Contacts of the helix formed by residues 346 - 367 (chain J) in PDB entry 5LK5
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 THR 346 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J GLN* 3.7 17.3 - - - +
94J GLN* 5.3 0.2 + - - -
96J THR* 4.9 0.2 - - - +
171J LEU* 4.8 4.0 - - - +
329J ASN* 3.4 40.0 - - - +
342J PHE* 2.7 40.6 + - + +
343J GLY* 3.3 7.5 + - - -
345J GLU* 1.3 81.6 - - + +
347J TRP* 1.3 72.7 + - - +
349J VAL* 3.0 11.7 + - - +
350J THR* 2.9 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 347 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344G ASN* 5.6 1.8 - - - -
96J THR* 4.0 20.1 - - + +
169J THR* 3.3 35.0 + - + -
170J HIS* 4.7 0.4 + - - -
171J LEU* 3.9 27.4 - - + -
187J ASP* 3.4 53.4 + - + -
188J ASN* 4.4 3.1 - - + -
343J GLY 3.1 11.3 + - - +
344J ASN* 4.0 15.9 - - - -
346J THR* 1.3 78.8 + - - +
348J GLY* 1.3 80.4 + - - +
350J THR* 3.2 10.0 - - - +
351J LYS* 3.0 64.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 348 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340G GLU* 5.3 1.6 - - - +
341G GLU* 4.5 5.4 + - - -
344G ASN* 2.8 32.1 + - - +
343J GLY 3.1 11.6 + - - -
344J ASN* 3.4 17.5 + - - -
346J THR 3.2 0.2 - - - -
347J TRP* 1.3 92.1 - - - +
349J VAL* 1.3 59.7 + - - +
351J LYS* 4.3 9.5 - - - +
352J ALA 5.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 349 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341G GLU* 3.6 42.6 - - + +
345G GLU* 3.6 37.9 - - + +
58J GLY* 5.5 0.9 - - - -
62J LYS* 4.2 24.0 - - + +
344J ASN 3.6 12.0 + - - +
345J GLU 3.4 20.4 - - - +
346J THR 3.0 7.9 + - - +
348J GLY* 1.3 79.1 - - - +
350J THR* 1.3 63.5 + - - +
351J LYS 3.5 0.2 - - - -
352J ALA 5.0 1.6 + - - -
353J ALA* 5.1 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 350 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J GLY* 3.8 5.9 - - - -
63J ASP* 3.2 37.1 + - - +
169J THR* 4.1 15.3 + - + -
329J ASN* 5.5 3.4 - - - +
346J THR 2.9 20.9 + - - +
347J TRP* 3.2 19.5 - - - +
349J VAL* 1.3 76.4 - - - +
351J LYS* 1.3 62.3 + - - +
352J ALA 3.4 0.9 + - - -
353J ALA 3.6 2.1 + - - -
354J GLU* 3.1 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 351 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G ASN 5.9 0.2 + - - -
340G GLU* 2.8 27.8 + - - +
344G ASN* 4.9 4.3 - - - +
168J PHE* 5.7 0.3 - - - -
169J THR* 6.1 1.1 - - - -
347J TRP* 3.0 60.1 + - + +
348J GLY* 4.4 11.0 - - - +
349J VAL 3.5 1.0 - - - -
350J THR* 1.3 77.9 - - - +
352J ALA* 1.3 64.0 + - - +
354J GLU* 3.6 8.3 - - - +
355J LYS* 3.2 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 352 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337G ALA* 4.2 25.5 - - + +
340G GLU* 3.3 35.4 - - + +
341G GLU* 5.6 1.3 - - - +
348J GLY 5.4 1.0 + - - -
349J VAL 5.0 1.4 + - - -
350J THR 3.6 0.6 - - - -
351J LYS* 1.3 77.8 - - - +
353J ALA* 1.3 61.4 + - - +
355J LYS* 3.4 7.2 + - - +
356J GLN* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337G ALA* 4.3 10.4 - - + +
341G GLU* 4.2 17.8 + - - +
57J TYR 3.9 0.4 - - - +
58J GLY* 3.7 27.8 - - - +
349J VAL 5.1 1.5 + - - +
350J THR 3.6 3.1 + - - +
351J LYS 3.5 0.2 - - - -
352J ALA* 1.3 75.3 - - - +
354J GLU* 1.3 65.8 + - - +
356J GLN* 3.3 9.7 + - - +
357J MET* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 354 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J PHE* 3.8 19.3 - - + -
57J TYR* 3.6 16.5 - - - -
58J GLY* 3.5 8.3 - - - +
63J ASP* 5.6 1.9 - - - +
98J LYS* 2.9 21.1 + - - +
168J PHE* 3.5 14.8 - - + +
169J THR* 2.5 50.8 + - - +
350J THR* 3.1 26.7 + - - +
351J LYS* 3.6 7.8 - - - +
353J ALA* 1.3 78.1 - - - +
355J LYS* 1.3 61.9 + - - +
357J MET* 3.4 2.1 + - - +
358J LYS* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 355 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168J PHE* 3.7 42.2 - - + -
