Contacts of the helix formed by residues 348 - 366 (chain A) in PDB entry 1DGB
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 ASP 348 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ARG 4.7 1.4 - - - +
218A HIS* 2.8 34.0 + - - +
219A THR 4.5 4.3 + - - +
233A LYS* 5.9 0.2 + - - -
297A PHE* 3.0 34.8 - - + +
299A LEU* 3.9 14.5 + - - +
346A SER* 2.9 19.0 + - - +
347A PRO* 1.3 73.6 - - - +
349A LYS* 1.3 57.9 + - - +
350A MET* 3.0 18.2 + - - +
351A LEU* 3.0 11.0 + - + +
352A GLN* 2.8 33.7 + - - +
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Residues in contact with LYS 349 (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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156A ARG 3.9 11.7 - - - +
157A ASP* 3.6 22.3 + - + +
158A PRO* 3.0 20.3 - - + +
297A PHE 4.7 0.6 + - - -
347A PRO 3.0 12.1 + - - +
348A ASP* 1.3 71.8 + - - +
350A MET* 1.3 66.3 + - - +
352A GLN* 2.8 11.8 + - - +
353A GLY 2.8 21.0 + - - -
432A PHE* 3.4 30.7 + - - +
434A THR* 3.5 20.9 - - + +
41C VAL* 4.5 12.8 + - + -
43C THR* 3.7 31.7 + - + +
46C PRO 4.0 17.4 + - - -
48C GLY 5.2 0.4 - - - +
50C LEU* 5.1 0.4 - - - +
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Residues in contact with MET 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A PHE* 3.8 11.4 - - + -
155A ILE* 3.6 24.9 - - + +
156A ARG* 3.5 20.0 - - - +
157A ASP 3.5 33.4 - - - +
158A PRO* 3.5 5.8 - - - +
218A HIS* 3.5 16.4 - - + -
299A LEU* 3.5 26.9 - - + -
348A ASP* 3.0 8.7 + - - +
349A LYS* 1.3 77.8 - - - +
351A LEU* 1.3 62.7 + - - +
353A GLY 3.2 0.5 + - - -
354A ARG* 3.0 25.9 + - - +
1200A HEM 3.2 33.3 - - + +
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Residues in contact with LEU 351 (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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218A HIS* 3.3 36.6 - - + +
219A THR 4.1 9.4 - - - +
220A PHE* 3.8 31.6 - - + -
336A PRO* 4.5 14.6 - - + +
339A MET* 5.9 0.2 - - + -
345A ALA* 3.9 9.6 - - + -
346A SER* 3.8 27.8 - - - +
348A ASP* 3.0 11.3 + - + +
350A MET* 1.3 76.4 - - - +
352A GLN* 1.3 68.5 + - - +
354A ARG* 2.9 18.2 + - + +
355A LEU* 2.9 29.2 + - + +
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Residues in contact with GLN 352 (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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345A ALA* 4.3 2.8 - - - +
346A SER 3.1 17.0 + - - +
347A PRO* 4.2 5.4 - - - +
348A ASP 2.8 25.6 + - - +
349A LYS* 3.1 11.0 - - - +
351A LEU* 1.3 72.0 - - - +
353A GLY* 1.3 59.0 + - - +
355A LEU* 3.0 36.0 - - - +
48C GLY 5.5 0.2 - - - +
49C PRO* 3.3 8.8 - - + +
50C LEU* 2.7 50.9 + - + +
52D VAL* 3.8 13.3 - - - +
53D GLN* 2.9 42.8 + - - +
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Residues in contact with GLY 353 (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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158A PRO* 4.1 7.9 - - - -
349A LYS 2.8 13.1 + - - -
350A MET 3.6 3.6 - - - -
352A GLN* 1.3 73.9 - - - +
354A ARG* 1.3 62.4 + - - +
355A LEU 2.9 5.3 + - - -
356A PHE* 3.0 15.8 + - - +
357A ALA* 3.3 12.2 + - - +
1200A HEM 4.8 3.1 - - - -
50C LEU* 4.0 4.6 - - - +
57C PHE* 3.9 27.1 - - - -
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Residues in contact with ARG 354 (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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146A VAL* 3.0 44.5 + - - +
