Contacts of the strand formed by residues 273 - 280 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A SER* 5.1 0.9 - - - -
272A TYR* 1.3 72.8 - - - +
274A PHE* 1.3 62.1 + - - -
275A TYR* 3.3 8.3 + - - -
292A THR* 3.5 0.5 - - - -
293A GLN 3.0 34.6 + - - -
294A PHE* 3.7 9.6 - - - -
298A ALA* 3.4 22.9 - - - +
301A SER* 3.7 13.5 - - - -
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 5.0 1.8 - - + -
183A PRO* 3.9 33.9 - - + -
190A PHE* 3.6 43.1 - + + -
266A ASN 4.8 0.7 - - - +
267A ILE* 3.5 10.9 - - + +
268A SER* 2.9 22.3 + - - -
273A GLY* 1.3 68.4 - - - -
275A TYR* 1.3 60.6 + - - +
290A ALA* 3.9 26.5 - - + -
291A ALA 3.8 5.2 - - - -
292A THR* 3.7 10.8 - - + -
294A PHE* 3.7 7.0 - - - -
301A SER* 4.5 2.4 + - - +
302A ALA* 3.8 23.0 - - + +
361A PHE* 3.5 39.3 - + - -
363A VAL* 5.3 3.6 - - + -
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Residues in contact with TYR 275 (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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267A ILE* 3.5 4.9 - - - -
268A SER* 3.4 20.6 - - - +
270A SER 3.4 22.4 - - - +
271A TYR* 3.7 34.3 - + - -
272A TYR 4.2 2.9 - - - +
273A GLY 3.3 10.0 + - - -
274A PHE* 1.3 75.0 - - - +
276A GLY* 1.3 62.5 + - - +
277A PHE* 4.0 19.1 - + + -
290A ALA* 3.3 6.2 - - - +
291A ALA* 2.9 64.0 + - + +
292A THR 4.4 1.1 - - - -
293A GLN* 4.2 12.1 - - + -
422A ILE* 4.0 4.5 - - - +
424A ASP 2.7 29.4 + - - -
425A PHE* 3.2 24.5 - + - -
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Residues in contact with GLY 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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185A LEU* 6.2 0.7 - - - -
188A MET* 3.2 24.8 - - - +
267A ILE* 3.4 11.5 - - - +
268A SER 3.2 9.1 + - - +
269A SER* 4.6 4.7 - - - -
275A TYR* 1.3 82.2 - - - +
277A PHE* 1.3 68.0 + - - +
289A PHE 3.1 12.6 - - - -
290A ALA* 4.1 2.0 - - - -
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Residues in contact with PHE 277 (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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188A MET* 4.8 3.3 - - - -
275A TYR* 4.0 18.4 - + + -
276A GLY* 1.3 78.1 - - - +
278A SER* 1.3 74.9 + - - +
279A TYR* 3.9 11.9 - + + -
288A TYR* 3.6 7.3 - - - -
289A PHE* 2.9 74.6 + + + +
290A ALA* 5.4 0.7 - - - -
291A ALA 5.5 0.9 - - - -
422A ILE* 4.3 2.9 - - + -
423A PRO* 3.8 24.5 - - + -
424A ASP* 3.7 54.3 - - + +
920A ARG* 6.0 0.4 - - - -
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Residues in contact with SER 278 (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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277A PHE* 1.3 84.8 - - - +
279A TYR* 1.3 63.1 + - - +
286A LYS* 3.3 37.4 + - - +
287A LYS 3.1 13.7 - - - -
288A TYR* 3.8 12.6 - - - -
424A ASP* 5.3 1.2 - - - +
920A ARG* 5.4 1.0 + - - -
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Residues in contact with TYR 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A PHE* 3.9 22.0 - + + -
278A SER* 1.3 75.9 - - - +
280A THR* 1.3 73.9 + - - +
281A ASP* 4.2 7.5 + - - -
286A LYS* 3.6 5.6 - - - +
287A LYS* 2.8 69.8 + - + +
288A TYR 4.5 1.8 - - - -
289A PHE* 4.3 18.5 - + + -
365A GLU* 4.2 11.4 + - - +
383A VAL* 3.3 35.0 - - + +
384A PRO* 4.8 2.9 - - - +
385A GLU* 4.2 17.3 - - - -
423A PRO* 4.4 6.1 - - + -
920A ARG* 3.3 27.4 - - - +
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Residues in contact with THR 280 (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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279A TYR* 1.3 88.9 + - - +
281A ASP* 1.3 76.2 + - - +
284A ASN* 3.8 33.7 - - - +
285A GLU 3.6 5.8 - - - +
286A LYS* 5.0 6.2 - - - +
385A GLU* 4.1 6.1 - - - +
920A ARG* 4.8 3.2 + - - +
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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