351J LYS 3.2 13.9 + - - +
352J ALA* 3.6 7.4 - - - +
354J GLU* 1.3 79.3 - - - +
356J GLN* 1.3 57.4 + - - +
358J LYS* 3.4 0.7 + - - +
359J ASP* 2.9 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 356 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335G ASP* 4.4 8.0 + - - +
336G GLU* 5.8 1.0 - - - +
337G ALA* 3.3 28.5 + - - +
352J ALA 3.0 16.3 + - - +
353J ALA* 3.3 6.3 + - - +
355J LYS* 1.3 75.2 - - - +
357J MET* 1.3 65.4 + - - +
359J ASP* 3.5 7.9 + - - +
360J LYS* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 357 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J LYS 3.5 11.4 - - - +
56J PHE* 4.0 7.2 - - + -
57J TYR* 3.5 57.4 - - + +
353J ALA 2.9 16.5 + - - +
354J GLU 3.9 3.4 - - - +
356J GLN* 1.3 76.3 - - - +
358J LYS* 1.3 62.0 + - - +
360J LYS* 3.4 24.8 + - - +
361J GLN* 3.1 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 358 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J PHE* 3.7 41.6 - - + +
100J GLU 5.2 3.0 + - - -
102J ASN* 5.3 4.4 + - - -
167J GLU* 3.0 27.3 + - - +
168J PHE* 3.7 30.3 - - + -
354J GLU 3.0 16.9 + - - +
355J LYS 3.9 0.4 - - - +
357J MET* 1.3 75.9 - - - +
359J ASP* 1.3 66.7 + - - +
361J GLN* 3.2 9.1 + - + +
362J ASP* 2.9 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 359 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168J PHE* 4.9 3.3 - - - -
355J LYS* 2.9 55.4 + - - +
356J GLN* 3.8 7.4 - - - +
358J LYS* 1.3 75.2 - - - +
360J LYS* 1.3 57.7 + - - +
362J ASP* 3.3 11.7 + - - +
363J GLU* 3.0 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 360 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356J GLN 3.2 10.2 + - - +
357J MET* 3.5 29.5 + - - +
359J ASP* 1.3 77.1 - - - +
361J GLN* 1.3 77.8 + - - +
363J GLU* 3.4 6.8 + - - +
364J GLU* 3.1 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 361 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J LYS* 3.0 32.5 + - - +
56J PHE* 3.7 23.9 - - - +
357J MET* 3.1 32.7 + - - +
358J LYS* 3.7 10.7 + - + +
360J LYS* 1.3 88.8 - - - +
362J ASP* 1.3 59.0 + - - +
364J GLU* 3.4 7.6 + - - +
365J GLN* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 362 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167J GLU* 4.4 3.5 - - - +
168J PHE* 5.8 0.3 - - - -
358J LYS* 2.9 52.4 + - - +
359J ASP* 3.6 11.6 - - - +
361J GLN* 1.3 73.7 - - - +
363J GLU* 1.3 67.1 + - - +
365J GLN* 3.3 8.6 + - - +
366J ARG* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 363 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359J ASP 3.0 15.4 + - - +
360J LYS* 3.6 10.1 - - - +
362J ASP* 1.3 76.9 - - + +
364J GLU* 1.3 66.0 + - + +
366J ARG* 2.9 54.8 + - - +
367J LEU* 3.4 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 364 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360J LYS* 3.1 35.8 + - + +
361J GLN* 3.9 6.5 - - - +
362J ASP 3.4 0.2 - - - -
363J GLU* 1.3 75.4 - - - +
365J GLN* 1.3 66.2 + - - +
367J LEU* 3.1 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 365 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361J GLN 3.0 14.5 + - - +
362J ASP* 3.4 13.0 - - - +
364J GLU* 1.3 76.8 - - - +
366J ARG* 1.3 62.4 + - - +
367J LEU 3.2 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 366 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362J ASP 3.1 12.5 + - - +
363J GLU* 2.9 41.1 + - - +
365J GLN* 1.3 76.7 - - - +
367J LEU* 1.3 88.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 367 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363J GLU* 3.5 25.8 - - + +
364J GLU* 3.1 26.1 + - - +
365J GLN 3.5 10.2 - - - +
366J ARG* 1.3 108.9 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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