Contacts of the helix formed by residues 346 - 367 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26F GLN* 3.7 17.3 - - - +
94F GLN* 5.3 0.3 + - - -
96F THR* 4.9 0.2 - - - +
171F LEU* 4.8 3.8 - - - +
329F ASN* 3.4 40.7 - - - +
342F PHE* 2.7 40.3 + - + +
343F GLY* 3.3 7.3 + - - -
345F GLU* 1.3 81.7 - - + +
347F TRP* 1.3 73.7 + - - +
349F VAL* 3.0 14.1 + - - +
350F THR* 3.0 18.1 + - - -
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Residues in contact with TRP 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C ASN* 5.7 1.6 - - - -
96F THR* 4.0 21.2 - - + +
169F THR* 3.3 35.6 + - + -
170F HIS* 4.7 0.4 - - - -
171F LEU* 3.9 30.7 - - + -
187F ASP* 3.4 51.0 + - + -
188F ASN* 4.3 3.4 - - + -
329F ASN* 5.5 0.2 - - - +
343F GLY 3.1 10.9 + - - +
344F ASN* 4.1 16.2 - - - -
346F THR* 1.3 79.1 + - - +
348F GLY* 1.3 73.5 + - - +
350F THR* 3.2 7.7 + - - -
351F LYS* 3.0 69.7 + - + +
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Residues in contact with GLY 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C GLU* 5.2 1.6 - - - +
341C GLU* 4.6 5.4 - - - +
344C ASN* 2.8 31.7 + - - +
343F GLY 3.1 10.4 + - - -
344F ASN* 3.4 17.7 + - - -
347F TRP* 1.3 93.7 - - - +
349F VAL* 1.3 58.6 + - - +
351F LYS* 4.3 8.8 - - - +
352F ALA* 5.3 1.4 + - - +
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Residues in contact with VAL 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C GLU* 3.7 40.0 - - + +
345C GLU* 3.6 38.4 - - + +
58F GLY* 5.5 0.9 - - - -
62F LYS* 4.2 25.1 - - + +
344F ASN 3.6 11.8 + - - +
345F GLU 3.4 20.4 - - - +
346F THR 3.0 8.1 + - - +
348F GLY* 1.3 79.3 - - - +
350F THR* 1.3 62.4 + - - +
351F LYS 3.5 0.2 - - - -
352F ALA 4.9 1.3 + - - -
353F ALA* 5.1 2.4 - - - +
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Residues in contact with THR 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F GLY* 3.8 6.1 - - - +
63F ASP* 2.7 40.4 + - - +
169F THR* 4.0 16.0 - - + +
329F ASN* 5.1 3.3 + - - -
346F THR 3.0 14.5 + - - -
347F TRP* 3.5 11.9 - - - -
349F VAL* 1.3 78.9 - - - +
351F LYS* 1.3 67.0 + - - +
352F ALA 3.3 1.1 + - - -
353F ALA 3.6 2.1 + - - -
354F GLU* 3.1 48.5 + - + +
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Residues in contact with LYS 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C GLU* 2.8 27.1 + - - +
344C ASN* 5.0 4.3 - - - +
168F PHE* 5.7 0.3 - - - -
169F THR* 6.0 0.9 - - - -
347F TRP* 3.0 55.8 + - + +
348F GLY* 4.3 10.8 - - - +
349F VAL 3.5 0.8 - - - -
350F THR* 1.3 81.6 - - - +
352F ALA* 1.3 64.2 + - - +
354F GLU* 3.6 7.7 - - - +
355F LYS* 3.2 23.6 + - + +
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Residues in contact with ALA 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C ALA* 4.3 23.2 - - + +
340C GLU* 3.6 34.5 - - + +
341C GLU* 5.6 4.0 - - + -
348F GLY 5.3 1.0 + - - +
349F VAL 4.9 1.8 + - - -
350F THR 3.3 0.6 + - - -
351F LYS* 1.3 77.8 - - - +
353F ALA* 1.3 61.3 + - - +
355F LYS* 3.4 6.8 + - - +
356F GLN* 3.0 29.2 + - - +
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Residues in contact with ALA 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C ALA* 4.5 7.9 - - + +
341C GLU* 3.8 21.6 + - - +
57F TYR 3.9 0.6 - - - +
58F GLY* 3.7 26.9 - - - +
349F VAL 5.1 2.4 + - - +
350F THR 3.6 3.0 + - - +
352F ALA* 1.3 75.8 - - - +
354F GLU* 1.3 66.6 + - - +
356F GLN* 3.3 8.2 + - - +
357F MET* 2.9 25.5 + - - +
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Residues in contact with GLU 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F PHE* 3.8 19.2 - - + -
57F TYR* 3.7 17.2 - - - -
58F GLY* 3.6 7.9 - - - +
63F ASP* 5.6 0.7 - - - +
98F LYS* 3.5 19.0 + - - +
168F PHE* 3.5 16.8 - - + +
169F THR* 2.5 52.2 + - - +
350F THR* 3.1 27.1 + - + +
351F LYS* 3.6 7.7 - - - +
353F ALA* 1.3 77.8 - - - +
355F LYS* 1.3 62.7 + - - +
357F MET* 3.5 2.1 + - - +
358F LYS* 3.0 23.6 + - - +
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Residues in contact with LYS 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F PHE* 3.7 42.5 - - + -
351F LYS 3.2 14.1 + - - +
352F ALA* 3.6 7.4 - - - +
354F GLU* 1.3 79.3 - - - +
