Contacts of the helix formed by residues 345 - 367 (chain P) in PDB entry 5GJQ
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 GLU 345 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344P THR* 1.3 81.4 - - - +
346P GLU* 1.3 54.8 + - + +
349P LYS* 2.7 41.1 - - - +
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Residues in contact with GLU 346 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342P GLY* 4.1 6.9 + - - -
345P GLU* 1.3 80.6 - - + +
347P GLY* 1.3 63.5 + - - +
349P LYS* 4.0 4.8 - - - +
350P ARG* 3.4 23.0 + - - +
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Residues in contact with GLY 347 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341P PHE* 4.7 4.9 - - - -
342P GLY* 2.8 21.5 + - - -
343P SER 2.8 27.1 - - - +
344P THR 3.9 0.6 + - - -
345P GLU 3.2 0.4 - - - -
346P GLU* 1.3 75.2 - - - +
348P GLU* 1.3 66.5 + - - +
349P LYS 3.0 0.9 - - - -
350P ARG* 2.8 22.0 + - - +
351P TRP* 3.5 3.8 + - - +
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Residues in contact with GLU 348 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343P SER 3.4 12.6 + - - +
344P THR* 2.7 30.9 + - - +
347P GLY* 1.3 70.1 - - - -
349P LYS* 1.3 61.1 + - - +
351P TRP* 3.2 30.7 + - + +
352P LYS* 3.6 13.1 + - + +
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Residues in contact with LYS 349 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240P TYR* 5.6 1.8 - - - +
344P THR 3.2 2.7 + - - +
345P GLU* 2.7 27.0 + - - +
346P GLU* 4.0 7.6 - - - +
347P GLY 3.0 0.8 + - - -
348P GLU* 1.3 77.7 - - - +
350P ARG* 1.3 60.8 + - + +
352P LYS* 3.6 8.1 + - - +
353P ASP* 3.6 23.1 + - - +
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Residues in contact with ARG 350 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240P TYR* 4.2 18.2 - - + +
276P LEU* 4.4 18.5 - - + +
341P PHE* 4.2 28.7 - - + -
342P GLY 5.3 0.2 - - - +
346P GLU 3.4 16.6 - - - +
347P GLY 2.8 9.2 + - - +
349P LYS* 1.3 74.9 - - + +
351P TRP* 1.3 66.6 + - - +
352P LYS 3.0 1.8 - - - -
353P ASP* 2.9 11.1 + - - +
354P LEU* 2.9 23.7 + - - +
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Residues in contact with TRP 351 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317P TRP* 2.5 49.8 - + - -
321P VAL* 3.5 27.8 - - + -
325P GLY* 5.9 3.4 - - - -
328P LEU* 5.2 6.7 - - + -
341P PHE* 4.1 19.1 - + + -
347P GLY 3.5 3.2 + - - +
348P GLU* 3.2 25.2 + - + +
350P ARG* 1.3 78.0 - - - +
352P LYS* 1.3 63.6 + - + +
354P LEU* 3.2 16.8 - - + -
355P LYS* 3.3 15.6 + - - +
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Residues in contact with LYS 352 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348P GLU* 3.8 16.4 - - + +
349P LYS* 3.6 8.2 + - - +
350P ARG 3.0 0.6 - - - -
351P TRP* 1.3 78.3 - - + +
353P ASP* 1.3 66.7 + - - +
355P LYS* 3.2 9.4 + - - +
356P ASN* 2.9 25.8 + - - -
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Residues in contact with ASP 353 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240P TYR* 2.8 35.8 + - + -
276P LEU* 4.2 16.2 - - + +
349P LYS* 3.6 14.9 + - - +
350P ARG* 2.9 9.4 + - - +
352P LYS* 1.3 73.7 - - - +
354P LEU* 1.3 58.8 + - - +
356P ASN* 2.5 34.2 + - - +
