Contacts of the helix formed by residues 358 - 373 (chain A) in PDB entry 3C6G
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 MET 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A GLU* 3.3 12.6 - - - +
340A ILE* 3.8 40.4 - - + +
343A ILE* 4.1 16.4 - - + -
344A MET* 3.6 30.7 - - + +
354A ASP* 3.5 13.5 - - - +
355A LYS 2.8 16.4 + - - +
357A LYS* 1.3 86.1 - - - +
359A PRO* 1.4 66.8 - - - +
360A TYR 3.3 2.7 - - - -
361A THR* 3.2 23.9 + - - +
362A GLU* 3.1 19.2 + - - +
459A PHE* 3.9 12.6 - - + -
463A THR* 4.4 5.6 - - + -
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Residues in contact with PRO 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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339A GLU* 3.3 9.0 - - - +
355A LYS 4.2 0.9 - - - +
356A CYS 4.6 5.2 - - - +
357A LYS* 3.5 8.1 - - - +
358A MET* 1.4 88.8 - - - +
360A TYR* 1.3 52.8 + - + +
362A GLU* 3.3 4.7 + - + +
363A ALA* 2.7 34.7 + - - +
426A LEU* 3.8 5.1 - - + +
430A GLY 3.1 28.5 - - - +
431A TYR* 3.7 13.7 - - + -
432A PHE* 3.4 31.4 - - + +
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Residues in contact with TYR 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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332A ILE* 3.6 32.4 - - - +
335A GLN* 3.6 38.0 - - + +
336A VAL* 3.9 15.5 - - + -
339A GLU* 2.8 21.7 + - + +
359A PRO* 1.3 78.9 - - + +
361A THR* 1.3 57.8 + - - +
363A ALA* 3.2 4.9 + - + +
364A VAL* 3.0 46.8 + - + +
422A PRO* 4.1 18.1 - - + +
423A GLU* 4.9 8.7 + - + -
426A LEU* 3.9 26.7 - - + +
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Residues in contact with THR 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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336A VAL* 3.4 27.5 + - + +
339A GLU* 2.9 22.6 + - - -
358A MET* 3.2 19.0 + - - +
360A TYR* 1.3 74.3 - - - +
362A GLU* 1.3 66.5 + - - +
364A VAL* 3.3 3.5 + - - +
365A LEU* 3.1 24.7 + - + +
459A PHE* 3.9 27.4 - - + -
462A PHE* 4.2 22.8 - - + -
463A THR* 4.2 7.6 - - + -
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Residues in contact with GLU 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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355A LYS* 3.4 51.3 + - + +
356A CYS* 4.9 3.5 - - - -
358A MET 3.1 9.9 + - - +
359A PRO* 3.7 8.4 - - + +
361A THR* 1.3 80.5 - - - +
363A ALA* 1.3 62.3 + - - +
365A LEU* 3.5 8.3 + - + +
366A HIS* 2.8 52.2 + - + -
432A PHE* 3.6 33.6 - - + +
455A ARG* 5.5 0.5 + - - -
459A PHE* 5.4 4.5 - - + -
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Residues in contact with ALA 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 PRO 2.7 21.4 + - - +
360A TYR* 3.3 11.4 - - + +
362A GLU* 1.3 70.1 - - - +
364A VAL* 1.3 66.3 + - - +
366A HIS 3.3 1.0 + - - -
367A GLU* 2.9 24.6 + - - +
422A PRO* 3.6 28.3 - - + +
425A PHE* 3.7 14.9 - - + -
426A LEU* 4.2 11.0 - - + -
432A PHE* 4.0 9.6 - - + -
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Residues in contact with VAL 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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326A MET* 3.7 26.7 - - + -
332A ILE* 3.9 10.3 - - + -
336A VAL* 3.7 13.5 - - + -
360A TYR* 3.0 42.9 + - + +
361A THR 3.7 6.1 - - - +
363A ALA* 1.3 73.9 - - - +
365A LEU* 1.3 65.1 + - + +
367A GLU* 3.0 4.0 + - - +
368A VAL* 2.9 36.6 + - + +
420A PHE* 4.6 4.4 - - + -
422A PRO* 4.0 13.7 - - + -
462A PHE* 4.1 17.0 - - + -
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Residues in contact with LEU 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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318A VAL* 5.3 5.7 - - + +
319A LEU* 5.5 2.0 - - + -
322A ALA* 4.9 10.3 - - + -
361A THR* 3.1 17.8 + - + +
362A GLU* 3.8 8.3 - - + +
364A VAL* 1.3 79.7 - - + +
366A HIS* 1.3 64.4 + - + +
368A VAL* 3.3 8.2 + - + +
369A LEU* 3.2 25.5 + - - +
455A ARG 5.5 0.2 - - - +
458A MET* 4.0 27.9 - - + +
459A PHE* 3.8 44.0 - - + +
462A PHE* 3.6 40.2 - - + -
