Contacts of the helix formed by residues 346 - 367 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D GLN* 3.7 17.0 - - - +
96D THR* 4.9 0.2 - - - +
171D LEU* 4.7 4.0 - - - +
329D ASN* 3.4 41.6 - - - +
342D PHE* 2.7 40.5 + - + +
343D GLY* 3.3 7.1 + - - -
345D GLU* 1.3 82.5 - - + +
347D TRP* 1.3 73.3 + - - +
348D GLY 3.1 0.4 - - - -
349D VAL* 3.0 5.4 + - - +
350D THR* 3.0 26.2 + - - -
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Residues in contact with TRP 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D THR* 4.0 16.1 - - + +
169D THR* 3.3 36.5 + - + -
170D HIS* 4.7 0.6 + - - -
171D LEU* 3.9 39.0 - - + -
187D ASP* 3.4 50.4 + - + -
188D ASN* 4.3 2.9 - - + -
329D ASN* 5.5 0.2 - - - +
343D GLY 3.0 11.1 + - - +
344D ASN* 4.1 16.2 - - - -
346D THR* 1.3 79.1 + - - +
348D GLY* 1.3 74.2 + - - +
350D THR* 3.1 7.8 + - - -
351D LYS* 3.0 69.6 + - + +
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Residues in contact with GLY 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D GLY 3.0 10.0 + - - -
344D ASN* 3.4 19.3 + - - -
346D THR 3.1 0.4 - - - -
347D TRP* 1.3 95.0 - - - +
349D VAL* 1.3 58.1 + - - +
351D LYS* 4.3 12.7 - - - +
352D ALA* 5.3 1.4 + - - +
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Residues in contact with VAL 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D GLY* 5.4 0.9 - - - -
59D ASP* 6.5 0.2 - - + -
62D LYS* 4.2 27.1 - - + +
344D ASN 3.6 11.4 - - - +
345D GLU* 3.4 22.4 - - + +
346D THR 3.0 9.0 + - - +
348D GLY* 1.3 80.0 - - - +
350D THR* 1.3 63.2 + - - +
351D LYS 3.4 0.2 - - - -
352D ALA* 5.0 2.0 + - - +
353D ALA* 5.0 7.1 + - - +
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Residues in contact with THR 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D GLY* 3.8 5.7 - - - +
63D ASP* 2.7 40.5 + - - +
169D THR* 4.0 16.7 - - + +
329D ASN* 5.1 3.5 + - - -
346D THR 3.0 14.3 + - - -
347D TRP* 3.5 10.9 - - - -
349D VAL* 1.3 79.0 - - - +
351D LYS* 1.3 65.4 + - - +
352D ALA 3.4 0.9 + - - -
353D ALA 3.6 2.1 + - - -
354D GLU* 3.0 48.4 + - + +
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Residues in contact with LYS 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D PHE* 5.7 0.3 - - - -
169D THR* 6.1 0.7 - - - -
347D TRP* 3.0 59.0 + - + +
348D GLY* 4.3 10.5 - - - +
349D VAL 3.4 1.0 - - - -
350D THR* 1.3 79.6 - - - +
352D ALA* 1.3 67.9 + - + +
354D GLU* 3.5 7.8 + - - +
355D LYS* 3.2 24.0 + - + +
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Residues in contact with ALA 352 (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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348D GLY 5.3 1.2 + - - +
349D VAL 5.0 1.4 + - - -
350D THR 3.6 0.4 - - - -
351D LYS* 1.3 84.0 - - + +
353D ALA* 1.3 60.6 + - - +
355D LYS* 3.4 7.3 + - - +
356D GLN* 3.0 32.2 + - - +
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Residues in contact with ALA 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D TYR 4.0 0.7 - - - +
58D GLY* 3.8 26.5 - - - +
349D VAL 5.0 6.4 + - - +
350D THR 3.6 3.4 + - - +
351D LYS 3.5 0.2 - - - -
352D ALA* 1.3 75.1 - - - +
354D GLU* 1.3 65.9 + - - +
356D GLN* 3.3 11.9 + - - +
357D MET* 3.0 24.6 + - - +
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Residues in contact with GLU 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D PHE* 3.8 18.7 - - + -
57D TYR* 3.7 16.5 - - - -
58D GLY* 3.6 7.0 - - - +
63D ASP* 5.6 0.7 - - - -
98D LYS* 2.9 21.1 + - - +
168D PHE* 3.5 14.6 - - + +
169D THR* 2.5 51.8 + - - +
350D THR* 3.0 27.9 + - + +
351D LYS* 3.6 7.4 - - - +
353D ALA* 1.3 76.9 - - - +
355D LYS* 1.3 57.2 + - - +
357D MET* 3.4 2.6 + - - +
358D LYS* 3.0 28.2 + - - +
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Residues in contact with LYS 355 (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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168D PHE* 3.7 40.8 - - + -
351D LYS 3.2 15.0 + - - +
352D ALA* 3.6 7.0 - - - +
354D GLU* 1.3 78.7 - - - +
356D GLN* 1.3 58.1 + - - +
358D LYS* 3.8 0.5 - - - +
359D ASP* 2.9 62.4 + - - +
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Residues in contact with GLN 356 (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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352D ALA* 3.0 19.1 + - - +
