Contacts of the strand formed by residues 272 - 278 (chain B) in PDB entry 1ES7
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 272 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B ILE 3.7 0.7 - - - +
263B ILE* 3.1 29.1 - - - +
264B GLU* 3.2 25.1 + - - +
270B GLU 4.0 12.3 + - - +
271B THR* 1.3 80.0 - - - +
273B LEU* 1.3 64.1 + - - +
274B ALA* 5.8 1.7 - - - +
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Residues in contact with LEU 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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241B SER* 4.6 7.4 + - - +
261B ALA* 4.6 5.2 - - + -
262B ILE 3.4 12.6 - - - +
263B ILE* 3.8 18.6 - - + -
272B THR* 1.3 78.1 - - - +
274B ALA* 1.3 87.0 + - - +
275B SER* 5.5 1.3 - - - -
311B LEU 4.3 21.1 - - - +
312B GLN* 5.1 7.0 - - + -
313B PRO* 4.9 1.6 - - + -
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Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B SER* 3.3 16.8 - - - +
242B GLY* 4.7 3.8 - - - -
243B HIS* 3.7 22.9 - - + +
261B ALA* 3.3 3.5 - - - -
262B ILE* 2.8 43.7 + - + +
264B GLU* 6.0 2.5 - - - +
272B THR* 5.8 2.0 - - - +
273B LEU* 1.3 80.0 - - - +
275B SER* 1.3 62.2 + - - +
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Residues in contact with SER 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TYR* 3.6 16.2 - - - -
240B CYS 3.6 3.1 - - - -
241B SER* 2.9 46.8 + - - +
243B HIS* 3.4 11.5 - - - +
260B PHE* 3.1 26.2 - - - -
261B ALA* 4.2 5.2 - - - -
273B LEU* 5.5 2.0 - - - -
274B ALA* 1.3 76.2 - - - +
276B GLY* 1.3 59.3 + - - +
308B ASN* 3.6 10.5 - - - -
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Residues in contact with GLY 276 (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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239B TYR 3.6 2.5 + - - -
240B CYS* 3.8 17.3 - - - -
243B HIS* 4.3 6.1 - - - -
253B CYS* 3.9 4.3 - - - -
259B CYS* 3.6 0.9 - - - -
260B PHE* 3.0 43.1 + - - -
275B SER* 1.3 78.1 - - - +
277B CYS* 1.3 58.6 + - - -
308B ASN* 3.4 8.4 + - - -
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Residues in contact with CYS 277 (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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52A ALA* 3.4 12.0 - - - +
53A ASP* 2.8 29.5 + - + -
54A HIS* 5.7 1.5 - - + -
238B CYS* 3.3 19.3 - - - -
243B HIS 5.2 1.2 + - - -
253B CYS* 2.0 66.3 - - + -
254B ILE 3.9 1.8 - - - +
255B THR* 3.6 20.4 - - - -
258B HIS 3.7 3.8 - - - -
260B PHE* 3.7 2.5 - - - -
276B GLY* 1.3 72.8 - - - -
278B MET* 1.3 60.8 + - - +
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Residues in contact with MET 278 (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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50A PRO* 4.3 5.8 - - + -
51A LEU 4.5 3.6 - - - +
52A ALA 4.9 0.2 - - - -
53A ASP 4.1 2.2 - - - +
255B THR* 3.2 5.0 + - - -
257B GLY* 3.1 3.3 - - - -
258B HIS* 2.9 39.8 + - - +
260B PHE* 4.0 17.3 - - + -
277B CYS* 1.3 75.9 - - - +
279B LYS* 1.3 73.5 + - - +
283B SER* 3.7 15.3 - - - -
286B GLN* 3.7 44.0 - - + +
287B CYS* 3.5 21.1 - - - -
299B ILE* 4.0 18.2 - - + -
301B CYS* 3.8 20.0 - - - -
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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