Contacts of the helix formed by residues 346 - 367 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C GLN* 3.7 17.0 - - - +
96C THR* 4.9 0.2 - - - +
171C LEU* 4.7 4.0 - - - +
329C ASN* 3.4 40.3 - - - +
342C PHE* 2.7 40.2 + - + +
343C GLY* 3.3 7.1 + - - -
345C GLU* 1.3 82.1 - - + +
347C TRP* 1.3 73.2 + - - +
348C GLY 3.1 0.4 - - - -
349C VAL* 3.0 13.9 + - - +
350C THR* 3.0 18.5 + - - -
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Residues in contact with TRP 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C THR* 4.0 14.5 - - + +
169C THR* 3.3 35.9 + - + -
170C HIS* 4.8 0.6 + - - -
171C LEU* 3.9 34.3 - - + -
187C ASP* 3.4 54.0 + - + -
188C ASN* 4.3 2.2 - - + -
329C ASN* 4.8 0.4 - - - +
343C GLY 3.1 11.1 + - - +
344C ASN* 4.0 16.4 - - - -
346C THR* 1.3 79.5 + - - +
348C GLY* 1.3 73.3 + - - +
350C THR* 3.2 7.1 + - - -
351C LYS* 3.0 70.3 + - + +
344F ASN* 5.5 2.7 - - - -
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Residues in contact with GLY 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C GLY 3.1 10.1 + - - -
344C ASN* 3.4 17.9 - - - -
346C THR 3.1 0.2 - - - -
347C TRP* 1.3 94.1 - - - +
349C VAL* 1.3 57.3 + - - +
351C LYS* 4.3 9.1 - - - +
352C ALA* 5.3 0.9 + - - +
340F GLU* 5.1 1.4 - - - +
341F GLU* 4.5 5.9 - - - +
344F ASN* 2.9 30.9 + - - +
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Residues in contact with VAL 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLY* 5.4 0.9 - - - -
59C ASP* 6.5 0.2 - - + -
62C LYS* 4.2 24.5 - - + +
344C ASN 3.5 9.8 + - - +
345C GLU 3.4 19.7 - - - +
346C THR 3.0 7.9 + - - +
348C GLY* 1.3 79.6 - - - +
350C THR* 1.3 63.5 + - - +
351C LYS 3.4 0.2 - - - -
352C ALA 5.0 1.1 + - - -
353C ALA* 5.0 1.2 - - - +
341F GLU* 3.6 40.7 - - + +
345F GLU* 3.6 40.6 - - + +
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Residues in contact with THR 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLY* 3.8 5.7 - - - +
63C ASP* 2.7 40.9 + - - +
169C THR* 4.0 17.1 - - + +
329C ASN* 5.2 3.5 + - - -
346C THR 3.0 14.1 + - - -
347C TRP* 3.5 11.5 - - - -
349C VAL* 1.3 78.9 - - - +
351C LYS* 1.3 65.1 + - - +
352C ALA 3.4 1.1 + - - -
353C ALA 3.6 1.9 + - - -
354C GLU* 3.0 48.2 + - + +
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Residues in contact with LYS 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C PHE* 5.8 0.2 - - - -
169C THR* 6.1 0.4 - - - -
347C TRP* 3.0 58.2 + - + +
348C GLY* 4.3 9.6 - - - +
349C VAL 3.4 1.2 - - - -
350C THR* 1.3 82.2 - - - +
352C ALA* 1.3 62.2 + - - +
354C GLU* 3.6 7.8 + - - +
355C LYS* 3.2 24.5 + - - +
188F ASN 5.9 0.4 + - - -
340F GLU* 2.7 28.0 + - - +
344F ASN* 4.9 4.5 - - - +
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Residues in contact with ALA 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C GLY 5.3 1.0 + - - +
349C VAL 5.0 1.2 + - - -
350C THR 3.4 0.6 + - - -
351C LYS* 1.3 78.1 - - - +
353C ALA* 1.3 59.9 + - - +
355C LYS* 3.4 7.3 + - - +
356C GLN* 3.0 28.6 + - - +
337F ALA* 4.0 26.9 - - + +
340F GLU* 3.5 35.0 - - + +
341F GLU* 5.4 3.6 - - + +
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Residues in contact with ALA 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C TYR 3.9 0.7 - - - +
58C GLY* 3.7 26.0 - - - +
349C VAL 5.0 1.3 - - - +
350C THR 3.6 3.5 + - - +
351C LYS 3.5 0.2 - - - -
352C ALA* 1.3 74.0 - - - +
354C GLU* 1.3 67.4 + - - +
356C GLN* 3.3 9.2 + - - +
357C MET* 3.0 24.9 + - - +
337F ALA* 4.2 7.9 - - + +
341F GLU* 3.5 23.3 + - - +
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Residues in contact with GLU 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C PHE* 3.8 19.2 - - + -
57C TYR* 3.6 16.4 - - - -
58C GLY* 3.5 7.7 - - - +
63C ASP* 5.6 0.7 - - - -
98C LYS* 3.5 19.3 + - - +
168C PHE* 3.5 16.3 - - + +
169C THR* 2.5 51.7 + - - +
350C THR* 3.0 29.0 + - + +
351C LYS* 3.6 7.5 - - - +
353C ALA* 1.3 77.7 - - - +
355C LYS* 1.3 61.5 + - - +
357C MET* 3.4 2.3 + - - +
358C LYS* 3.0 23.9 + - - +
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Residues in contact with LYS 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C PHE* 3.7 39.9 - - + -
351C LYS* 3.2 15.2 + - + +
352C ALA* 3.6 6.7 - - - +
354C GLU* 1.3 79.0 - - - +
356C GLN* 1.3 58.4 + - - +
