Contacts of the helix formed by residues 348 - 366 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156D ARG 4.6 1.6 - - - +
218D HIS* 2.9 31.0 + - - +
219D THR 4.5 3.8 + - - +
233D LYS* 5.7 0.3 + - - -
297D PHE* 2.9 37.3 - - + +
299D LEU* 3.8 15.9 + - - +
346D SER* 2.9 18.8 + - - +
347D PRO* 1.3 71.9 - - - +
349D LYS* 1.3 67.5 + - - +
350D MET* 3.0 21.0 + - - +
351D LEU* 2.9 13.5 + - + +
352D GLN* 2.9 21.4 + - - +
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Residues in contact with LYS 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B VAL* 4.0 14.0 + - + -
43B THR* 4.0 23.0 + - + -
46B PRO 3.8 21.7 + - - -
48B GLY 5.3 0.7 - - - +
50B LEU* 4.8 1.9 - - - +
156D ARG 3.7 17.7 - - - +
157D ASP* 3.9 20.2 + - + +
158D PRO* 2.9 18.2 - - + +
295D ASN* 6.1 2.7 - - - +
297D PHE 4.7 0.4 + - - -
347D PRO 2.8 12.3 + - - +
348D ASP* 1.3 71.9 + - - +
350D MET* 1.3 64.7 + - - +
352D GLN* 3.1 10.3 + - - +
353D GLY 2.9 18.7 + - - -
432D PHE* 3.0 34.6 + - - +
434D THR* 3.4 20.4 - - + +
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Residues in contact with MET 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D PHE* 3.8 15.3 - - + -
155D ILE* 3.4 31.4 - - + +
156D ARG* 3.5 16.2 - - - +
157D ASP 3.1 40.6 - - - +
158D PRO* 3.5 6.5 - - - +
218D HIS* 3.6 15.9 - - + -
299D LEU* 3.7 15.9 - - + -
348D ASP* 3.0 11.7 + - - +
349D LYS* 1.3 73.5 - - - +
351D LEU* 1.3 64.6 + - - +
353D GLY* 3.0 11.6 + - - -
354D ARG* 3.1 17.0 + - - +
1203D HEM 3.4 29.3 - - + +
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Residues in contact with LEU 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D HIS* 3.3 34.0 + - + +
219D THR 3.8 17.9 - - - +
220D PHE* 3.6 34.8 - - + -
336D PRO* 4.4 16.2 - - + +
339D MET* 5.8 0.2 - - + -
345D ALA* 3.8 20.6 - - + -
346D SER* 4.0 5.4 - - - +
348D ASP* 2.9 11.7 + - + +
350D MET* 1.3 79.0 - - - +
352D GLN* 1.3 63.8 + - - +
354D ARG* 2.9 16.7 + - + +
355D LEU* 2.9 35.0 + - + +
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Residues in contact with GLN 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 3.9 9.9 - - - +
53A GLN* 2.8 50.6 + - - +
49B PRO* 3.7 3.0 - - + +
50B LEU* 3.2 43.8 + - + +
345D ALA* 4.3 3.4 - - - +
346D SER 3.0 21.8 + - - +
347D PRO* 3.9 6.8 - - - +
348D ASP 2.9 21.5 + - - +
349D LYS* 3.3 9.9 - - - +
351D LEU* 1.3 74.8 - - - +
353D GLY* 1.3 63.3 + - - +
355D LEU* 3.1 31.9 - - - +
356D PHE 3.9 1.2 + - - -
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Residues in contact with GLY 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU* 3.9 6.0 - - - +
57B PHE* 3.9 26.0 - - - -
158D PRO* 4.0 8.3 - - - -
349D LYS 2.9 12.4 + - - -
350D MET 3.0 4.4 + - - -
352D GLN* 1.3 77.4 - - - +
354D ARG* 1.3 60.0 + - - +
356D PHE* 3.1 16.9 + - - +
357D ALA* 3.2 14.6 + - - +
1203D HEM 5.1 3.4 - - - -
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Residues in contact with ARG 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D VAL* 3.0 45.1 + - - +