357P ARG* 2.8 24.1 + - + +
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Residues in contact with LEU 354 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275P ILE* 3.8 28.7 - - + -
276P LEU* 3.9 13.4 - - + +
305P LEU* 5.8 2.9 - - + -
309P PHE* 4.7 7.6 - - + -
317P TRP* 3.0 35.9 - - + -
320P LEU* 5.3 2.5 - - + -
328P LEU* 4.6 9.6 - - + -
341P PHE* 4.0 18.2 - - + -
350P ARG 2.9 16.5 + - - +
351P TRP* 3.2 20.0 - - + +
353P ASP* 1.3 72.3 - - - +
355P LYS* 1.3 63.9 + - - +
357P ARG* 3.3 4.7 + - + +
358P VAL* 2.9 33.3 + - + +
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Residues in contact with LYS 355 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317P TRP* 4.5 25.7 - - + +
351P TRP 3.3 10.4 + - - +
352P LYS* 3.2 12.5 + - - +
353P ASP 3.1 0.6 - - - -
354P LEU* 1.3 80.8 - - - +
356P ASN* 1.3 65.4 + - - +
358P VAL* 3.1 9.6 + - + +
359P VAL* 3.0 34.7 + - + +
384P LEU* 5.8 6.1 - - + -
392P PHE* 4.7 9.2 - - + -
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Residues in contact with ASN 356 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352P LYS* 2.9 21.2 + - - -
353P ASP* 2.5 18.1 + - - +
355P LYS* 1.3 69.1 - - - +
357P ARG* 1.3 76.7 + - - +
359P VAL* 2.8 15.2 + - - +
360P GLU* 2.8 20.1 + - + +
392P PHE* 4.3 23.1 - - + -
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Residues in contact with ARG 357 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240P TYR* 5.6 4.6 - - - -
275P ILE 3.6 14.1 - - - +
276P LEU* 2.5 30.7 + - + +
277P ALA 3.4 13.2 - - - -
278P PRO* 3.2 39.6 - - - +
279P PHE 4.7 1.6 - - - +
309P PHE* 4.7 12.8 - - + -
353P ASP* 2.8 26.4 + - - +
354P LEU* 3.7 9.9 - - + +
356P ASN* 1.3 83.3 - - - +
358P VAL* 1.3 57.6 + - - +
360P GLU* 3.3 33.5 + - - +
361P HIS* 2.9 28.8 + - - +
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Residues in contact with VAL 358 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309P PHE* 4.3 17.9 - - + -
315P MET* 3.8 27.8 - - + -
317P TRP* 4.1 43.1 - - + +
354P LEU* 2.9 25.0 + - + +
355P LYS* 3.3 9.9 - - + +
356P ASN 3.1 0.2 - - - -
357P ARG* 1.3 74.3 - - - +
359P VAL* 1.3 69.4 + - + +
361P HIS* 2.8 17.3 + - - +
362P ASN* 3.0 21.4 + - - +
383P ASP* 5.7 1.3 - - - +
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Residues in contact with VAL 359 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355P LYS* 3.0 22.7 + - + +
356P ASN 2.8 12.1 + - - +
358P VAL* 1.3 74.0 - - + +
360P GLU* 1.3 64.1 + - - +
361P HIS 2.9 0.9 + - - -
362P ASN* 3.1 4.9 + - - +
363P ILE* 2.9 29.5 + - + +
382P LEU* 4.7 7.9 - - + +
384P LEU* 4.0 11.7 - - + -
392P PHE* 3.4 50.0 - - + -
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Residues in contact with GLU 360 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278P PRO* 4.3 4.7 - - - +
279P PHE* 4.2 18.5 + - + +
356P ASN* 2.8 23.3 + - + +
357P ARG* 3.3 40.5 + - - +
359P VAL* 1.3 72.5 - - + +
361P HIS* 1.3 50.6 + - - +
363P ILE* 3.9 0.3 - - - +
364P ARG* 2.6 38.7 + - - +
392P PHE* 5.4 3.3 - - + -
396P LEU* 4.2 38.7 - - + +
401P THR* 5.8 0.7 - - - -
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Residues in contact with HIS 361 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308P LEU 4.4 2.4 + - - -
