Contacts of the helix formed by residues 278 - 285 (chain J) in PDB entry 5LS6
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 LEU 278 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274J ARG* 3.4 34.2 + - - +
275J GLU 3.5 4.0 - - - +
276J GLN 3.3 0.4 - - - -
277J SER* 1.3 76.4 - - - +
279J HIS* 1.3 56.4 + - - +
280J SER 3.5 1.6 - - - -
281J PHE* 3.9 8.7 - - + -
282J HIS* 3.0 53.2 + - + +
442J VAL* 4.0 12.8 - - + -
658L LEU* 3.1 49.8 - - + +
661L VAL* 3.4 26.5 - - + -
662L SER* 4.2 8.7 - - - +
665L ASP* 3.8 0.4 - - - +
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Residues in contact with HIS 279 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259J GLU* 5.4 11.7 + - + +
261J THR* 5.6 0.7 - - - +
275J GLU* 3.1 21.9 + - - +
276J GLN* 3.2 22.1 + - + +
277J SER 3.4 0.4 - - - -
278J LEU* 1.3 74.2 - - - +
280J SER* 1.3 59.4 + - - +
282J HIS* 4.9 2.2 - - - -
283J THR* 2.8 67.6 + - + +
605L ASP 6.1 1.1 - - - -
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Residues in contact with SER 280 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276J GLN 4.8 0.6 + - - -
277J SER 4.9 0.8 + - - -
278J LEU* 3.5 0.4 - - - +
279J HIS* 1.3 81.8 - - - +
281J PHE* 1.3 63.7 + - - +
283J THR* 3.9 6.7 - - - -
284J LEU* 3.0 33.4 + - - +
605L ASP 4.3 9.7 + - - -
606L VAL* 3.9 12.0 - - - +
610L GLU* 2.8 33.9 + - - -
614L MET* 3.6 19.1 - - - +
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Residues in contact with PHE 281 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277J SER 4.4 9.4 - - - -
278J LEU* 3.6 12.5 + - + +
279J HIS 3.2 0.4 - - - -
280J SER* 1.3 79.9 - - - +
282J HIS* 1.3 65.6 + - - +
285J PHE* 3.1 30.5 + - - +
292J TYR* 3.3 31.6 - + + -
610L GLU* 3.7 35.2 - - + -
613L VAL* 4.0 20.6 - - + -
614L MET* 5.1 5.2 - - + -
655L ASN* 3.6 16.6 - - - -
658L LEU* 4.1 14.4 - - + -
659L HIS* 3.5 33.4 - - + -
662L SER* 3.4 20.4 - - - +
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Residues in contact with HIS 282 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274J ARG* 4.1 6.7 + - - -
275J GLU* 3.8 21.3 - - - +
278J LEU* 3.0 40.9 + - + +
279J HIS* 4.3 1.3 - - - +
281J PHE* 1.3 77.7 - - - +
283J THR* 1.3 64.0 + - - +
284J LEU 3.3 0.7 + - - -
285J PHE 4.3 1.2 + - - +
301J ALA* 3.7 13.0 - - - +
306J TYR* 3.5 46.3 + + + +
662L SER* 3.4 18.3 + - - -
665L ASP* 3.2 41.9 + - + -
666L PHE* 3.5 19.9 - - - -
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Residues in contact with THR 283 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279J HIS* 2.8 52.5 + - + +
280J SER* 3.5 11.2 - - - +
282J HIS* 1.3 78.7 - - - +
284J LEU* 1.3 71.1 + - + +
285J PHE 4.6 0.4 - - - +
300J HIS* 3.1 40.8 + - + +
301J ALA* 4.4 3.4 + - - -
306J TYR* 5.6 2.0 - - - -
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Residues in contact with LEU 284 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280J SER* 3.0 17.4 + - - +
282J HIS 3.2 0.2 - - - -
283J THR* 1.3 84.6 - - + +
285J PHE* 1.3 69.1 + - - +
286J CYS* 5.0 0.9 - - - +
292J TYR* 3.8 13.7 - - + -
293J ASP* 3.3 58.8 + - + +
300J HIS* 4.9 6.6 + - + +
600L ILE* 4.9 1.8 - - + -
603L PHE* 4.6 26.2 - - + -
605L ASP* 5.8 0.7 - - - +
606L VAL* 4.5 17.3 - - + -
614L MET* 4.0 24.9 - - + -
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Residues in contact with PHE 285 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281J PHE 3.1 19.0 + - - +
282J HIS 4.6 3.8 - - - +
283J THR 4.6 2.6 - - - +
284J LEU* 1.3 83.8 + - - +
286J CYS* 1.3 89.0 + - - +
287J ARG* 3.8 3.1 + - - -
290J PHE* 3.3 27.8 - - - -
291J LYS 4.7 0.2 - - - -
292J TYR* 3.6 38.7 - + + +
300J HIS* 5.2 2.1 - - - -
301J ALA* 4.6 10.0 + - - +
617L TRP* 4.3 4.0 - - - -
662L SER* 4.8 1.1 - - - +
663L MET* 3.3 32.5 - - + -
666L PHE* 3.5 43.3 - + + -
668L LEU* 3.4 23.6 - - + -
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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