Contacts of the strand formed by residues 286 - 293 (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 LYS 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B SER* 3.7 19.5 + - - +
279B TYR 3.4 14.1 - - - +
280B THR* 4.1 9.2 - - + +
284B ASN 4.3 0.8 + - - +
285B GLU* 1.3 74.0 - - - +
287B LYS* 1.3 67.4 + - - +
288B TYR* 2.7 48.3 + - + -
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Residues in contact with LYS 287 (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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278B SER* 3.2 5.2 - - - -
279B TYR* 3.0 64.1 + - + +
281B ASP* 3.7 28.9 + - + +
285B GLU* 3.5 17.2 + - + +
286B LYS* 1.3 81.7 - - - +
288B TYR* 1.3 64.3 + - - +
365B GLU* 2.9 43.1 + - + +
384B PRO* 5.7 6.3 - - - +
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Residues in contact with TYR 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 3.9 32.3 - - + +
186B THR* 5.0 25.3 + - + +
188B MET* 4.5 7.4 - - + -
277B PHE 3.7 4.5 - - - -
278B SER* 3.5 24.7 - - - -
279B TYR* 5.0 0.5 - - - -
286B LYS* 2.7 44.8 + - + -
287B LYS* 1.3 78.4 - - - +
289B PHE* 1.3 69.7 + - - +
325B TYR* 3.6 37.4 + - - +
364B GLY* 4.1 3.8 - - - -
365B GLU* 4.5 4.2 + - - +
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Residues in contact with PHE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 3.8 4.1 - - - +
188B MET* 4.8 1.4 - - - +
276B GLY* 3.2 2.4 - - - -
277B PHE* 2.8 77.0 + + + +
279B TYR* 4.6 9.6 - + + -
288B TYR* 1.3 80.2 - - - +
290B ALA* 1.3 73.8 + - - +
291B ALA* 4.4 0.4 - - + -
362B ILE* 3.4 32.8 - - + -
363B VAL 3.7 4.5 - - - -
364B GLY* 4.2 9.2 - - - -
365B GLU 4.6 3.6 - - - -
366B MET* 3.7 31.9 - - + -
383B VAL* 4.3 20.9 - - + -
420B VAL* 4.9 0.7 - - + -
421B ALA 5.7 0.7 - - - -
422B ILE* 3.6 24.7 - - + -
423B PRO* 4.5 5.6 - - + -
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Residues in contact with ALA 290 (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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185B LEU* 4.2 20.6 - - + -
188B MET* 6.2 0.4 - - + -
267B ILE* 4.7 6.3 - - + -
274B PHE* 3.7 25.4 - - + -
275B TYR 3.3 9.6 - - - +
276B GLY* 4.3 4.3 - - - -
277B PHE* 5.1 0.2 - - - -
289B PHE* 1.3 78.4 - - - +
291B ALA* 1.3 63.3 + - - +
362B ILE* 3.5 4.9 - - - +
363B VAL* 2.9 37.0 + - + +
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Residues in contact with ALA 291 (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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274B PHE* 3.3 6.5 - - - -
275B TYR* 3.0 50.5 + - + +
277B PHE* 5.3 1.1 - - + -
289B PHE* 4.4 3.3 - - + -
290B ALA* 1.3 75.7 - - - +
292B THR* 1.3 67.7 + - - +
361B PHE 3.6 8.7 - - - -
362B ILE* 3.7 18.8 - - + -
422B ILE* 4.2 17.9 - - + -
425B PHE* 6.1 1.1 - - + -
437B THR* 5.8 1.8 - - + -
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Residues in contact with THR 292 (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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273B GLY 3.5 2.7 - - - -
274B PHE* 4.0 4.5 - - + -
275B TYR* 4.4 3.6 - - - -
291B ALA* 1.3 83.0 - - - +
293B GLN* 1.3 64.5 + - - +
294B PHE* 3.8 24.2 - - + -
360B ALA* 3.1 30.8 - - - +
361B PHE* 3.2 50.2 + - + +
362B ILE* 4.9 1.3 - - - +
425B PHE* 4.7 7.6 - - - -
432B ASN* 4.6 11.0 + - - -
437B THR* 4.8 4.7 + - - +
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Residues in contact with GLN 293 (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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271B TYR 3.7 23.1 - - - +
272B TYR* 3.6 8.8 - - + -
273B GLY* 2.9 34.3 + - - -
275B TYR* 4.3 5.1 - - + -
292B THR* 1.3 75.1 - - - +
294B PHE* 1.3 59.9 + - - +
295B GLU* 2.8 46.1 + - - +
298B ALA* 3.4 4.3 - - - +
425B PHE* 3.9 16.2 - - + -
427B ALA* 4.9 7.1 - - + +
430B MET* 3.3 36.7 - - - +
432B ASN* 5.8 0.4 - - - -
1127B 7O2 4.3 10.7 - - - +
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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