Contacts of the helix formed by residues 42 - 50 (chain D) in PDB entry 4DQ0
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 GLY 42 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D CYS* 2.8 23.9 + - - -
40D GLY 3.1 1.7 - - - -
41D ASN* 1.3 80.1 + - - +
43D ARG* 1.3 66.0 + - - +
44D ASN 3.2 3.5 + - - -
45D SER* 3.4 5.4 + - - -
46D LEU* 2.9 33.2 + - - +
68D VAL* 4.0 15.5 - - - -
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Residues in contact with ARG 43 (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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179C ASP* 4.8 3.4 + - - +
202C NHE 3.4 28.9 + - - -
9D PHE* 5.1 4.2 - - - +
10D THR* 5.8 0.2 - - - +
15D LEU* 4.4 13.0 - - + +
16D THR* 3.1 43.1 - - - +
17D ARG 2.9 27.9 + - - -
18D THR* 4.2 10.4 + - - +
19D HIS* 3.7 23.7 - - - +
39D CYS 5.0 3.6 + - - +
41D ASN* 2.8 19.4 + - - +
42D GLY* 1.3 76.2 - - - +
44D ASN* 1.3 83.2 + - - +
46D LEU* 3.9 3.6 - - - +
47D TYR* 3.2 23.2 + - - +
102D THR* 4.7 4.4 + - - -
103D VAL* 3.7 19.6 - - - +
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Residues in contact with ASN 44 (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 THR* 3.5 10.4 - - - +
19D HIS* 2.9 34.3 + - - +
22D VAL* 3.6 20.2 - - + +
36D ASP* 3.8 12.0 + - - +
39D CYS 5.2 1.6 + - - +
42D GLY 3.2 0.4 - - - -
43D ARG* 1.3 87.3 - - - +
45D SER* 1.3 62.3 + - - +
47D TYR* 3.3 5.5 + - - +
48D LEU* 2.9 36.6 + - - +
100D LEU* 4.0 14.3 - - + +
102D THR* 3.2 25.5 + - - -
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Residues in contact with SER 45 (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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36D ASP* 2.6 37.0 + - - +
39D CYS* 3.6 2.1 - - - +
42D GLY* 3.4 9.8 + - - -
44D ASN* 1.3 77.3 - - - +
46D LEU* 1.3 58.4 + - - +
48D LEU* 3.9 4.3 - - - +
49D ALA* 2.8 34.0 + - - +
55D VAL* 3.6 19.0 - - - +
57D ALA* 3.2 22.0 - - - +
68D VAL* 5.8 1.1 - - - -
80D LEU* 4.0 8.7 - - - +
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Residues in contact with LEU 46 (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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9D PHE* 3.5 31.9 - - + -
15D LEU* 3.7 27.8 - - + -
41D ASN 4.8 2.2 - - - +
42D GLY* 2.9 25.3 + - - +
43D ARG 3.9 2.2 - - - +
45D SER* 1.3 74.3 - - - +
47D TYR* 1.3 56.3 + - - +
49D ALA* 3.3 2.6 + - - +
50D ALA* 2.7 37.9 + - - +
68D VAL* 4.6 10.1 - - + +
71D ILE* 3.8 30.3 - - + -
72D LYS 5.1 0.2 - - - +
77D LEU* 3.7 24.7 - - + +
80D LEU* 3.9 17.3 - - + -
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Residues in contact with TYR 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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4D ARG 3.8 13.5 - - - -
5D ASP* 4.1 20.0 - - - -
6D GLU* 4.3 1.3 - - - -
9D PHE* 3.7 12.9 - - + -
18D THR* 3.7 25.1 - - + +
22D VAL* 4.3 5.2 - - + -
23D LEU* 3.9 23.6 - - + +
26D VAL* 3.8 26.9 - - + +
43D ARG 3.2 16.4 + - - +
44D ASN 3.6 2.5 - - - +
46D LEU* 1.3 80.2 - - - +
48D LEU* 1.3 83.8 + - + +
50D ALA* 3.3 0.3 + - - +
51D ASN* 2.6 53.5 + - + +
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Residues in contact with LEU 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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22D VAL* 4.2 8.3 - - + -
26D VAL* 3.5 32.5 - - + -
34D THR* 4.3 9.0 - - + -
36D ASP* 5.7 0.7 - - + +
44D ASN 2.9 21.9 + - - +
45D SER* 3.9 4.3 - - - +
47D TYR* 1.3 86.9 - - + +
49D ALA* 1.3 57.5 + - - +
51D ASN* 2.8 17.4 + - - -
53D TYR* 3.2 43.7 + - + -
55D VAL* 3.9 11.9 - - + -
98D PHE* 4.3 9.9 - - + -
100D LEU* 3.9 36.1 - - + -
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Residues in contact with ALA 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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45D SER 2.8 22.3 + - - +
46D LEU 3.8 2.7 - - - +
48D LEU* 1.3 68.6 - - - +
50D ALA* 1.3 58.9 + - - +
51D ASN 3.0 8.9 + - - -
52D GLY 3.7 2.6 + - - -
53D TYR 3.5 15.0 - - - +
55D VAL* 3.9 6.4 - - + +
77D LEU* 4.0 12.1 - - + +
79D ASN* 2.9 30.1 + - - +
80D LEU* 4.0 26.9 - - + -
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Residues in contact with ALA 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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4D ARG* 3.8 26.9 + - + +
9D PHE* 3.5 26.5 - - + -
46D LEU 2.7 21.8 + - - +
47D TYR 3.6 5.4 - - - +
49D ALA* 1.3 72.7 - - - +
51D ASN* 1.3 67.7 + - - +
52D GLY 3.8 0.7 - - - -
77D LEU* 3.9 11.2 - - + +
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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