Contacts of the helix formed by residues 54 - 65 (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 54 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431B ARG* 2.7 39.8 + - - +
41D VAL* 3.1 16.5 - - - +
42D ILE* 2.8 40.8 + - + +
50D LEU* 4.2 3.8 - - + -
51D LEU* 3.4 14.5 + - - +
52D VAL* 3.0 4.8 - - - +
53D GLN* 1.3 76.7 - - - +
55D VAL* 1.3 58.8 + - - +
56D VAL* 3.6 0.2 - - - +
57D PHE* 3.2 22.8 + - + +
58D THR* 3.3 20.6 + - - -
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Residues in contact with VAL 55 (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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337A SER* 3.6 42.6 - - - +
339A MET* 6.1 1.8 - - + -
355A LEU* 4.4 17.5 - - + +
29D THR* 5.6 5.6 - - + -
52D VAL 4.0 9.4 - - - +
53D GLN 2.8 18.4 + - - +
54D ASP* 1.3 69.8 - - - +
56D VAL* 1.3 67.3 + - + +
57D PHE 3.0 1.6 - - - -
58D THR* 4.2 8.1 - - - +
59D ASP* 2.7 38.3 + - + +
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A GLU* 3.9 9.0 - - - +
159B ILE* 4.4 6.3 - - + -
431B ARG* 3.4 20.0 - - - +
29D THR* 4.4 17.0 - - + -
34D PRO 5.9 0.2 - - - +
35D VAL* 3.6 41.3 - - + -
36D GLY 5.7 0.4 - - - +
37D ASP 4.7 0.4 - - - +
38D LYS* 4.2 15.0 - - + -
54D ASP* 3.6 6.7 - - - +
55D VAL* 1.3 86.7 - - + +
57D PHE* 1.3 64.1 + - - +
59D ASP* 3.4 7.2 - - - +
60D GLU* 3.2 21.2 + - + +
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Residues in contact with PHE 57 (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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158B PRO* 3.6 33.9 - - + -
159B ILE* 3.9 24.9 - - + -
162B PRO* 6.3 0.2 - - + -
353B GLY* 3.9 15.3 - - - -
356B PHE* 4.6 14.1 - + + -
52C VAL* 6.0 2.0 - - + -
41D VAL* 3.8 17.3 - - + -
50D LEU* 4.2 24.0 - - + -
51D LEU 6.1 0.2 - - - -
54D ASP* 3.2 28.0 + - - +
55D VAL 3.0 0.2 - - - -
56D VAL* 1.3 78.1 - - - +
58D THR* 1.3 82.5 + - - +
60D GLU* 3.0 5.4 + - - +
61D MET* 2.8 54.4 + - + +
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Residues in contact with THR 58 (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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356A PHE* 5.0 11.7 - - + -
359A PRO* 6.0 3.1 - - + -
363A ARG* 4.6 13.2 - - - +
356B PHE* 3.6 32.5 - - + -
52D VAL* 4.6 7.3 + - - +
54D ASP 3.3 12.4 + - - -
55D VAL* 3.3 11.1 + - - -
57D PHE* 1.3 87.2 - - - +
59D ASP* 1.3 57.7 + - - +
61D MET* 4.4 3.6 - - - -
62D ALA* 2.6 37.7 + - - +
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Residues in contact with ASP 59 (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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363A ARG* 4.2 17.2 + - - +
371A LEU* 4.8 8.5 - - - +
387A GLN* 3.1 17.5 + - - +
29D THR* 3.5 12.6 - - + -
30D GLY* 2.9 33.9 + - - -
31D ALA* 5.1 0.7 + - - +
55D VAL* 2.7 23.8 + - + +
56D VAL* 3.4 8.4 - - - +
58D THR* 1.3 75.4 - - - +
60D GLU* 1.3 61.3 + - - +
62D ALA* 3.9 2.3 - - - +
63D HIS* 3.4 19.4 + - - +
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Residues in contact with GLU 60 (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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386A TYR* 4.1 19.0 + - - +
