Contacts of the strand formed by residues 258 - 264 (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 HIS 258 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236B LEU* 3.8 7.6 - - - -
255B THR* 3.7 4.0 - - - +
257B GLY* 1.3 80.1 - - - +
259B CYS* 1.3 66.8 + - - +
277B CYS* 3.7 3.8 - - - -
278B MET* 2.9 37.3 + - + +
280B TYR* 4.1 13.5 - + - -
283B SER* 3.2 37.6 + - - -
287B CYS* 4.5 6.2 - - - -
301B CYS* 4.0 23.1 - - + +
302B CYS* 3.6 9.9 + - - +
303B ARG* 3.3 32.6 - - + +
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Residues in contact with CYS 259 (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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236B LEU* 3.6 14.4 - - - -
237B LYS 3.8 6.5 - - - -
238B CYS* 2.0 49.4 - - - -
258B HIS* 1.3 75.7 - - - +
260B PHE* 1.3 60.0 + - - +
276B GLY 3.6 1.6 - - - -
301B CYS* 3.2 5.9 - - - +
302B CYS* 2.9 30.1 + - - -
304B THR 4.0 2.0 - - - -
306B LEU 4.6 1.3 - - - -
307B CYS* 3.6 27.1 - - - -
308B ASN* 2.9 20.0 - - - +
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Residues in contact with PHE 260 (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* 3.6 25.6 - - + -
52A ALA* 4.8 7.0 - - + -
243B HIS* 3.6 37.2 - + - -
259B CYS* 1.3 74.0 - - - +
261B ALA* 1.3 66.9 - - - +
262B ILE* 4.0 7.6 - - + -
275B SER* 3.1 21.7 - - - -
276B GLY* 3.0 49.2 + - - -
277B CYS 3.7 11.4 - - - -
278B MET* 4.0 37.0 - - + -
299B ILE* 4.2 8.3 - - + -
300B GLU 3.1 11.9 - - - +
301B CYS* 4.2 3.1 - - - -
302B CYS* 5.7 0.4 - - - -
308B ASN* 2.4 23.9 + - - +
311B LEU* 5.4 1.1 - - - -
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Residues in contact with ALA 261 (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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260B PHE* 1.3 76.0 - - - +
262B ILE* 1.3 65.0 + - - +
273B LEU* 4.6 4.5 - - + -
274B ALA 3.3 8.7 - - - +
275B SER* 4.2 3.6 - - - +
298B THR 3.9 0.2 - - - +
299B ILE* 3.4 2.4 - - - +
300B GLU 3.0 28.4 + - - -
308B ASN* 4.5 3.8 - - - +
311B LEU* 3.8 37.0 - - + +
313B PRO* 3.9 16.4 - - + +
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Residues in contact with ILE 262 (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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49A PHE* 4.2 20.0 - - + +
50A PRO* 4.2 20.4 - - + -
243B HIS* 4.7 2.7 - - - +
260B PHE* 4.0 17.0 - - + -
261B ALA* 1.3 77.7 - - - +
263B ILE* 1.3 72.3 + - - +
264B GLU* 4.0 26.4 - - + +
272B THR 3.7 0.7 - - - +
273B LEU* 3.4 5.9 - - - +
274B ALA* 2.8 52.8 + - + +
297B ARG* 4.4 7.9 - - + -
298B THR 3.2 17.3 - - - +
299B ILE* 4.1 9.9 - - + -
313B PRO* 4.5 1.5 - - - +
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Residues in contact with ILE 263 (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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262B ILE* 1.3 73.8 - - - +
264B GLU* 1.3 65.2 + - - +
271B THR* 6.1 2.7 - - - -
272B THR 3.1 13.2 - - - +
273B LEU* 3.8 23.6 - - + -
297B ARG* 3.0 28.1 - - - +
298B THR* 3.1 18.9 + - - +
312B GLN 5.7 0.2 - - - -
313B PRO* 3.0 40.6 - - + +
314B THR* 3.2 5.6 - - - +
315B LEU* 3.1 42.0 - - + +
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Residues in contact with GLU 264 (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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49A PHE* 3.9 17.0 - - - +
262B ILE* 4.0 24.1 - - + +
263B ILE* 1.3 79.1 - - - +
265B GLU* 1.3 66.3 + - - +
270B GLU 4.5 0.7 - - - +
271B THR* 3.2 27.4 - - - +
272B THR* 3.2 24.5 + - - +
295B LEU* 6.2 1.8 - - + -
296B ARG 3.7 8.7 - - - -
297B ARG* 4.1 15.3 + - + -
315B LEU* 4.3 4.4 - - - +
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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