Contacts of the strand formed by residues 273 - 280 (chain B) in PDB entry 5MJ6
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 GLY 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B SER* 5.1 0.9 - - - -
272B TYR* 1.3 72.7 - - - +
274B PHE* 1.3 64.1 + - - -
275B TYR* 3.4 6.9 + - - -
292B THR* 3.5 1.9 - - - -
293B GLN 2.9 38.9 + - - -
294B PHE* 3.9 9.9 - - - -
298B ALA* 3.6 9.5 - - - +
301B SER* 3.6 20.0 - - - -
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Residues in contact with PHE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 5.0 3.4 - - + -
183B PRO* 4.1 33.9 - - + -
190B PHE* 4.2 32.7 - + + -
266B ASN 4.9 0.5 - - - +
267B ILE* 3.5 15.5 - - + +
268B SER* 2.9 23.6 + - - -
273B GLY* 1.3 69.8 - - - -
275B TYR* 1.3 56.9 + - - +
290B ALA* 3.7 31.0 - - + -
291B ALA* 3.3 17.5 - - - -
292B THR* 4.0 6.3 - - + -
294B PHE* 4.0 3.4 - - - -
301B SER* 4.4 4.6 + - - +
302B ALA* 4.0 20.8 - - + +
361B PHE* 3.8 38.6 - + - -
363B VAL* 5.1 4.9 - - + -
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Residues in contact with TYR 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ILE* 3.6 4.9 - - - -
268B SER* 3.4 16.2 - - - +
270B SER 3.3 28.3 - - - +
271B TYR* 3.6 28.7 - + - -
272B TYR 4.1 3.4 - - - +
273B GLY 3.4 9.6 + - - -
274B PHE* 1.3 74.0 - - - +
276B GLY* 1.3 62.8 + - - +
277B PHE* 4.0 19.7 - + + -
290B ALA* 3.3 2.8 - - - +
291B ALA* 3.0 57.1 + - + +
292B THR 4.4 2.5 - - - -
293B GLN* 4.3 11.2 - - + -
422B ILE* 3.9 4.7 - - - +
424B ASP* 2.5 32.0 + - + -
425B PHE* 3.3 22.8 - + - -
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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
----------------------------------------------------------
188B MET* 3.7 20.5 - - - +
267B ILE* 3.4 8.6 - - - +
268B SER 3.0 16.0 + - - +
269B SER* 4.8 6.4 - - - -
270B SER 5.2 0.3 - - - +
275B TYR* 1.3 78.7 - - - +
277B PHE* 1.3 67.3 + - - +
289B PHE 3.2 9.9 - - - -
290B ALA* 4.1 2.9 - - - -
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Residues in contact with PHE 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B MET* 3.8 9.1 - - - +
275B TYR* 4.0 15.7 - + + -
276B GLY* 1.3 78.1 - - - +
278B SER* 1.3 67.9 + - - +
279B TYR* 4.6 4.9 - + - -
288B TYR* 3.7 2.9 - - - -
289B PHE* 2.8 76.6 + + + +
290B ALA* 4.8 2.5 - - - -
291B ALA* 5.4 0.4 - - + -
422B ILE* 3.8 5.4 - - + -
423B PRO* 3.5 31.6 - - + -
424B ASP* 3.5 52.0 - - + +
920B ARG* 3.8 9.0 - - - +
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Residues in contact with SER 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B MET* 5.2 0.4 - - - +
277B PHE* 1.3 74.9 - - - +
279B TYR* 1.3 61.6 - - - +
286B LYS* 3.7 23.0 + - - +
287B LYS 3.2 8.5 - - - -
288B TYR* 3.5 31.0 - - - -
920B ARG* 3.1 20.4 + - - -
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Residues in contact with TYR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B PHE* 4.6 13.0 - + + -
278B SER* 1.3 75.7 - - - +
280B THR* 1.3 90.2 + - - +
281B ASP* 4.3 5.8 - - + +
286B LYS* 3.4 10.8 - - - +
287B LYS* 3.0 60.2 + - + +
288B TYR 5.0 0.4 - - - -
289B PHE* 4.6 13.9 - + + -
365B GLU* 4.4 3.8 + - - +
383B VAL* 3.2 43.6 - - + +
384B PRO* 4.1 9.2 - - - +
385B GLU* 4.4 11.6 - - - +
386B LYS* 6.4 0.4 - - - -
423B PRO* 4.8 8.7 - - + -
440B GLU* 6.1 0.2 - - - -
920B ARG* 4.4 20.0 - - - +
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Residues in contact with THR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR* 1.3 90.7 + - - +
281B ASP* 1.3 76.8 + - - +
284B ASN* 3.6 28.7 - - + +
285B GLU 3.6 7.4 - - - +
286B LYS* 4.1 10.8 - - + +
385B GLU* 4.0 5.5 - - - +
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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