356F GLN* 1.3 57.5 + - - +
358F LYS* 3.4 0.9 + - - +
359F ASP* 2.9 61.7 + - - +
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Residues in contact with GLN 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C ASP* 4.5 6.1 + - - +
337C ALA* 3.2 29.6 + - - +
352F ALA 3.0 15.7 + - - +
353F ALA* 3.6 6.9 - - - +
355F LYS* 1.3 73.9 - - - +
357F MET* 1.3 64.8 + - - +
359F ASP* 3.4 9.6 + - - +
360F LYS* 3.2 22.3 + - - +
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Residues in contact with MET 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F LYS 4.6 0.2 - - - +
56F PHE* 3.9 15.3 - - + -
57F TYR* 3.5 58.1 - - + +
58F GLY 5.6 2.2 - - - +
353F ALA 2.9 16.7 + - - +
354F GLU 3.9 3.6 - - - +
356F GLN* 1.3 77.3 - - - +
358F LYS* 1.3 62.2 + - - +
360F LYS* 3.4 24.4 + - - +
361F GLN* 3.1 33.3 + - - +
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Residues in contact with LYS 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F PHE* 3.7 39.9 - - + +
100F GLU 5.5 2.0 + - - -
102F ASN* 5.4 3.4 + - - -
167F GLU* 3.0 31.8 + - - +
168F PHE* 3.7 26.9 - - + -
354F GLU 3.0 16.9 + - - +
355F LYS 3.8 0.4 - - - +
357F MET* 1.3 76.4 - - - +
359F ASP* 1.3 66.6 + - - +
361F GLN* 3.2 9.7 + - + +
362F ASP* 2.9 49.2 + - - +
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Residues in contact with ASP 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F PHE* 4.9 3.3 - - - -
355F LYS* 2.9 55.5 + - - +
356F GLN* 3.8 7.2 - - - +
358F LYS* 1.3 75.9 - - - +
360F LYS* 1.3 57.6 + - - +
362F ASP* 3.3 12.4 + - - +
363F GLU* 3.0 30.0 + - - +
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Residues in contact with LYS 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356F GLN 3.2 12.9 + - - +
357F MET* 3.5 36.5 - - - +
358F LYS 3.1 0.6 - - - -
359F ASP* 1.3 77.5 - - - +
361F GLN* 1.3 71.2 + - - +
363F GLU* 3.4 17.3 + - - +
364F GLU* 3.0 49.0 + - - +
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Residues in contact with GLN 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F LYS* 3.0 30.1 + - - +
56F PHE* 3.7 27.3 - - - +
357F MET* 3.1 22.6 + - + +
358F LYS* 3.7 10.2 + - + +
360F LYS* 1.3 90.7 - - - +
362F ASP* 1.3 59.0 + - - +
364F GLU* 3.4 9.7 + - + +
365F GLN* 3.0 27.7 + - - +
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Residues in contact with ASP 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F GLU* 4.5 3.5 - - - +
168F PHE* 5.8 0.3 - - - -
358F LYS* 2.9 52.7 + - - +
359F ASP* 3.6 11.6 - - - +
361F GLN* 1.3 75.2 - - - +
363F GLU* 1.3 65.1 + - - +
365F GLN* 3.3 8.6 + - - +
366F ARG* 3.0 22.9 + - - +
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Residues in contact with GLU 363 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359F ASP 3.0 14.5 + - - +
360F LYS* 3.4 16.1 - - - +
362F ASP* 1.3 76.0 - - - +
364F GLU* 1.3 95.0 + - - +
366F ARG* 3.2 16.7 + - - +
367F LEU* 3.3 29.2 + - + +
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Residues in contact with GLU 364 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360F LYS* 3.0 45.2 + - + +
361F GLN* 3.9 7.6 - - - +
362F ASP 3.4 0.2 - - - -
363F GLU* 1.3 92.5 - - - +
365F GLN* 1.3 63.4 + - - +
367F LEU* 3.2 26.6 + - - +
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Residues in contact with GLN 365 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361F GLN 3.0 14.5 + - - +
362F ASP* 3.4 13.5 - - - +
364F GLU* 1.3 77.9 - - - +
366F ARG* 1.3 60.3 + - - +
367F LEU 3.2 6.1 + - - -
116J SER* 5.4 9.7 - - - -
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Residues in contact with ARG 366 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362F ASP 3.0 13.8 + - - +
363F GLU* 3.2 13.4 + - - +
365F GLN* 1.3 75.0 - - - +
367F LEU* 1.3 63.5 + - + +
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Residues in contact with LEU 367 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363F GLU* 3.5 33.4 - - + +
364F GLU* 3.2 19.6 + - - +
365F GLN 3.2 6.5 - - - -
366F ARG* 1.3 86.8 - - + +
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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