218D HIS* 3.1 42.1 + - - -
220D PHE* 5.8 1.2 - - - -
336D PRO* 3.9 21.3 - - + +
350D MET 3.1 10.9 + - - +
351D LEU* 2.9 10.4 + - + +
353D GLY* 1.3 69.8 - - - +
355D LEU* 1.3 67.9 + - - +
356D PHE 2.9 3.6 + - - -
357D ALA* 3.4 8.6 + - - +
358D TYR* 2.7 61.0 + - + +
1203D HEM 3.0 49.0 - - + +
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Residues in contact with LEU 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 4.4 7.9 - - + -
53A GLN* 4.2 23.3 - - + +
55A VAL* 4.4 20.3 - - + +
336D PRO 4.6 1.8 - - - -
337D SER* 3.6 40.1 + - - +
339D MET* 4.6 5.2 - - + -
345D ALA* 4.3 13.5 - - + -
351D LEU* 2.9 36.0 + - + +
352D GLN* 3.1 44.4 - - - +
354D ARG* 1.3 76.7 - - - +
356D PHE* 1.3 58.6 + - - +
359D PRO* 3.6 7.6 - - - +
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Residues in contact with PHE 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 4.1 20.0 - - + -
58A THR* 5.2 11.9 - - + -
57B PHE* 4.6 10.8 - + + -
58B THR* 3.8 27.8 - - + -
61B MET* 4.0 24.0 - - + -
62B ALA* 4.2 8.3 - - + -
65B ASP* 3.8 17.0 - - - -
356C PHE* 4.0 27.6 - + - -
363C ARG* 5.3 2.2 - - - -
353D GLY 3.1 8.6 + - - +
354D ARG 2.9 0.8 + - - -
355D LEU* 1.3 80.0 - - - +
357D ALA* 1.3 78.9 + - - +
359D PRO* 3.3 18.0 - - - +
360D ASP* 3.4 35.2 + - + +
363D ARG* 5.4 1.7 + - - -
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Residues in contact with ALA 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B MET* 4.1 7.2 - - + -
65B ASP* 3.5 28.0 - - - +
353D GLY 3.2 10.8 + - - +
354D ARG 3.4 2.2 + - - +
356D PHE* 1.3 81.5 - - - +
358D TYR* 1.3 59.0 + - + +
360D ASP* 3.1 2.9 + - - +
361D THR* 2.7 35.8 + - - -
1203D HEM 4.0 27.8 - - + -
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Residues in contact with TYR 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D VAL* 4.1 7.2 - - + -
334D PHE* 3.4 17.9 - - + +
335D ASP* 3.3 9.4 - - - +
336D PRO* 3.2 19.1 - - + -
354D ARG* 2.7 53.5 + - + -
357D ALA* 1.3 73.2 - - + +
359D PRO* 1.3 71.3 - - + +
361D THR* 3.0 7.6 - - - +
362D HIS* 2.8 28.0 + - + -
1203D HEM 1.8 95.8 + + + -
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Residues in contact with PRO 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A THR* 6.0 4.0 - - + -
335D ASP* 3.0 17.9 - - - +
336D PRO* 5.1 0.2 - - + -
337D SER* 3.9 13.2 - - - +
355D LEU 3.6 18.2 - - - +
356D PHE* 3.3 15.7 - - - +
358D TYR* 1.3 89.3 - - + +
360D ASP* 1.3 60.8 + - - +
362D HIS* 3.1 3.6 + - - +
363D ARG* 3.0 53.8 + - - +
370D TYR* 3.3 16.3 - - - +
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Residues in contact with ASP 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ARG* 4.5 0.7 + - - -
62B ALA* 3.6 7.8 - - - +
65B ASP* 2.6 22.9 - - - +
66B ARG* 2.8 45.8 + - - -
360C ASP* 4.2 10.7 - - - +
363C ARG* 5.1 2.3 + - - -
356D PHE* 3.5 33.3 - - + +
357D ALA 3.1 8.7 + - - +
359D PRO* 1.3 79.7 - - - +
361D THR* 1.3 62.9 + - - +
