Contacts of the helix formed by residues 278 - 285 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ARG* 3.0 34.3 + - - +
275A GLU 3.6 2.0 - - - +
277A SER* 1.3 76.0 - - - +
279A HIS* 1.3 62.5 + - - +
280A SER 3.2 3.1 - - - -
281A PHE* 3.0 21.2 + - + -
282A HIS* 3.2 47.9 + - + +
442A VAL* 4.2 9.6 - - + -
658C LEU* 3.3 48.2 - - + +
661C VAL* 3.7 24.7 - - + -
662C SER* 4.4 4.9 - - - +
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Residues in contact with HIS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLU* 4.6 23.1 - - + +
275A GLU* 2.8 33.5 + - - +
276A GLN* 3.3 18.3 + - - +
278A LEU* 1.3 73.1 - - - +
280A SER* 1.3 64.3 + - - +
282A HIS* 4.6 0.8 - - - +
283A THR* 3.0 52.1 + - + +
605C ASP* 5.3 8.5 + - - -
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A THR* 5.6 4.7 + - - -
276A GLN 4.7 2.1 + - - -
278A LEU 3.2 0.4 - - - -
279A HIS* 1.3 83.9 - - - +
281A PHE* 1.3 61.1 + - - +
283A THR* 3.4 9.1 - - - +
284A LEU* 3.2 27.1 - - - +
605C ASP 4.7 4.0 + - - -
606C VAL* 4.5 15.6 - - - +
610C GLU* 2.6 41.3 + - - -
614C MET* 3.5 11.9 - - - +
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Residues in contact with PHE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A SER 4.4 2.9 - - - -
278A LEU* 3.0 21.0 + - + +
280A SER* 1.3 76.0 - - - +
282A HIS* 1.3 62.2 + - - +
285A PHE* 2.9 36.2 + - - +
292A TYR* 3.5 26.0 - + + -
610C GLU* 3.6 40.6 - - + -
613C VAL* 4.1 17.5 - - + -
614C MET* 4.0 13.5 - - + -
655C ASN* 3.6 18.4 - - + -
658C LEU* 3.8 17.3 - - + -
659C HIS* 3.8 26.5 - - + -
662C SER* 3.7 21.3 - - - +
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Residues in contact with HIS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG* 4.4 3.0 + - - -
275A GLU* 3.5 29.2 + - - +
278A LEU* 3.2 42.0 + - + +
279A HIS 4.6 1.1 - - - +
281A PHE* 1.3 77.7 - - - +
283A THR* 1.3 63.5 + - - +
284A LEU 3.2 1.0 + - - -
285A PHE 3.8 3.3 + - - +
301A ALA* 3.6 12.1 - - - +
306A TYR* 3.4 40.7 + + + +
662C SER* 3.8 21.6 + - - -
665C ASP* 3.2 29.1 + - + -
666C PHE* 3.5 26.3 - - - -
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Residues in contact with THR 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A HIS* 3.0 43.8 + - + +
280A SER* 3.4 12.6 - - - +
282A HIS* 1.3 79.6 - - - +
284A LEU* 1.3 69.8 + - + +
285A PHE 3.9 1.0 - - - +
300A HIS* 3.3 34.9 + - - +
301A ALA* 4.7 5.2 + - - -
306A TYR* 5.6 2.2 - - - -
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Residues in contact with LEU 284 (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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280A SER 3.2 17.5 - - - +
281A PHE 3.4 0.8 + - - -
282A HIS 3.2 0.2 - - - -
283A THR* 1.3 89.2 - - + +
285A PHE* 1.3 62.2 + - - +
286A CYS 3.7 0.2 + - - -
292A TYR* 3.3 14.2 - - + -
293A ASP* 3.0 53.7 + - + +
300A HIS* 5.4 2.2 - - + -
600C ILE* 4.6 2.7 - - + -
603C PHE* 3.9 28.5 - - + -
605C ASP* 5.7 0.2 - - - +
606C VAL* 3.9 28.3 - - + -
614C MET* 4.2 17.0 - - + -
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Residues in contact with PHE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE 2.9 19.5 + - - +
282A HIS 3.8 7.5 + - - +
283A THR 5.0 0.7 - - - +
284A LEU* 1.3 76.5 - - - +
286A CYS* 1.3 82.0 + - - +
287A ARG* 3.9 3.3 + - - -
290A PHE* 3.5 32.8 - - + -
291A LYS 3.8 4.7 - - - -
292A TYR* 3.5 30.9 - + + -
300A HIS 5.5 0.9 - - - -
301A ALA* 5.0 7.8 + - - +
617C TRP* 4.1 6.3 - - - -
662C SER* 4.5 1.8 - - - +
663C MET* 3.3 33.9 - - + -
666C PHE* 3.5 43.8 - + + -
668C LEU* 3.8 20.4 - - + -
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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