Contacts of the helix formed by residues 273 - 285 (chain D) 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 GLN 273 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272D VAL* 1.3 83.6 - - - +
274D ARG* 1.3 72.2 + - - +
275D GLU* 3.5 3.8 - - + +
276D GLN* 3.3 23.5 + - + +
277D SER* 3.1 19.3 + - - -
438D SER 5.4 0.2 - - - -
441D ARG* 3.9 34.2 - - - +
473D GLU* 4.9 3.8 + - - -
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Residues in contact with ARG 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D GLN* 1.3 80.7 + - - +
275D GLU* 1.3 68.2 + - - +
277D SER* 3.2 12.8 + - - -
278D LEU* 3.3 25.2 + - + +
282D HIS* 4.5 4.4 + - - -
306D TYR 5.3 1.0 + - - -
307D LYS* 6.2 2.0 - - - +
441D ARG* 3.5 20.7 - - + +
442D VAL* 2.7 38.1 + - - +
445D GLY* 3.5 20.6 + - - -
446D THR* 3.8 12.7 - - - +
661F VAL* 3.1 20.6 - - - +
665F ASP* 3.1 40.9 + - - -
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Residues in contact with GLU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D GLN* 3.5 2.5 - - + +
274D ARG* 1.3 82.6 + - - +
276D GLN* 1.3 61.0 + - + +
278D LEU* 3.8 3.0 - - - -
279D HIS* 2.8 44.0 + - - +
282D HIS* 3.7 28.1 + - - +
306D TYR* 4.2 17.8 + - - -
307D LYS* 4.8 7.3 - - - -
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Residues in contact with GLN 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D THR* 3.1 23.5 + - - +
272D VAL* 3.2 28.2 - - + +
273D GLN* 3.3 29.0 + - + +
274D ARG 3.2 0.6 - - - -
275D GLU* 1.3 78.1 - - + +
277D SER* 1.3 65.2 + - - +
279D HIS* 3.5 16.6 - - - +
280D SER* 4.9 1.0 + - - -
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Residues in contact with SER 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D THR* 4.5 10.4 - - - +
264D ILE* 4.3 8.4 - - - +
272D VAL* 4.0 6.8 + - - +
273D GLN 3.1 12.0 + - - -
274D ARG 3.2 2.7 + - - -
276D GLN* 1.3 77.4 - - - +
278D LEU* 1.3 59.7 + - - +
280D SER* 4.9 1.0 + - - -
281D PHE* 4.1 2.3 - - - -
438D SER* 3.5 26.9 - - - -
442D VAL* 3.7 25.1 - - - +
610F GLU* 3.6 12.6 - - - +
658F LEU* 3.4 26.3 - - - +
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Residues in contact with LEU 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D ARG* 3.3 29.1 + - + +
275D GLU 3.8 0.7 - - - +
277D SER* 1.3 75.5 - - - +
279D HIS* 1.3 54.8 + - - +
280D SER 3.2 2.7 - - - -
281D PHE* 2.7 34.2 + - + -
282D HIS* 3.1 32.1 + - + +
442D VAL* 4.3 6.1 - - + -
658F LEU* 3.3 52.0 - - + +
661F VAL* 3.7 25.1 - - + -
662F SER* 4.1 5.8 - - - +
665F ASP* 3.8 15.0 - - - +
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Residues in contact with HIS 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D GLU* 3.6 36.2 + - - -
261D THR* 5.3 2.2 - - - +
275D GLU* 2.8 34.8 + - - +
276D GLN* 3.5 15.5 - - - +
277D SER 3.5 1.0 - - - -
278D LEU* 1.3 74.7 - - - +
280D SER* 1.3 69.4 + - - +
282D HIS* 4.2 1.7 - - - +
283D THR* 3.1 48.6 + - + +
605F ASP* 5.1 10.3 + - - -