216A GLY 4.9 0.2 + - - -
218A HIS* 3.1 42.6 + - - -
220A PHE* 5.8 1.2 - - - -
336A PRO* 3.9 21.0 - - + +
350A MET 3.0 12.9 + - - +
351A LEU* 2.9 13.9 + - + +
353A GLY* 1.3 70.9 - - - +
355A LEU* 1.3 63.7 + - - +
356A PHE 3.1 0.9 + - - -
357A ALA* 3.4 8.9 + - - -
358A TYR* 2.7 65.3 + - + +
1200A HEM 3.0 51.5 - - + +
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Residues in contact with LEU 355 (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 PRO* 4.4 3.1 - - + -
337A SER* 3.6 41.3 + - - +
339A MET* 4.4 9.6 - - + -
345A ALA* 4.1 13.2 - - + -
351A LEU* 2.9 27.9 + - + +
352A GLN* 3.0 47.3 - - - +
354A ARG* 1.3 78.8 - - - +
356A PHE* 1.3 56.2 + - - +
359A PRO* 3.9 8.0 - - - +
52D VAL* 4.3 9.0 - - + -
53D GLN* 4.4 16.6 - - - +
55D VAL* 4.4 21.2 - - + +
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Residues in contact with PHE 356 (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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352A GLN 4.1 0.4 + - - +
353A GLY 3.0 6.8 + - - +
355A LEU* 1.3 80.4 - - - +
357A ALA* 1.3 69.6 + - - +
358A TYR 3.5 0.6 + - - -
359A PRO* 3.5 6.6 - - - +
360A ASP* 3.2 54.5 + - + +
363A ARG* 5.1 1.5 + - - -
356B PHE* 3.9 30.7 - + - -
360B ASP* 5.6 0.2 - - - -
363B ARG* 5.2 2.5 - - - -
57C PHE* 4.5 14.6 - + + -
58C THR* 3.9 26.5 - - + -
61C MET* 4.0 22.4 - - + -
62C ALA* 4.2 10.3 - - + -
65C ASP* 3.8 7.6 - - - -
52D VAL* 4.4 17.0 - - + -
58D THR* 5.0 11.4 - - + -
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Residues in contact with ALA 357 (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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353A GLY 3.3 9.6 + - - +
354A ARG* 3.4 2.9 + - - +
356A PHE* 1.3 81.3 - - - +
358A TYR* 1.3 60.9 + - + +
360A ASP* 3.0 3.6 + - - +
361A THR* 2.7 35.4 + - - -
1200A HEM 3.9 31.0 - - + -
61C MET* 4.2 6.7 - - + -
65C ASP* 3.3 26.4 - - - +
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Residues in contact with TYR 358 (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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146A VAL* 4.0 7.6 - - + -
334A PHE* 3.2 17.5 - - + +
335A ASP* 3.3 11.9 - - - +
336A PRO* 3.2 17.9 - - + -
354A ARG* 2.7 52.6 + - + -
357A ALA* 1.3 75.5 - - + +
359A PRO* 1.3 72.9 - - + +
360A ASP 3.0 0.2 + - - -
361A THR* 3.1 7.9 - - - +
362A HIS* 2.9 24.9 + - + -
1200A HEM 1.7 98.1 + + + -
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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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335A ASP* 3.0 15.7 - - + +
336A PRO* 5.3 0.2 - - + -
337A SER* 4.0 11.2 - - - +
354A ARG 4.5 0.7 - - - +
355A LEU 3.9 17.9 - - - +
356A PHE* 3.5 10.5 - - - +
358A TYR* 1.3 91.8 - - + +
360A ASP* 1.3 62.8 + - - +
362A HIS* 3.3 1.9 + - - +
363A ARG* 3.0 54.6 + - - +
370A TYR* 3.3 19.7 - - - +
58D THR* 6.0 3.4 - - + -
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Residues in contact with ASP 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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356A PHE* 3.2 42.7 + - + +
357A ALA 3.0 9.9 + - - +
359A PRO* 1.3 78.8 - - - +
361A THR* 1.3 61.7 + - - +
363A ARG* 3.2 27.2 + - - +
364A HIS* 3.6 4.3 + - - +
360B ASP* 4.2 9.2 - - - +
