Contacts of the helix formed by residues 346 - 366 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H GLN* 3.7 16.4 - - - +
96H THR* 4.9 0.2 - - - +
171H LEU* 4.8 3.8 - - - +
329H ASN* 3.4 42.9 - - - +
342H PHE* 2.7 39.0 + - + +
343H GLY* 3.3 7.7 + - - -
344H ASN 3.3 0.2 - - - -
345H GLU* 1.3 81.8 - - + +
347H TRP* 1.3 73.5 + - - +
349H VAL* 3.0 8.3 + - - +
350H THR* 3.0 25.7 + - - -
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Residues in contact with TRP 347 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H THR* 4.0 20.8 - - + +
169H THR* 3.3 34.6 + - + -
170H HIS* 4.3 1.1 + - - -
171H LEU* 3.9 29.2 - - + -
187H ASP* 3.4 48.8 + - + -
188H ASN* 4.4 2.9 - - + -
329H ASN* 4.8 0.4 - - - +
343H GLY 3.1 10.9 + - - +
344H ASN* 4.1 16.2 - - - -
346H THR* 1.3 78.6 + - - +
348H GLY* 1.3 73.4 + - - +
350H THR* 3.1 7.5 + - - -
351H LYS* 3.0 79.9 + - + +
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Residues in contact with GLY 348 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343H GLY 3.0 11.0 + - - -
344H ASN* 3.4 17.9 + - - -
346H THR 3.2 0.4 - - - -
347H TRP* 1.3 94.9 - - - +
349H VAL* 1.3 59.7 + - - +
351H LYS* 4.3 11.6 - - - +
352H ALA* 5.3 1.4 + - - +
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Residues in contact with VAL 349 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H GLY* 5.4 1.0 - - - -
62H LYS* 4.9 22.7 - - + +
344H ASN 3.6 14.9 + - - +
345H GLU* 3.2 26.0 - - - +
346H THR* 3.0 12.4 + - - +
348H GLY* 1.3 76.8 - - - +
350H THR* 1.3 66.9 + - - +
351H LYS 3.4 0.4 - - - -
352H ALA* 4.8 3.0 + - - +
353H ALA* 4.9 7.6 + - - +
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Residues in contact with THR 350 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H GLY* 3.8 5.7 - - - -
63H ASP* 2.7 39.4 + - - +
169H THR* 4.0 17.5 - - + +
329H ASN* 5.2 3.5 + - - -
346H THR 3.0 14.9 + - - -
347H TRP* 3.1 11.7 + - - -
349H VAL* 1.3 79.9 - - - +
351H LYS* 1.3 64.9 + - - +
352H ALA 3.4 0.7 + - - -
353H ALA 3.5 2.1 + - - -
354H GLU* 3.0 49.0 + - + +
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Residues in contact with LYS 351 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H PHE* 5.7 0.2 - - - -
169H THR* 6.0 1.1 - - - -
170H HIS* 5.8 3.2 - - - -
187H ASP* 4.5 8.1 + - - +
347H TRP* 3.0 61.8 + - + +
348H GLY* 4.3 9.4 - - - +
349H VAL 3.4 0.6 - - - -
350H THR* 1.3 78.9 - - - +
352H ALA* 1.3 66.0 + - + +
354H GLU* 3.5 7.6 + - - +
355H LYS* 3.2 24.6 + - + +
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Residues in contact with ALA 352 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348H GLY 5.3 1.3 + - - +
349H VAL 4.8 2.2 + - - +
350H THR 3.4 0.4 + - - -
351H LYS* 1.3 78.9 - - + +
353H ALA* 1.3 61.3 + - - +
355H LYS* 3.4 8.0 + - - +
356H GLN* 3.0 29.1 + - - +
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Residues in contact with ALA 353 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H TYR 4.0 0.3 - - - +
58H GLY* 3.7 26.7 - - - +
349H VAL 4.9 6.6 + - - +
350H THR 3.5 3.0 + - - +
351H LYS 3.5 0.2 - - - -
352H ALA* 1.3 76.4 - - - +
354H GLU* 1.3 66.6 + - - +
356H GLN* 3.3 10.6 + - - +
357H MET* 2.9 25.6 + - - +
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Residues in contact with GLU 354 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H PHE* 3.8 19.8 - - + -
57H TYR* 3.7 16.0 - - - -
58H GLY* 3.6 7.9 - - - +
63H ASP* 5.6 1.2 - - - +
98H LYS* 2.9 20.6 + - - +
168H PHE* 3.5 15.4 - - + +
169H THR* 2.5 51.1 + - - +
350H THR* 3.0 27.7 + - + +
351H LYS* 3.6 7.9 - - - +
353H ALA* 1.3 76.6 - - - +
355H LYS* 1.3 57.1 + - - +
357H MET* 3.5 2.3 + - - +
358H LYS* 3.0 28.8 + - - +
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Residues in contact with LYS 355 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASP* 4.7 9.9 + - - -
168H PHE* 3.7 41.5 - - + -
351H LYS* 3.2 15.5 + - + +
352H ALA* 3.6 6.7 - - - +
354H GLU* 1.3 80.1 - - - +
356H GLN* 1.3 57.8 + - - +