353D ALA* 3.3 10.3 + - - +
355D LYS* 1.3 75.1 - - - +
357D MET* 1.3 64.7 + - - +
359D ASP* 3.4 9.0 + - - +
360D LYS* 3.2 22.7 + - - +
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Residues in contact with MET 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D LYS 3.5 12.1 - - - +
56D PHE* 4.0 6.7 - - + -
57D TYR* 3.5 57.2 - - + +
353D ALA 3.0 16.3 + - - +
354D GLU 3.9 3.8 - - - +
356D GLN* 1.3 76.2 - - - +
358D LYS* 1.3 61.7 + - - +
360D LYS* 3.4 10.5 + - + +
361D GLN* 3.1 46.2 + - + +
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Residues in contact with LYS 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D PHE* 3.7 42.7 - - + -
100D GLU 5.6 1.6 + - - -
102D ASN* 5.5 3.8 + - - -
167D GLU* 3.0 28.8 + - - +
168D PHE* 3.7 26.7 - - + -
354D GLU 3.0 18.1 + - - +
355D LYS 3.8 0.4 - - - +
357D MET* 1.3 74.8 - - - +
359D ASP* 1.3 66.6 + - - +
361D GLN* 3.2 8.6 + - + +
362D ASP* 2.9 49.8 + - - +
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Residues in contact with ASP 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D PHE* 4.9 3.1 - - - -
355D LYS* 2.9 55.9 + - - +
356D GLN* 3.8 7.6 - - - +
358D LYS* 1.3 76.3 - - - +
360D LYS* 1.3 61.3 + - - +
362D ASP* 3.3 12.3 + - - +
363D GLU* 2.9 34.9 + - + +
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Residues in contact with LYS 360 (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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356D GLN 3.2 12.0 + - - +
357D MET* 3.6 13.0 - - + +
358D LYS 3.2 0.2 - - - -
359D ASP* 1.3 79.6 - - - +
361D GLN* 1.3 64.3 - - + +
363D GLU* 3.4 9.1 + - + +
364D GLU* 3.1 44.8 + - + +
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Residues in contact with GLN 361 (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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55D LYS* 3.0 29.9 + - - +
56D PHE* 3.7 23.9 - - - +
357D MET* 3.1 34.1 + - + +
358D LYS* 3.2 10.1 + - + +
360D LYS* 1.3 78.4 - - + +
362D ASP* 1.3 60.7 + - - +
364D GLU* 3.5 16.0 + - - +
365D GLN* 3.0 29.5 + - - +
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Residues in contact with ASP 362 (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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167D GLU* 4.5 2.8 - - - +
168D PHE* 5.9 0.3 - - - -
358D LYS* 2.9 53.3 + - - +
359D ASP* 3.6 10.9 - - - +
361D GLN* 1.3 75.5 - - - +
363D GLU* 1.3 65.2 + - + +
365D GLN* 3.3 8.3 + - - +
366D ARG* 3.0 22.7 + - - +
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Residues in contact with GLU 363 (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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359D ASP* 2.9 29.7 + - - +
360D LYS* 3.4 9.4 - - - +
362D ASP* 1.3 77.2 - - - +
364D GLU* 1.3 64.3 + - + +
366D ARG* 3.2 16.4 + - - +
367D LEU* 3.2 21.0 - - + +
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Residues in contact with GLU 364 (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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360D LYS* 3.1 50.7 + - + +
361D GLN* 3.9 14.6 - - - +
363D GLU* 1.3 80.1 - - + +
365D GLN* 1.3 63.6 + - - +
367D LEU* 3.1 29.3 + - + +
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Residues in contact with GLN 365 (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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361D GLN 3.0 14.9 + - - +
362D ASP* 3.4 13.0 - - - +
364D GLU* 1.3 76.8 - - - +
366D ARG* 1.3 58.0 + - - +
367D LEU 3.0 9.9 + - - +
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Residues in contact with ARG 366 (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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362D ASP 3.0 12.7 + - - +
363D GLU* 3.2 13.9 + - - +
365D GLN* 1.3 75.1 - - - +
367D LEU* 1.3 60.4 + - + +
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Residues in contact with LEU 367 (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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363D GLU* 3.2 20.6 - - + +
364D GLU* 3.1 19.1 + - + +
365D GLN 3.0 5.7 + - - +
366D ARG* 1.3 83.6 - - + +
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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