358C LYS* 3.8 0.5 - - - +
359C ASP* 2.9 61.7 + - - +
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Residues in contact with GLN 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C ALA 3.0 15.7 + - - +
353C ALA* 3.6 7.3 - - - +
355C LYS* 1.3 79.1 - - - +
357C MET* 1.3 60.8 + - - +
359C ASP* 3.4 8.7 + - - +
360C LYS* 3.2 22.5 + - - +
335F ASP* 3.8 12.3 + - - +
337F ALA* 3.2 28.0 + - - +
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Residues in contact with MET 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C PHE* 3.9 13.9 - - + -
57C TYR* 3.5 59.9 - - + +
58C GLY 5.6 1.6 - - - +
353C ALA 3.0 16.5 + - - +
354C GLU 3.8 3.8 - - - +
356C GLN* 1.3 77.7 - - - +
358C LYS* 1.3 62.2 + - - +
360C LYS* 3.3 26.2 + - - +
361C GLN* 3.1 33.6 + - - +
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Residues in contact with LYS 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C PHE* 3.7 40.0 - - + +
100C GLU 5.5 2.0 + - - -
102C ASN* 5.4 5.7 - - - +
167C GLU* 3.0 27.9 + - - +
168C PHE* 3.6 30.1 - - + -
354C GLU 3.0 17.5 + - - +
355C LYS 3.8 0.2 - - - +
357C MET* 1.3 76.1 - - - +
359C ASP* 1.3 66.3 + - - +
361C GLN* 3.3 8.6 + - + +
362C ASP* 2.9 49.5 + - - +
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Residues in contact with ASP 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C PHE* 4.9 3.3 - - - -
355C LYS* 2.9 55.4 + - - +
356C GLN* 3.8 7.8 - - - +
358C LYS* 1.3 75.8 - - - +
360C LYS* 1.3 61.4 + - - +
362C ASP* 3.3 11.9 + - - +
363C GLU* 3.0 33.2 + - + +
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Residues in contact with LYS 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C GLN 3.2 13.1 + - - +
357C MET* 3.6 36.7 - - - +
358C LYS 3.1 0.8 - - - -
359C ASP* 1.3 76.0 - - - +
361C GLN* 1.3 71.0 - - - +
363C GLU* 3.3 16.9 + - - +
364C GLU* 3.1 48.9 + - + +
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Residues in contact with GLN 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C LYS* 3.0 39.3 + - - +
56C PHE* 3.7 26.7 - - - +
357C MET* 3.1 24.8 + - + +
358C LYS* 3.3 10.6 + - + +
360C LYS* 1.3 89.2 - - - +
362C ASP* 1.3 60.0 + - - +
364C GLU* 3.9 13.2 - - - +
365C GLN* 3.0 28.8 + - - +
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Residues in contact with ASP 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C GLU* 4.5 3.3 - - - +
168C PHE* 5.8 0.3 - - - -
358C LYS* 2.9 54.0 + - - +
359C ASP* 3.6 11.0 - - - +
361C GLN* 1.3 74.7 - - - +
363C GLU* 1.3 66.3 + - + +
365C GLN* 3.3 8.6 + - - +
366C ARG* 3.0 22.7 + - - +
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Residues in contact with GLU 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B SER* 3.2 36.8 + - - +
45B ASP* 5.8 2.0 - - - +
359C ASP* 3.0 18.2 + - + +
360C LYS* 3.6 25.2 - - - +
362C ASP* 1.3 75.9 - - + +
364C GLU* 1.3 64.1 + - + +
366C ARG* 3.2 18.1 + - - +
367C LEU* 3.4 18.3 + - - +
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Residues in contact with GLU 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C LYS* 3.1 47.7 + - + +
361C GLN* 3.9 12.6 - - - +
362C ASP 3.3 0.2 - - - -
363C GLU* 1.3 76.4 - - + +
365C GLN* 1.3 63.4 + - - +
367C LEU* 3.2 28.4 + - + +
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Residues in contact with GLN 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A SER* 5.4 9.9 - - - -
310A ASN* 5.2 10.1 - - - +
361C GLN 3.0 15.2 + - - +
362C ASP* 3.4 13.2 - - - +
364C GLU* 1.3 77.7 - - - +
366C ARG* 1.3 61.7 + - - +
367C LEU 3.2 5.9 + - - -
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Residues in contact with ARG 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C ASP 3.0 12.9 + - - +
363C GLU* 3.2 12.5 + - - +
365C GLN* 1.3 75.1 - - - +
367C LEU* 1.3 64.2 + - + +
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Residues in contact with LEU 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LYS* 3.9 20.2 - - + +
42B HIS 4.2 9.0 - - - +
43B LYS* 4.2 9.2 - - - -
44B SER* 3.8 36.3 - - - +
363C GLU 3.5 17.5 - - - +
364C GLU* 3.2 19.2 + - + +
365C GLN 3.1 5.8 - - - -
366C ARG* 1.3 86.9 - - + +
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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