309P PHE* 3.8 28.3 + + + +
310P THR 5.3 0.4 - - - -
311P THR 3.7 23.9 + - - -
312P MET* 4.9 0.2 - - - -
313P GLU 3.5 19.0 + - - -
315P MET* 3.3 33.3 - - + +
357P ARG 2.9 13.8 + - - +
358P VAL* 2.8 15.1 + - - +
360P GLU* 1.3 74.7 - - - +
362P ASN* 1.3 65.6 + - - +
364P ARG* 2.9 31.1 + - - +
365P ILE* 2.9 29.1 + - + +
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Residues in contact with ASN 362 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313P GLU 3.8 1.9 - - - +
314P LEU* 3.4 19.4 - - + +
315P MET* 2.8 48.3 + - - +
316P ARG 4.0 6.7 - - - +
358P VAL* 3.0 19.8 + - - +
359P VAL* 3.9 3.7 - - - +
361P HIS* 1.3 73.8 - - - +
363P ILE* 1.3 65.9 + - - +
365P ILE* 3.0 5.1 + - - +
366P MET* 2.9 27.0 + - - +
381P LEU 4.6 7.9 + - - -
382P LEU* 3.2 25.8 - - + +
383P ASP* 4.9 6.3 + - - -
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Residues in contact with ILE 363 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359P VAL 2.9 16.7 + - - +
362P ASN* 1.3 77.5 - - - +
364P ARG* 1.3 62.0 + - - +
366P MET* 4.1 9.1 - - - +
367P ALA* 3.6 19.2 + - - +
382P LEU* 3.9 14.8 - - + +
392P PHE* 5.9 4.7 - - + -
393P LEU* 4.7 17.0 - - + +
396P LEU* 3.7 26.9 - - + -
402P ILE* 4.0 20.3 - - + +
415P PHE* 5.1 10.4 - - + -
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Residues in contact with ARG 364 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279P PHE* 3.0 55.1 - - + -
310P THR 5.6 0.8 + - - -
312P MET* 3.3 31.7 - - - +
360P GLU 2.6 23.3 + - - +
361P HIS* 2.9 23.8 + - - +
363P ILE* 1.3 80.3 - - - +
365P ILE* 1.3 74.5 + - - +
367P ALA* 3.9 8.8 - - - +
368P LYS* 3.8 23.3 - - - +
396P LEU* 5.7 0.9 - - + -
401P THR 5.8 3.1 - - - +
402P ILE* 4.9 9.4 - - + +
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Residues in contact with ILE 365 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312P MET* 4.1 17.5 - - + -
313P GLU 4.3 9.6 - - - +
314P LEU* 5.5 3.1 - - + -
361P HIS* 2.9 30.8 + - + +
362P ASN* 3.0 5.4 + - - +
364P ARG* 1.3 102.3 - - - +
366P MET* 1.3 56.3 + - - +
367P ALA 3.0 1.8 - - - -
368P LYS* 2.4 39.9 + - + +
369P TYR* 3.3 22.2 + - + -
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Residues in contact with MET 366 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312O MET* 6.1 0.2 - - - -
314P LEU* 4.4 16.0 - - + +
362P ASN 2.9 23.3 + - - +
363P ILE* 4.1 8.3 - - - +
365P ILE* 1.3 73.6 - - - +
367P ALA* 1.3 63.7 + - - +
368P LYS 3.0 1.4 + - - -
369P TYR* 5.2 1.1 - - - -
370P TYR* 3.1 54.4 + - + +
373P ILE* 5.4 5.2 - - + -
378P MET* 6.0 2.9 - - + -
381P LEU* 5.4 5.4 - - + -
382P LEU* 4.9 11.2 - - + -
415P PHE* 4.3 21.7 - - + -
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Residues in contact with ALA 367 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363P ILE 3.6 11.1 + - - +
364P ARG 3.9 12.1 - - - +
365P ILE 3.0 0.4 + - - -
366P MET* 1.3 78.4 - - - +
368P LYS* 1.3 62.5 + - + +
370P TYR 4.3 5.7 - - - +
402P ILE* 4.6 18.8 - - + -
403P PHE 5.7 2.7 - - - +
415P PHE* 4.6 28.2 - - + +
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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