387A GLN* 4.0 24.5 - - + +
159B ILE* 3.4 19.7 - - - +
162B PRO* 4.2 24.3 - - + +
163B SER* 4.6 2.1 + - - -
38D LYS* 2.8 48.5 + - + +
56D VAL 3.2 8.6 + - - +
57D PHE* 3.0 8.6 + - + +
59D ASP* 1.3 75.7 - - - +
61D MET* 1.3 68.2 + - - +
63D HIS* 3.2 4.3 + - - +
64D PHE* 3.0 21.4 + - + +
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Residues in contact with MET 61 (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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158B PRO 4.9 1.1 - - - +
161B PHE* 4.6 0.4 - - + -
162B PRO* 4.2 17.0 - - + -
356B PHE* 4.0 21.3 - - + -
357B ALA* 4.1 4.9 - - + -
1201B HEM 3.7 27.4 - - + -
57D PHE* 2.8 50.0 + - + +
58D THR* 3.8 2.2 - - - +
60D GLU* 1.3 74.7 - - - +
62D ALA* 1.3 57.8 + - - +
64D PHE* 3.0 44.6 + - + +
65D ASP* 2.8 51.1 + - - +
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Residues in contact with ALA 62 (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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363A ARG* 3.2 42.6 - - - +
356B PHE* 4.2 8.0 - - + -
360B ASP* 3.7 12.8 - - - +
58D THR 2.6 22.5 + - - +
59D ASP 3.9 1.3 - - - +
61D MET* 1.3 73.2 - - - +
63D HIS* 1.3 62.8 + - - +
65D ASP 3.4 3.1 + - - -
66D ARG* 2.8 34.0 + - - +
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Residues in contact with HIS 63 (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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363A ARG* 5.3 0.4 - - - +
368A PRO* 4.3 15.2 - - + +
369A ASN* 2.7 28.5 + - - -
372A HIS* 5.4 0.4 + - - -
387A GLN* 3.5 31.7 - - + +
388A ARG* 3.0 41.9 + - - -
389A ASP 3.2 14.4 - - - -
390A GLY* 4.6 4.0 - - - -
59D ASP 3.4 5.8 + - - +
60D GLU 3.2 7.4 + - - +
62D ALA* 1.3 75.8 - - - +
64D PHE* 1.3 68.2 + - - +
66D ARG* 2.9 17.7 + - + +
67D GLU* 3.3 9.2 + - - +
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Residues in contact with PHE 64 (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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73B VAL* 3.6 42.5 - - + +
74B VAL* 4.1 3.1 - - + -
161B PHE* 3.8 21.8 - + - -
162B PRO* 3.9 26.5 - - + -
165B ILE* 3.8 36.8 - - + -
166B HIS* 4.2 4.7 - + - -
1201B HEM 4.5 3.1 - - + -
60D GLU 3.0 12.8 + - - +
61D MET* 3.0 37.2 - - + +
63D HIS* 1.3 76.4 + - - +
65D ASP* 1.3 62.9 + - - +
66D ARG 2.9 5.9 + - - -
67D GLU* 3.2 40.9 + - - +
68D ARG* 5.5 0.2 - - - -
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Residues in contact with ASP 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 5.0 5.1 - - - +
356B PHE* 3.9 3.6 - - - -
357B ALA* 3.0 30.3 - - - +
360B ASP* 2.6 28.8 - - - +
361B THR* 2.7 36.6 + - - -
364B HIS* 3.4 11.6 - - - -
1201B HEM 4.0 7.6 - - - +
61D MET* 2.8 40.7 + - - +
62D ALA 3.5 3.8 - - - +
63D HIS 3.1 0.6 - - - -
64D PHE* 1.3 79.1 - - - +
66D ARG* 1.3 59.4 + - - +
67D GLU 3.7 0.7 - - - -
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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