Contacts of the helix formed by residues 46 - 55 (chain D) in PDB entry 1D1T
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 CYS 46 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44D GLY 3.6 1.7 + - - +
45D ILE* 1.3 78.8 - - - +
47D ARG* 1.3 62.8 + - - +
48D THR* 3.6 10.5 - - - -
49D ASP* 2.8 33.6 + - - +
50D ASP 3.6 1.6 + - - -
67D HIS* 3.5 12.8 - - + +
68D GLU* 4.4 6.5 - - + +
174D CYS* 3.7 1.6 - - - -
362D LEU* 4.6 0.5 - - - +
369D ARG* 3.3 27.4 - - - +
376D ZN 2.3 37.2 - - - -
511D ACT 3.7 1.8 - - - -
4377D NAD 3.9 10.1 - - - -
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Residues in contact with ARG 47 (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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45D ILE 4.3 0.6 + - - -
46D CYS* 1.3 74.1 - - - +
48D THR* 1.3 63.5 + - - +
50D ASP* 2.9 30.9 + - - +
51D HIS* 3.2 35.6 + - - +
54D LYS* 5.1 1.2 - - - +
269D ILE 5.1 2.5 - - - +
362D LEU* 3.6 45.3 + - + +
363D ASN* 3.0 27.9 + - - +
369D ARG* 4.3 0.2 - - - +
4377D NAD 2.8 74.6 + - - +
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Residues in contact with THR 48 (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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46D CYS* 3.1 2.0 + - - -
47D ARG* 1.3 76.7 - - - +
49D ASP* 1.3 62.6 + - - +
51D HIS* 3.2 22.8 + - - +
52D VAL* 3.6 8.5 + - - +
57D MET* 3.7 27.5 - - + +
67D HIS* 4.0 2.7 - - - -
140D PHE* 4.5 6.1 - - + -
141D LEU* 4.8 0.2 - - + -
294D VAL* 5.1 4.0 - - + -
376D ZN 3.7 5.2 - - - -
511D ACT 3.0 45.8 + - + +
4377D NAD 2.8 24.4 + - - +
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Residues in contact with ASP 49 (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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44D GLY 4.2 2.3 - - - +
46D CYS* 2.8 24.9 + - - +
48D THR* 1.3 77.5 - - - +
50D ASP* 1.3 63.0 + - - +
52D VAL* 3.0 25.3 + - - +
53D ILE* 3.6 7.8 + - - +
65D VAL* 3.8 6.2 - - + +
66D GLY* 3.2 23.3 + - - -
67D HIS* 2.9 34.9 + - - -
140D PHE* 3.5 7.2 - - - -
146D PHE* 3.5 16.8 - - + -
359D PHE* 4.0 19.1 - - + -
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Residues in contact with ASP 50 (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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46D CYS 3.6 1.2 + - - -
47D ARG* 2.9 39.2 + - - +
49D ASP* 1.3 78.5 - - - +
51D HIS* 1.3 60.2 + - - +
53D ILE* 2.9 14.6 + - - +
54D LYS* 2.8 59.9 + - - +
359D PHE* 3.9 16.2 - - + -
362D LEU* 4.0 14.4 - - + -
363D ASN* 3.1 23.4 + - - -
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Residues in contact with HIS 51 (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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47D ARG* 3.2 34.3 + - + +
48D THR* 3.3 15.0 - - - +
49D ASP 3.1 0.6 - - - -
50D ASP* 1.3 79.5 - - + +
52D VAL* 1.3 56.6 + - - +
54D LYS* 3.9 5.6 - - + -
55D GLY 2.9 23.2 + - - -
56D THR* 3.0 32.1 + - - +
57D MET* 3.3 18.2 + - + +
269D ILE 5.1 2.3 + - - -
270D GLY* 5.7 0.9 - - - -
294D VAL* 4.2 21.4 + - + +
296D PRO* 6.4 0.2 - - - +
4377D NAD 3.1 37.4 + - - -
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Residues in contact with VAL 52 (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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14D LEU* 3.7 22.9 - - + -
17D GLN* 4.2 0.9 - - - +
48D THR 4.1 2.0 - - - +
49D ASP 3.0 13.2 + - - +
51D HIS* 1.3 78.3 - - - +
53D ILE* 1.3 65.7 + - - +
55D GLY* 3.3 9.4 + - - -
57D MET* 4.0 19.4 - - + +
59D SER* 4.3 7.6 - - - -
61D PHE* 3.9 31.4 - - + -
63D VAL* 4.3 4.3 - - + -
65D VAL* 3.8 13.0 - - + -
140D PHE* 3.4 39.5 - - + -
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Residues in contact with ILE 53 (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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14D LEU* 4.0 21.5 - - + -
16D GLU 6.0 0.4 - - - -
17D GLN* 3.9 1.3 - - - +
18D LYS* 2.8 33.0 + - - +
19D GLN 3.6 25.1 - - - +
20D PRO* 5.6 1.8 - - + -
21D PHE* 3.6 33.2 - - + -
49D ASP 3.8 9.6 - - - +
50D ASP* 2.9 14.1 + - - +
52D VAL* 1.3 77.5 - - - +
54D LYS* 1.3 69.5 + - - +
55D GLY 3.1 1.2 + - - -
61D PHE* 6.0 0.4 - - - -
359D PHE* 4.0 22.7 - - + -
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Residues in contact with LYS 54 (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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18D LYS* 3.8 21.8 - - - +
47D ARG* 5.1 0.9 - - - +
50D ASP* 2.8 52.8 + - - +
51D HIS* 4.0 9.2 - - + +
53D ILE* 1.3 78.5 - - - +
55D GLY* 1.3 60.1 + - - +
56D THR* 3.4 17.3 + - + +
363D ASN* 3.8 18.9 + - - +
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Residues in contact with GLY 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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17D GLN* 3.9 27.1 + - - -
18D LYS* 4.9 1.6 - - - -
51D HIS 2.9 6.6 + - - -
52D VAL 3.7 8.3 - - - -
53D ILE 3.1 4.7 + - - -
54D LYS* 1.3 79.3 - - - +
56D THR* 1.3 60.3 + - - +
57D MET 3.2 11.5 + - - +
297D SER* 5.2 2.6 - - - -
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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