363D ARG* 3.0 29.7 + - - +
364D HIS* 3.5 6.1 + - - +
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Residues in contact with THR 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ASP* 2.9 38.2 + - - -
73D VAL* 4.5 6.9 + - - +
357D ALA 2.7 17.4 + - - +
358D TYR 3.0 15.0 - - - +
360D ASP* 1.3 73.6 + - - +
362D HIS* 1.3 62.2 + - - +
364D HIS* 3.0 6.4 + - - +
365D ARG* 2.8 29.7 + - - +
1203D HEM 3.7 53.1 + - + +
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Residues in contact with HIS 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D ALA* 3.4 31.1 - - + +
334D PHE 3.1 29.1 + - - -
335D ASP* 2.8 16.0 + - - -
358D TYR* 2.8 27.8 + - + +
359D PRO 3.3 5.2 - - - +
360D ASP 3.1 0.2 - - - -
361D THR* 1.3 74.8 - - - +
363D ARG* 1.3 60.8 + - - +
364D HIS 3.0 1.8 - - - -
365D ARG* 3.7 9.6 - - - +
366D LEU* 2.8 33.6 + - + +
367D GLY 3.2 4.3 + - - +
370D TYR* 3.6 21.5 - - + -
1203D HEM 2.6 41.0 + - + -
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Residues in contact with ARG 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A THR* 4.9 9.5 - - - +
59A ASP* 4.5 20.2 + - - +
62A ALA* 3.2 30.6 - - - +
63A HIS* 6.0 0.4 - - - +
66A ARG* 3.6 45.8 - - - +
66B ARG* 5.1 0.9 - - - +
356C PHE* 5.0 3.2 - - - -
360C ASP* 4.9 2.4 + - - -
356D PHE* 5.4 1.8 + - - -
359D PRO* 3.0 39.6 + - - +
360D ASP* 3.0 28.2 + - - +
362D HIS* 1.3 75.9 - - - +
364D HIS* 1.3 56.6 + - - +
367D GLY* 3.1 33.4 + - - +
368D PRO* 3.7 9.6 + - + +
370D TYR* 3.9 17.3 + - + -
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Residues in contact with HIS 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ASP 3.6 18.6 - - - +
66B ARG* 3.6 44.8 + - + +
68B ARG* 3.0 28.9 + - + -
368C PRO* 4.1 7.7 - - + +
391C PRO* 3.7 24.5 - - + -
70D PRO* 4.4 12.5 - - + +
360D ASP 3.5 3.4 + - - +
361D THR* 3.0 9.8 + - - +
362D HIS 3.0 0.6 - - - -
363D ARG* 1.3 81.1 - - - +
365D ARG* 1.3 72.6 + - + +
366D LEU 3.5 0.9 + - - -
367D GLY* 4.4 1.4 + - - -
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Residues in contact with ARG 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ILE* 4.0 16.6 - - + +
70D PRO* 3.1 45.9 - - + +
71D GLU 3.9 1.1 - - - -
72D ARG* 3.5 32.7 - - - +
330D GLU* 2.6 29.1 + - - -
332D ILE 3.1 22.8 + - - -
361D THR* 2.8 21.2 + - - +
362D HIS* 3.7 11.8 - - - +
364D HIS* 1.3 82.3 - - + +
366D LEU* 1.3 79.6 + - + +
1203D HEM 2.9 38.7 + - - +
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Residues in contact with LEU 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A PRO* 4.9 6.5 - - - +
392A MET* 3.0 32.0 + - + +
69D ILE* 4.0 15.9 - - + -
331D GLN* 3.4 42.2 - - + +
333D ALA* 3.7 23.8 - - + -
362D HIS* 2.8 19.7 + - + +
364D HIS 4.5 1.8 - - - -
365D ARG* 1.3 105.4 - - + +
367D GLY* 1.3 57.3 + - - +
370D TYR* 3.5 17.3 - - + -
373D ILE* 4.3 4.0 - - + -
376D ASN* 4.0 6.5 - - - +
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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