358H LYS* 3.4 1.0 + - - +
359H ASP* 2.9 62.0 + - - +
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Residues in contact with GLN 356 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352H ALA 3.0 18.2 + - - +
353H ALA* 3.6 10.4 - - - +
355H LYS* 1.3 75.1 - - - +
357H MET* 1.3 64.0 + - - +
359H ASP* 3.4 9.5 + - - +
360H LYS* 3.1 23.1 + - + +
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Residues in contact with MET 357 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H LYS 3.5 12.3 - - - +
56H PHE* 4.0 7.2 - - + -
57H TYR* 3.5 58.1 - - + +
353H ALA 2.9 16.9 + - - +
354H GLU 3.8 3.6 - - - +
356H GLN* 1.3 77.3 - - - +
358H LYS* 1.3 63.0 + - - +
360H LYS* 3.2 25.0 - - + +
361H GLN* 3.1 44.3 + - + +
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Residues in contact with LYS 358 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H PHE* 3.7 42.3 - - + +
100H GLU 5.6 1.6 + - - -
102H ASN* 5.5 3.2 + - - -
167H GLU* 3.0 28.2 + - - +
168H PHE* 3.7 27.1 - - + -
354H GLU 3.0 17.7 + - - +
355H LYS 3.8 0.4 - - - +
356H GLN 3.3 0.2 - - - -
357H MET* 1.3 76.0 - - - +
359H ASP* 1.3 66.8 + - - +
361H GLN* 3.3 9.7 + - + +
362H ASP* 2.9 49.9 + - - +
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Residues in contact with ASP 359 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASP* 5.1 7.9 - - - +
168H PHE* 4.9 2.9 - - - -
355H LYS* 2.9 54.7 + - - +
356H GLN* 3.4 7.4 + - - +
358H LYS* 1.3 75.7 - - - +
360H LYS* 1.3 56.9 + - - +
362H ASP* 3.3 11.8 + - - +
363H GLU* 3.0 29.5 + - - +
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Residues in contact with LYS 360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356H GLN 3.1 13.7 + - - +
357H MET* 3.2 28.6 - - - +
359H ASP* 1.3 76.2 - - - +
361H GLN* 1.3 75.4 + - + +
363H GLU* 3.3 7.4 + - - +
364H GLU* 3.0 25.9 + - + +
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Residues in contact with GLN 361 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H LYS* 3.0 39.7 + - - +
56H PHE* 3.7 23.5 - - - +
357H MET* 3.1 33.3 + - + +
358H LYS* 3.3 11.1 + - + +
360H LYS* 1.3 94.8 - - + +
362H ASP* 1.3 59.4 + - - +
364H GLU* 3.3 15.2 - - - +
365H GLN* 3.0 28.1 + - - +
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Residues in contact with ASP 362 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASP* 5.8 0.5 - - - +
167H GLU* 4.6 2.6 - - - +
168H PHE* 5.9 0.2 - - - -
358H LYS* 2.9 55.4 + - - +
359H ASP* 3.6 11.0 - - - +
361H GLN* 1.3 75.5 - - - +
363H GLU* 1.3 63.8 + - - +
365H GLN* 3.3 8.2 + - - +
366H ARG* 3.1 22.6 + - - +
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Residues in contact with GLU 363 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ASN 5.7 1.6 - - - +
359H ASP 3.0 13.0 + - - +
360H LYS* 3.4 11.9 - - - +
362H ASP* 1.3 76.5 - - - +
364H GLU* 1.3 58.6 + - - +
366H ARG* 2.6 67.7 + - - +
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Residues in contact with GLU 364 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360H LYS* 3.0 14.9 + - + +
361H GLN* 3.3 23.8 - - - +
363H GLU* 1.3 77.0 - - + +
365H GLN* 1.3 72.3 + - - +
366H ARG 3.2 6.4 + - - +
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Residues in contact with GLN 365 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361H GLN 3.0 14.9 + - - +
362H ASP* 3.4 13.7 - - - +
364H GLU* 1.3 84.6 + - - +
366H ARG* 1.3 58.8 + - + +
116I SER* 5.1 12.7 - - - -
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Residues in contact with ARG 366 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ASN* 5.7 7.1 - - - +
201B ASP* 5.7 3.2 + - - -
362H ASP 3.1 11.7 + - - +
363H GLU* 2.6 59.9 + - - +
364H GLU 3.8 4.8 - - - +
365H GLN* 1.3 79.6 - - - +
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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
------------------------------------------------------------
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