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Residues in contact with SER 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D THR* 5.0 8.7 + - - -
276D GLN 4.9 0.7 + - - -
277D SER 4.9 1.1 + - - -
278D LEU 3.0 1.4 + - - -
279D HIS* 1.3 85.0 - - - +
281D PHE* 1.3 58.1 + - - +
283D THR* 3.9 5.1 - - - +
284D LEU* 3.2 28.4 - - - +
605F ASP 4.6 9.7 + - - -
606F VAL* 4.3 20.7 - - - +
607F ASN 4.8 0.2 + - - -
610F GLU* 2.7 32.6 + - - -
614F MET* 3.2 11.7 - - - +
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Residues in contact with PHE 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D SER 4.1 0.7 - - - -
278D LEU* 2.7 32.7 + - + +
280D SER* 1.3 73.1 - - - +
282D HIS* 1.3 59.5 - - - +
283D THR 3.3 0.2 - - - -
284D LEU 3.3 0.7 + - - -
285D PHE* 2.8 36.0 + - - +
292D TYR* 3.4 30.3 - + + -
610F GLU* 3.6 31.2 - - + -
613F VAL* 4.2 16.8 - - + -
614F MET* 4.2 9.2 - - + -
655F ASN* 4.1 6.3 - - + -
658F LEU* 3.5 37.2 - - + -
659F HIS* 4.0 21.3 - - + -
662F SER* 3.7 21.5 - - - +
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Residues in contact with HIS 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D ARG* 4.5 4.4 + - - -
275D GLU* 3.7 23.4 + - - +
278D LEU* 3.1 30.9 + - + +
279D HIS 4.2 2.7 - - - +
281D PHE* 1.3 79.9 - - - +
283D THR* 1.3 64.4 + - - +
284D LEU 3.1 0.9 + - - -
285D PHE 3.6 2.8 + - - +
301D ALA* 3.4 21.0 - - - +
306D TYR* 3.5 48.0 + + + +
662F SER* 4.0 13.4 - - - -
665F ASP* 3.1 38.2 + - + -
666F PHE* 3.5 19.7 - - - -
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Residues in contact with THR 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D HIS* 3.1 42.5 + - + +
280D SER* 3.9 10.5 - - - +
282D HIS* 1.3 80.6 - - - +
284D LEU* 1.3 72.3 + - + +
285D PHE 4.8 0.5 - - - +
300D HIS* 3.3 40.0 + - + +
301D ALA* 4.3 7.3 + - - -
306D TYR* 5.5 1.8 - - - -
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Residues in contact with LEU 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D SER* 3.2 22.4 - - - +
281D PHE 3.3 0.8 + - - +
282D HIS 3.1 0.6 - - - -
283D THR* 1.3 87.5 - - + +
285D PHE* 1.3 61.1 + - - +
286D CYS* 5.3 0.2 - - - +
292D TYR* 3.4 17.4 - - + -
293D ASP* 2.8 59.8 + - + +
300D HIS* 5.4 1.1 - - - -
600F ILE* 4.7 2.2 - - + -
603F PHE* 4.3 26.2 - - + -
605F ASP* 5.9 0.2 - - - +
606F VAL* 4.4 21.1 - - + -
614F MET* 4.0 12.6 - - + -
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Residues in contact with PHE 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D PHE 2.8 18.5 + - - +
282D HIS 3.6 7.5 + - - +
283D THR 4.8 1.4 - - - +
284D LEU* 1.3 78.1 - - - +
286D CYS* 1.3 71.5 + - - +
287D ARG* 3.8 4.3 + - - -
290D PHE* 3.4 39.3 - - + -
291D LYS 3.8 5.6 - - - -
292D TYR* 3.5 30.9 - + + +
300D HIS 5.6 0.2 - - - -
301D ALA* 4.7 8.8 + - - +
617F TRP* 3.9 7.2 - - - -
662F SER* 4.6 1.6 - - - +
663F MET* 3.3 30.7 - - - -
666F PHE* 3.5 45.0 - + + -
668F LEU* 3.8 19.7 - - + -
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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