Contacts of the helix formed by residues 346 - 367 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLN* 3.9 6.3 - - - +
171A LEU* 4.8 4.0 - - - +
329A ASN* 3.4 42.8 - - - +
342A PHE* 2.7 49.3 + - + +
343A GLY* 3.3 7.4 + - - -
345A GLU* 1.3 82.1 - - + +
347A TRP* 1.3 73.3 + - - +
348A GLY 3.2 0.4 - - - -
349A VAL* 3.0 5.7 + - - +
350A THR* 3.0 26.9 + - - -
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Residues in contact with TRP 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A THR* 4.0 15.9 - - + +
169A THR* 3.3 36.6 + - + -
170A HIS* 4.7 0.6 + - - -
171A LEU* 3.9 31.0 - - + -
187A ASP* 3.4 57.8 + - + -
188A ASN* 4.3 3.1 - - + -
329A ASN* 5.0 0.2 + - - -
343A GLY 3.0 10.6 + - - +
344A ASN* 4.1 15.0 - - - -
346A THR* 1.3 79.6 + - - +
348A GLY* 1.3 73.6 + - - +
350A THR* 3.2 6.9 + - - -
351A LYS* 3.0 69.7 + - + +
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Residues in contact with GLY 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLY 3.0 10.6 + - - -
344A ASN* 3.3 19.5 - - - -
346A THR 3.2 0.4 - - - -
347A TRP* 1.3 92.5 - - - +
349A VAL* 1.3 59.0 + - - +
351A LYS* 4.3 12.8 - - - +
352A ALA* 5.3 1.4 + - - +
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY* 5.4 0.9 - - - -
59A ASP* 6.5 0.2 - - + -
62A LYS* 4.2 27.8 - - + +
344A ASN 3.7 11.7 - - - +
345A GLU* 3.4 22.7 - - - +
346A THR 3.0 8.8 + - - +
348A GLY* 1.3 78.5 - - - +
350A THR* 1.3 62.6 + - - +
351A LYS 3.4 0.2 - - - -
352A ALA 4.9 2.4 + - - -
353A ALA* 5.0 7.1 + - - +
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Residues in contact with THR 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY* 3.8 5.7 - - - +
63A ASP* 2.7 40.9 + - - +
169A THR* 4.0 15.4 - - + +
329A ASN* 5.3 2.1 + - - -
346A THR 3.0 15.0 + - - -
347A TRP* 3.5 10.7 - - - -
349A VAL* 1.3 79.8 - - - +
351A LYS* 1.3 65.8 + - - +
352A ALA 3.4 1.1 + - - -
353A ALA 3.6 1.9 + - - -
354A GLU* 3.0 48.5 + - + +
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Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE* 5.8 0.2 - - - -
169A THR* 6.1 0.7 - - - -
347A TRP* 3.0 56.9 + - + +
348A GLY* 4.3 11.0 - - - +
349A VAL 3.4 1.0 - - - -
350A THR* 1.3 82.4 - - - +
352A ALA* 1.3 68.7 + - + +
354A GLU* 3.5 8.2 + - - +
355A LYS* 3.2 24.0 + - + +
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Residues in contact with ALA 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A GLY 5.3 0.8 + - - -
349A VAL 4.9 1.4 + - - -
350A THR 3.6 0.6 - - - -
351A LYS* 1.3 84.2 - - + +
353A ALA* 1.3 61.6 + - - +
355A LYS* 3.4 7.3 + - - +
356A GLN* 3.0 31.7 + - - +
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Residues in contact with ALA 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR 4.0 0.7 - - - +
58A GLY* 3.7 26.5 - - - +
349A VAL 5.0 6.4 + - - +
350A THR 3.6 2.8 + - - +
351A LYS 3.5 0.2 - - - -
352A ALA* 1.3 75.1 - - - +
354A GLU* 1.3 66.3 + - - +
356A GLN* 3.3 11.4 + - - +
357A MET* 2.9 25.1 + - - +
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Residues in contact with GLU 354 (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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56A PHE* 3.8 19.1 - - + -
57A TYR* 3.7 17.1 - - - -
58A GLY* 3.6 7.9 - - - +
63A ASP* 5.7 1.0 - - - +
98A LYS* 3.5 18.7 + - - +
168A PHE* 3.5 16.7 - - + +
169A THR* 2.5 52.2 + - - +
350A THR* 3.0 27.3 + - + +
351A LYS* 3.6 7.1 - - - +
352A ALA 3.3 0.2 - - - -
353A ALA* 1.3 77.1 - - - +
355A LYS* 1.3 61.1 + - - +
357A MET* 3.5 2.1 + - - +
358A LYS* 3.0 24.1 + - - +
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Residues in contact with LYS 355 (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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168A PHE* 3.7 41.0 - - + -
351A LYS 3.2 14.6 + - - +
352A ALA* 3.6 7.9 - - - +
354A GLU* 1.3 79.8 - - - +
356A GLN* 1.3 57.8 + - - +
358A LYS* 3.4 1.2 + - - +
359A ASP* 2.9 61.8 + - - +
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Residues in contact with GLN 356 (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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352A ALA* 3.0 18.0 + - - +
353A ALA* 3.6 10.0 - - - +
354A GLU 3.3 0.2 - - - -
355A LYS* 1.3 74.4 - - - +
357A MET* 1.3 65.7 + - - +
359A ASP* 3.4 9.6 + - - +
