Contacts of the strand formed by residues 267 - 272 (chain B) in PDB entry 1E2R
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 GLN 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A MET* 4.6 8.8 - - - +
294A TYR* 5.9 0.3 - - - +
136B GLU* 4.7 3.6 - - - +
137B PHE 2.9 28.4 + - - +
142B MET* 3.4 7.7 - - - +
238B ILE* 3.0 25.1 + - - +
262B ALA* 2.9 29.7 + - + +
265B PRO* 2.9 39.2 + - - +
266B PRO* 1.3 73.9 - - - +
268B TYR* 1.3 61.8 + - - +
269B VAL* 4.8 2.5 - - + -
281B ILE* 4.0 16.8 - - + +
282B GLN 3.1 19.3 - - - +
283B SER* 4.2 2.4 - - - -
284B THR* 3.5 6.4 + - - +
285B ARG* 5.9 0.3 + - - -
300B VAL* 3.6 7.2 - - - +
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Residues in contact with TYR 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ILE* 3.6 29.4 - - + -
260B ALA 3.2 13.5 - - - +
261B GLY* 4.2 6.5 - - - -
267B GLN* 1.3 73.9 - - - +
269B VAL* 1.3 71.1 + - - +
270B ILE* 4.5 8.7 - - + -
281B ILE* 3.5 0.7 - - - +
282B GLN* 2.9 74.0 + - + +
283B SER 5.3 1.1 - - - -
284B THR* 3.9 14.8 - - + -
300B VAL* 4.4 7.0 - - + -
303B ILE* 5.0 0.2 - - + -
314B VAL* 4.2 12.3 - - + -
323B LEU* 3.7 23.8 - - + +
325B VAL* 3.1 38.3 - - + +
335B THR* 4.4 5.7 - - - +
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B MET* 3.3 44.2 - - + -
238B ILE* 4.1 22.9 - - + +
259B ILE* 3.2 4.2 - - - -
260B ALA 2.9 35.4 + - - +
267B GLN* 4.6 3.4 - - + +
268B TYR* 1.3 81.3 - - - +
270B ILE* 1.3 75.9 - - - +
271B MET* 3.8 14.0 - - + +
278B PRO* 4.4 7.0 - - + -
280B LYS 3.3 11.2 - - - +
281B ILE* 4.0 12.8 - - + -
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Residues in contact with ILE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B TYR* 3.7 31.9 - - + -
258B ALA 3.5 7.0 - - - +
259B ILE* 4.1 17.7 - - + -
268B TYR* 4.5 8.7 - - + -
269B VAL* 1.3 76.1 - - - +
271B MET* 1.3 62.8 + - - +
279B LYS* 2.8 25.0 + - - +
280B LYS* 2.9 25.9 + - + +
282B GLN* 6.1 0.2 - - + -
312B PHE* 4.3 15.3 - - + -
325B VAL* 4.0 26.0 - - + -
327B TYR* 4.7 3.4 - - + -
330B LEU* 3.9 31.2 - - + -
333B LEU* 5.2 1.3 - - + -
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Residues in contact with MET 271 (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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220B VAL* 4.5 9.6 - - + -
236B ILE* 3.8 26.9 - - + -
238B ILE* 4.0 9.6 - - + -
245B ILE* 4.7 2.0 - - + -
257B TYR* 3.3 11.5 - - - -
258B ALA* 2.8 43.3 + - + +
259B ILE 3.9 5.8 - - - -
260B ALA* 3.7 39.0 - - + +
269B VAL* 3.8 16.8 - - + +
270B ILE* 1.3 79.0 - - - +
272B ASP* 1.3 65.1 + - - +
273B GLY 3.3 0.3 + - - -
276B LEU* 3.7 29.8 - - + +
277B GLU 3.2 9.4 - - - +
278B PRO* 4.3 3.6 - - + -
279B LYS* 4.4 0.9 - - - -
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Residues in contact with ASP 272 (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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256B LYS 4.0 6.7 - - - +
257B TYR* 4.2 7.1 - - - -
258B ALA* 5.1 0.2 - - - +
271B MET* 1.3 70.6 - - - +
273B GLY* 1.3 61.2 + - - +
274B GLU* 2.9 31.4 + - - +
275B THR* 3.1 28.8 + - - +
276B LEU* 2.8 29.5 + - - +
277B GLU* 2.9 24.1 + - + +
279B LYS* 4.0 10.4 - - + +
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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
------------------------------------------------------------
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