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Residues in contact with HIS 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 GLU* 2.8 50.9 + - + +
363A ALA 3.8 3.4 - - - +
365A LEU* 1.3 78.0 - - + +
367A GLU* 1.3 56.8 + - - +
369A LEU* 3.3 14.1 + - + +
370A ARG* 2.9 28.6 + - - +
425A PHE* 3.7 17.1 - - + -
432A PHE* 3.4 35.3 - + + -
438A LEU* 3.5 23.6 - - + +
455A ARG* 2.8 33.7 + - - -
458A MET* 6.4 1.6 - - + -
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Residues in contact with GLU 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 ALA 2.9 18.2 + - - +
364A VAL 3.0 4.2 + - - +
366A HIS* 1.3 74.3 - - - +
368A VAL* 1.3 59.9 + - - +
370A ARG* 2.8 38.8 + - - -
371A PHE* 3.0 32.9 + - - +
419A VAL 3.3 0.9 - - - +
420A PHE* 3.6 18.0 - - + -
421A HIS 2.8 34.2 + - - +
422A PRO* 3.7 14.8 - - + -
424A ARG* 3.0 18.8 + - - -
425A PHE* 3.3 14.0 - - + -
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Residues in contact with VAL 368 (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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318A VAL* 3.8 31.4 - - + +
321A TRP* 3.9 20.2 - - + +
322A ALA* 4.1 23.1 - - + +
325A PHE* 5.3 2.9 - - + -
326A MET* 5.8 0.2 - - + -
364A VAL* 2.9 29.0 + - + +
365A LEU* 3.5 9.9 - - + +
367A GLU* 1.3 74.9 - - - +
369A LEU* 1.3 59.4 + - - +
372A CYS* 2.9 37.8 + - + +
374A ILE* 4.3 2.8 - - + +
420A PHE* 4.1 18.2 - - + -
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Residues in contact with LEU 369 (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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318A VAL* 3.6 35.9 - - + -
365A LEU 3.2 11.3 + - - +
366A HIS* 3.3 24.0 + - + +
368A VAL* 1.3 80.4 - - - +
370A ARG* 1.3 63.0 + - - +
373A ASN* 3.3 20.8 + - - +
374A ILE* 4.7 6.8 + - + -
408A HIS* 4.3 5.2 + - - -
438A LEU* 4.6 3.1 - - + -
440A PRO* 3.9 35.4 - - + +
441A PHE* 4.1 14.4 - - + -
455A ARG* 5.2 4.0 - - - +
458A MET* 4.2 21.5 - - + -
601A HEM 4.5 9.6 - - + -
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Residues in contact with ARG 370 (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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366A HIS 2.9 17.6 + - - +
367A GLU* 2.8 39.1 + - - +
369A LEU* 1.3 78.5 - - - +
371A PHE* 1.3 67.9 - - - +
373A ASN* 3.1 19.6 + - - -
408A HIS* 2.7 53.1 + - + +
409A PHE* 3.8 7.3 - - - -
414A TRP* 3.5 36.6 - - + -
417A PRO* 3.0 37.4 + - - +
419A VAL 3.3 10.9 + - - -
424A ARG* 3.6 11.9 - - - +
425A PHE* 4.3 1.6 - - + -
438A LEU* 3.6 19.9 - - + +
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Residues in contact with PHE 371 (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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325A PHE* 3.7 39.0 - + - -
367A GLU 3.0 19.8 + - - +
368A VAL 4.4 0.4 - - - +
370A ARG* 1.3 100.2 - - - +
372A CYS* 1.3 63.6 + - - +
373A ASN* 3.6 6.3 + - - -
409A PHE* 4.1 18.2 - + - -
417A PRO 4.0 3.6 - - - -
418A GLU* 3.4 30.3 - - - -
420A PHE* 3.7 30.7 - + + -
481A LEU* 6.0 1.3 - - + -
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Residues in contact with CYS 372 (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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321A TRP* 3.7 53.5 + - + -
325A PHE* 4.0 18.4 - - - -
368A VAL* 2.9 26.2 + - - +
371A PHE* 1.3 81.9 - - - +
373A ASN* 1.3 75.3 + - - +
374A ILE* 3.4 8.6 + - + -
420A PHE* 5.8 0.4 - - - -
489A LEU* 3.3 19.1 - - - +
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Residues in contact with ASN 373 (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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368A VAL 4.1 0.2 + - - -
369A LEU 3.3 11.5 + - - -
370A ARG 3.1 20.5 + - - -
371A PHE 3.7 6.1 + - - -
372A CYS* 1.3 80.6 - - - +
374A ILE* 1.3 66.9 + - - +
375A VAL 3.2 4.7 + - - +
376A PRO* 3.4 20.6 - - + +
404A LEU* 4.2 0.3 - - - +
405A TYR* 3.5 28.3 + - + -
408A HIS* 2.6 32.8 + - - -
409A PHE* 3.6 20.2 - - - -
440A PRO* 6.3 1.3 - - - -
489A LEU* 3.3 18.6 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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