360A LYS* 3.2 35.7 + - - +
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Residues in contact with MET 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS 3.5 12.1 - - - +
56A PHE* 4.0 6.7 - - + -
57A TYR* 3.5 57.9 - - + +
353A ALA 2.9 16.5 + - - +
354A GLU 3.9 3.8 - - - +
356A GLN* 1.3 77.6 - - - +
358A LYS* 1.3 61.6 + - - +
360A LYS* 3.4 15.5 + - - +
361A GLN* 3.1 46.2 + - + +
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Residues in contact with LYS 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 3.7 43.8 - - + +
100A GLU 5.6 1.4 + - - -
102A ASN* 5.6 4.4 - - - +
167A GLU* 3.0 27.9 + - - +
168A PHE* 3.7 26.7 - - + -
354A GLU 3.0 17.7 + - - +
355A LYS 3.8 0.4 - - - +
357A MET* 1.3 75.0 - - - +
359A ASP* 1.3 65.5 + - - +
361A GLN* 3.2 8.9 + - + +
362A ASP* 2.9 50.3 + - - +
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Residues in contact with ASP 359 (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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168A PHE* 4.9 3.3 - - - -
355A LYS* 2.9 56.4 + - - +
356A GLN* 3.4 7.8 + - - +
358A LYS* 1.3 75.7 - - - +
360A LYS* 1.3 61.9 + - - +
362A ASP* 3.4 11.5 + - - +
363A GLU* 3.0 31.2 + - + +
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Residues in contact with LYS 360 (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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356A GLN* 3.2 26.8 + - - +
357A MET* 3.6 19.3 - - - +
358A LYS 3.2 0.2 - - - -
359A ASP* 1.3 75.5 - - - +
361A GLN* 1.3 60.5 + - + +
363A GLU* 3.4 8.7 + - + +
364A GLU* 3.0 48.3 + - + +
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Residues in contact with GLN 361 (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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55A LYS* 3.0 34.7 + - - +
56A PHE* 3.7 23.3 - - - +
357A MET* 3.1 35.7 + - + +
358A LYS* 3.2 9.8 + - + +
360A LYS* 1.3 78.7 - - + +
362A ASP* 1.3 58.4 + - - +
364A GLU* 3.5 8.2 + - - +
365A GLN* 3.0 28.9 + - - +
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Residues in contact with ASP 362 (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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167A GLU* 4.5 2.6 - - - +
168A PHE* 5.9 0.3 - - - -
358A LYS* 2.9 53.2 + - - +
359A ASP* 3.6 10.7 - - - +
361A GLN* 1.3 74.9 - - - +
363A GLU* 1.3 65.2 + - + +
365A GLN* 3.3 8.8 + - - +
366A ARG* 3.1 21.7 + - - +
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Residues in contact with GLU 363 (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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359A ASP* 3.0 20.7 + - + +
360A LYS* 3.4 11.0 + - + +
362A ASP* 1.3 76.1 - - + +
364A GLU* 1.3 65.8 + - + +
366A ARG* 3.2 17.8 + - - +
367A LEU* 3.4 25.6 + - + +
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Residues in contact with GLU 364 (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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360A LYS* 3.0 37.5 + - + +
361A GLN* 3.9 7.4 - - - +
363A GLU* 1.3 77.7 - - - +
365A GLN* 1.3 63.2 + - - +
367A LEU* 3.1 33.7 + - - +
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Residues in contact with GLN 365 (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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361A GLN 3.0 15.1 + - - +
362A ASP* 3.4 13.2 - - - +
364A GLU* 1.3 76.1 - - - +
366A ARG* 1.3 62.2 + - - +
367A LEU 3.2 7.6 + - - +
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Residues in contact with ARG 366 (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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362A ASP 3.1 12.9 + - - +
363A GLU* 3.2 13.2 + - - +
365A GLN* 1.3 76.3 - - - +
367A LEU* 1.3 61.8 + - + +
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Residues in contact with LEU 367 (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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363A GLU* 3.6 26.2 - - + +
364A GLU* 3.1 26.9 + - - +
365A GLN 3.5 10.2 - - - +
366A ARG* 1.3 81.9 - - + +
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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
------------------------------------------------------------
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