363B ARG* 5.4 1.2 + - - -
62C ALA* 3.6 2.8 - - - +
65C ASP* 2.7 20.3 - - - +
66C ARG* 2.7 48.6 + - - -
66D ARG* 4.4 1.4 + - - -
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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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73A VAL* 4.6 6.4 + - - +
357A ALA 2.7 17.1 + - - +
358A TYR* 3.1 20.0 - - - +
360A ASP* 1.3 74.0 + - - +
362A HIS* 1.3 59.6 + - + +
364A HIS* 3.2 5.0 + - - +
365A ARG* 2.9 30.1 + - - +
1200A HEM 3.5 49.6 + - + +
65C ASP* 3.0 38.0 + - - -
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Residues in contact with HIS 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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333A ALA* 3.5 28.4 - - + +
334A PHE 3.0 20.1 + - - -
335A ASP* 2.7 32.2 + - - -
358A TYR* 2.9 20.6 + + + +
359A PRO 3.6 0.7 - - - +
361A THR* 1.3 74.3 - - + +
363A ARG* 1.3 62.4 + - - +
364A HIS 2.9 5.6 - - - -
365A ARG* 4.2 10.1 - - - +
366A LEU* 3.1 16.9 + - + +
367A GLY 3.0 17.8 + - - +
370A TYR* 3.5 29.3 - - + -
1200A HEM 2.8 36.0 + - - +
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Residues in contact with ARG 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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356A PHE* 5.1 1.6 + - - -
359A PRO* 3.0 44.0 + - - +
360A ASP* 3.2 20.0 + - - +
362A HIS* 1.3 77.2 - - - +
364A HIS* 1.3 57.1 + - - +
367A GLY* 3.2 29.4 - - - +
368A PRO* 3.7 11.8 + - - +
370A TYR* 4.0 16.7 + - + -
356B PHE* 5.2 2.8 - - - -
360B ASP* 5.1 2.4 + - - -
66C ARG* 5.1 1.1 - - - +
58D THR* 4.5 10.5 + - - +
59D ASP* 4.2 24.2 + - - +
62D ALA* 3.2 29.9 - - - +
63D HIS* 5.9 0.4 - - - +
66D ARG* 3.7 44.8 + - - +
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Residues in contact with HIS 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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70A PRO* 4.2 10.7 - - + +
360A ASP 3.6 5.3 + - - +
361A THR* 3.3 11.0 - - - +
362A HIS 2.9 1.4 - - - -
363A ARG* 1.3 79.9 - - - +
365A ARG* 1.3 85.4 + - + +
366A LEU 3.1 3.5 + - - -
367A GLY* 4.1 2.4 + - - -
368B PRO* 4.2 7.7 - - + +
391B PRO* 4.0 18.2 - - + -
65C ASP 3.7 15.7 - - - +
66C ARG* 3.7 47.2 + - + +
68C ARG* 2.9 29.3 + - + -
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Residues in contact with ARG 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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69A ILE* 3.8 17.1 - - - +
70A PRO* 3.5 47.2 + - + +
71A GLU 4.8 1.3 - - - +
72A ARG* 3.2 33.9 - - - +
330A GLU* 2.8 24.9 + - - -
332A ILE 2.8 27.3 + - - -
361A THR* 2.9 21.4 + - - +
362A HIS* 4.2 7.4 - - - -
364A HIS* 1.3 81.9 - - + +
366A LEU* 1.3 92.7 + - + +
1200A HEM 2.8 40.4 + - - +
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Residues in contact with LEU 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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69A ILE* 4.1 13.2 - - + -
331A GLN* 3.5 32.8 - - + +
333A ALA* 3.9 20.0 - - + -
362A HIS* 3.1 12.3 + - + +
364A HIS 4.2 1.8 - - - -
365A ARG* 1.3 119.5 - - + +
367A GLY* 1.3 60.5 + - - +
370A TYR* 3.5 25.6 - - + -
373A ILE* 4.3 14.6 - - + -
391D PRO* 4.9 6.6 - - - +
392D MET* 3.4 27.0 + - - +
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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