Contacts of the helix formed by residues 330 - 344 (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 GLY 330 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329G GLU* 1.3 73.4 - - - +
331G ALA* 1.3 67.8 + - - +
332G LYS 3.7 0.4 - - - -
333G GLU* 3.8 11.7 + - - +
334G PHE* 3.1 37.4 + - - -
422G PRO* 3.7 9.2 - - - +
423G ASN* 4.5 1.6 - - - -
467G TYR* 2.7 23.2 + - - -
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Residues in contact with ALA 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318G LYS* 4.0 5.4 - - - +
325G TYR* 3.0 48.5 - - - +
326G GLN* 3.8 15.7 - - - -
327G HIS* 4.0 8.5 - - - +
328G LEU 3.0 18.6 + - - +
330G GLY* 1.3 81.4 - - - +
332G LYS* 1.3 61.7 + - - +
335G ALA* 3.8 4.9 - - - +
467G TYR* 4.1 6.0 - - - -
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Residues in contact with LYS 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315G LEU 4.5 3.7 + - - -
316G ASP* 2.6 53.5 + - - +
317G ASN* 3.8 7.5 + - - +
318G LYS* 4.2 22.5 - - + +
325G TYR* 3.8 24.9 + - - +
331G ALA* 1.3 79.3 - - - +
333G GLU* 1.3 64.1 + - + +
334G PHE 3.6 0.2 - - - -
335G ALA* 3.9 2.8 - - - +
336G ALA* 3.1 28.5 + - + +
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Residues in contact with GLU 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G GLU* 5.1 10.4 - - - +
330G GLY 3.8 15.0 + - - +
331G ALA 3.4 0.8 - - - +
332G LYS* 1.3 83.9 - - + +
334G PHE* 1.3 55.1 + - - +
336G ALA* 3.6 7.1 - - - +
337G ALA* 2.8 30.5 + - - +
422G PRO* 5.5 4.7 - - + -
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Residues in contact with PHE 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330G GLY* 3.1 29.7 + - - +
333G GLU* 1.3 74.1 - - - +
335G ALA* 1.3 56.2 + - - +
336G ALA 3.2 0.9 - - - -
337G ALA* 3.4 8.1 - - + -
338G LEU* 2.6 63.3 + - + +
341G GLU* 4.0 17.9 - - - -
422G PRO* 3.7 34.8 - - + -
423G ASN* 4.4 19.5 - - + +
467G TYR* 3.6 12.8 - - - +
471G VAL* 4.5 10.8 - - + -
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Residues in contact with ALA 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325G TYR* 4.0 6.3 - - + +
330G GLY 3.7 3.8 + - - -
331G ALA 3.8 15.5 - - - +
332G LYS 3.9 4.9 - - - +
334G PHE* 1.3 79.0 - - - +
336G ALA* 1.3 59.3 + - - +
338G LEU* 4.1 5.4 - - - +
339G THR* 3.5 13.9 + - - -
449G ASP* 3.4 24.4 - - + +
451G PHE* 3.9 31.0 - - + -
467G TYR* 4.1 9.3 + - + -
470G ARG* 4.7 2.2 + - - +
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Residues in contact with ALA 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332G LYS* 3.1 18.1 + - + +
333G GLU* 3.6 9.4 - - - +
334G PHE 3.2 0.2 - - - -
335G ALA* 1.3 76.7 - - - +
337G ALA* 1.3 60.4 + - - +
339G THR* 5.0 1.0 - - - -
340G ALA* 3.1 27.5 + - - +
449G ASP* 5.3 0.7 - - - -
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Residues in contact with ALA 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333G GLU 2.8 21.0 + - - +
334G PHE* 3.2 19.7 + - + +
336G ALA* 1.3 74.2 - - - +
338G LEU* 1.3 53.0 + - - +
340G ALA* 3.3 5.1 + - - +
341G GLU* 2.5 53.0 + - + +
422G PRO* 5.5 2.9 - - + -
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Residues in contact with LEU 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334G PHE* 2.6 51.5 + - + +
335G ALA* 3.5 5.1 + - - +
336G ALA 3.5 0.4 - - - -
337G ALA* 1.3 73.6 - - - +
339G THR* 1.3 52.9 + - - +
341G GLU* 3.2 17.7 + - + +
342G ARG* 2.6 35.7 + - - +
467G TYR* 5.9 0.4 - - + -
470G ARG* 3.5 24.6 + - + +
471G VAL* 4.6 9.9 - - + -
474G SER* 3.4 39.0 - - - +
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Residues in contact with THR 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335G ALA 3.5 5.3 + - - -
336G ALA* 5.0 1.6 - - - -
337G ALA 3.5 0.2 - - - -
338G LEU* 1.3 73.0 - - - +
340G ALA* 1.3 57.1 + - - +
342G ARG* 3.7 10.3 - - + -
343G ILE* 2.8 37.4 + - + +
448G TYR* 5.7 10.5 - - + -
449G ASP* 2.4 32.2 + - - +
470G ARG* 2.9 18.3 + - - +
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Residues in contact with ALA 340 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336G ALA 3.1 21.4 + - - +
337G ALA* 3.3 5.1 + - - +
339G THR* 1.3 76.8 - - - +
341G GLU* 1.3 61.4 + - - +
343G ILE* 3.2 23.6 - - + +
344G LYS* 3.5 20.3 - - - +
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Residues in contact with GLU 341 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334G PHE* 4.0 15.9 - - - -
337G ALA* 2.5 44.8 + - + +
338G LEU* 3.3 19.8 + - + +
340G ALA* 1.3 71.4 - - - +
342G ARG* 1.3 63.4 - - - +
344G LYS* 3.6 26.3 + - + +
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Residues in contact with ARG 342 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338G LEU* 2.6 22.4 + - - +
339G THR* 3.3 15.0 + - + +
341G GLU* 1.3 75.2 - - - +
343G ILE* 1.3 63.6 + - - +
344G LYS 3.1 8.3 + - - +
345G THR* 4.8 2.3 + - - -
470G ARG* 5.0 13.2 - - - +
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Residues in contact with ILE 343 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310G ASN* 5.5 9.4 - - - +
339G THR* 2.8 22.3 + - + +
340G ALA* 3.2 25.8 - - + +
342G ARG* 1.3 72.8 - - - +
344G LYS* 1.3 63.3 + - + +
345G THR* 3.4 9.7 + - - -
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Residues in contact with LYS 344 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340G ALA* 3.5 18.6 - - - +
341G GLU* 3.6 19.8 + - + +
342G ARG 3.1 9.5 + - - +
343G ILE* 1.3 78.4 - - + +
345G THR* 1.3 61.9 + - - +
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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