 3.9 4.0 - - - +
100A ASP 3.1 27.4 - - - +
101A HIS* 3.5 36.3 - - + -
103A MET* 3.5 24.0 - - + -
104A ALA* 4.1 10.3 - - - +
107A SER* 6.1 0.2 - - - -
231A PHE 2.9 12.1 + - - +
232A ASP* 4.7 0.4 - - - -
233A VAL* 3.0 32.0 + - - +
274A ASP* 3.8 22.4 - - + -
275A ILE* 1.3 85.0 - - - +
277A GLU* 1.3 65.3 + - + +
278A VAL* 3.3 7.2 + - - +
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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