Contacts of the helix formed by residues 278 - 285 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274G ARG* 3.0 34.8 + - + +
275G GLU* 3.8 2.9 - - - +
277G SER* 1.3 73.9 - - - +
279G HIS* 1.3 63.3 + - - +
280G SER 3.4 2.7 - - - -
281G PHE* 3.2 10.8 + - + +
282G HIS* 3.0 53.3 + - + +
442G VAL* 4.2 10.8 - - + -
658I LEU* 3.4 48.9 - - + +
661I VAL* 3.6 25.1 - - + -
662I SER* 4.2 7.6 - - - +
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Residues in contact with HIS 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259G GLU 5.5 7.0 - - - -
275G GLU* 3.2 24.4 + - - +
276G GLN* 3.5 16.4 - - - +
277G SER 3.4 3.2 - - - -
278G LEU* 1.3 76.7 - - - +
280G SER* 1.3 65.8 + - - +
282G HIS* 4.2 1.7 - - - +
283G THR* 2.9 53.5 + - + +
605I ASP* 6.0 4.0 - - - -
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Residues in contact with SER 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G GLN 4.9 0.6 + - - -
277G SER 4.8 1.2 + - - -
278G LEU 3.4 0.4 - - - -
279G HIS* 1.3 82.4 - - - +
281G PHE* 1.3 66.1 - - - +
283G THR* 3.4 5.5 - - - +
284G LEU* 3.1 32.1 + - - +
605I ASP* 4.4 6.8 + - - -
606I VAL* 3.9 17.9 - - - +
610I GLU* 2.7 32.2 + - - -
614I MET* 3.8 17.2 - - - +
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Residues in contact with PHE 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G SER 4.3 2.0 - - - -
278G LEU* 3.2 20.4 + - + +
280G SER* 1.3 74.4 - - - +
282G HIS* 1.3 68.6 + - - +
285G PHE* 3.1 30.3 + - - +
292G TYR* 3.4 32.1 - + - +
610I GLU* 3.8 34.8 - - + -
613I VAL* 4.1 16.8 - - + -
614I MET* 4.3 5.8 - - + -
655I ASN* 3.8 15.9 - - + -
658I LEU* 3.7 24.5 - - + -
659I HIS* 3.6 28.9 - - + -
662I SER* 3.6 20.9 - - - +
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Residues in contact with HIS 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G ARG* 4.4 4.9 + - - -
275G GLU* 3.3 24.4 + - - +
278G LEU* 3.0 42.0 + - + +
279G HIS* 4.2 2.9 - - - +
281G PHE* 1.3 78.4 - - - +
283G THR* 1.3 62.0 + - - +
285G PHE 4.2 1.9 - - - +
301G ALA* 3.4 20.1 - - - +
306G TYR* 3.2 42.3 - + + +
662I SER* 4.1 9.1 - - - -
665I ASP* 3.1 42.2 + - + -
666I PHE* 3.4 19.8 - - - -
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Residues in contact with THR 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G HIS* 2.9 49.6 + - + +
280G SER* 3.4 9.0 - - - +
282G HIS* 1.3 80.5 - - - +
284G LEU* 1.3 70.5 + - + +
285G PHE 4.3 0.9 - - - +
300G HIS* 3.6 36.1 + - + +
301G ALA* 3.9 9.1 + - - +
306G TYR* 5.5 1.6 - - - -
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Residues in contact with LEU 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G SER* 3.1 18.5 + - - +
283G THR* 1.3 84.4 - - + +
285G PHE* 1.3 65.0 + - - +
286G CYS* 3.8 1.0 + - - +
292G TYR* 3.6 16.6 - - + -
293G ASP* 3.2 57.0 + - + +
300G HIS* 5.2 4.0 - - - -
600I ILE* 4.8 2.2 - - + -
603I PHE* 3.8 42.2 - - + -
606I VAL* 4.4 13.5 - - + -
614I MET* 3.8 18.2 - - + -
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Residues in contact with PHE 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G PHE 3.1 18.8 + - - +
282G HIS 4.2 7.1 - - - +
283G THR 3.8 3.1 - - - +
284G LEU* 1.3 78.1 - - - +
286G CYS* 1.3 80.1 + - - +
287G ARG* 4.0 4.5 + - - -
290G PHE* 3.8 28.0 - - - -
291G LYS 4.5 1.6 - - - -
292G TYR* 3.5 40.3 - + + +
300G HIS* 5.4 0.9 - - - -
301G ALA* 4.8 8.5 + - - +
617I TRP* 4.2 5.8 - - - -
662I SER* 4.6 1.3 - - - +
663I MET* 3.6 28.0 - - - -
666I PHE* 3.5 43.2 - + + -
668I LEU* 3.6 23.8 - - + -
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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