Contacts of the helix formed by residues 39 - 48 (chain E) in PDB entry 1DWK
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 ALA 39 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E LEU* 1.3 73.2 - - - +
40E GLU* 1.3 67.0 + - - +
41E ALA* 4.1 3.8 - - + +
42E PHE* 3.0 3.3 + - - -
43E VAL* 3.0 21.7 + - - +
127E LYS* 6.2 0.4 - - - +
128E LEU 5.8 0.2 - - - +
201E SO4 3.5 18.6 - - - +
156F PHE* 2.8 48.3 + - + +
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Residues in contact with GLU 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E PHE 4.7 4.9 - - - +
30E ALA* 4.0 23.0 - - - +
33E ALA* 3.9 19.7 - - + -
38E LEU 3.7 0.6 + - - -
39E ALA* 1.3 72.0 - - - +
41E ALA* 1.3 59.9 + - + +
43E VAL* 4.2 0.2 - - - +
44E THR* 2.7 41.0 + - - +
130E VAL* 4.0 7.1 + - - +
201E SO4 2.8 37.0 + - - +
111G LEU* 4.2 20.9 - - + +
114G GLU* 4.7 1.4 - - - +
115G LYS* 2.6 39.9 + - - -
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Residues in contact with ALA 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ALA* 3.1 2.4 - - + +
40E GLU* 1.3 82.5 - - + +
42E PHE* 1.3 61.7 + - - +
45E ALA* 3.1 24.9 + - - +
128E LEU* 3.6 37.9 - - + +
129E ASP* 4.9 4.7 - - - -
130E VAL* 5.7 2.0 - - + +
201E SO4 5.0 0.6 + - - -
156F PHE* 4.6 4.0 - - + -
104G TYR* 3.8 3.5 - - + -
107G THR* 3.8 11.7 - - + +
111G LEU* 4.1 19.1 - - + -
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Residues in contact with PHE 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E LEU* 4.2 17.9 - - + -
39E ALA* 3.0 9.2 + - - +
41E ALA* 1.3 79.9 - - - +
43E VAL* 1.4 67.0 + - - +
45E ALA* 3.3 5.5 + - - +
46E ALA* 3.0 19.1 + - - +
51E GLN* 3.5 38.9 - - + +
52E ALA 3.5 26.5 - - - -
53E LEU* 4.4 5.8 - - + -
54E PRO* 4.8 0.2 - - + -
153F THR* 5.1 2.5 - - + -
154F LYS 4.0 6.7 - - - -
155F PRO* 3.6 38.6 - - + -
156F PHE* 3.7 50.1 - + + +
104G TYR* 4.4 0.9 - - - -
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Residues in contact with VAL 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E PHE 5.6 0.4 - - - +
32E ILE* 4.4 9.0 - - + -
33E ALA* 3.9 24.5 - - + -
36E THR* 3.7 16.4 - - + +
38E LEU* 3.6 29.8 - - + -
39E ALA 3.0 15.2 + - - +
40E GLU 4.2 0.2 - - - +
42E PHE* 1.4 73.8 - - - +
44E THR* 1.3 64.2 + - - +
46E ALA* 3.1 3.8 + - - +
47E LEU* 3.0 27.9 + - + +
53E LEU* 4.4 14.4 - - + -
61E VAL* 4.2 21.3 - - + -
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Residues in contact with THR 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E PHE* 3.5 46.5 + - + +
40E GLU* 2.7 23.8 + - - -
43E VAL* 1.3 75.1 - - - +
45E ALA* 1.3 64.7 + - - +
47E LEU* 3.1 13.1 + - - +
48E LEU* 3.0 36.4 + - + +
107G THR* 3.8 23.3 - - + +
110G ALA* 4.3 8.7 - - + -
111G LEU* 3.9 6.7 - - + +
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Residues in contact with ALA 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ALA 3.1 20.1 + - - +
42E PHE 3.6 4.0 - - - +
44E THR* 1.3 77.3 - - - +
46E ALA* 1.3 60.8 + - - +
48E LEU* 3.2 5.2 + - - +
49E GLY 3.1 5.4 + - - -
50E GLN* 2.8 34.8 + - + +
51E GLN* 3.8 17.5 - - + -
103G VAL 4.7 0.7 - - - +
104G TYR* 3.8 15.3 - - + -
107G THR* 3.2 17.4 + - - +
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Residues in contact with ALA 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ARG* 2.8 23.4 + - - +
42E PHE 3.0 10.8 + - - +
43E VAL 3.1 8.3 + - - +
45E ALA* 1.3 75.0 - - - +
47E LEU* 1.4 64.3 + - - +
49E GLY 3.0 4.3 + - - -
51E GLN* 3.4 30.0 - - + +
53E LEU* 3.6 36.6 - - + +
75E LEU* 3.8 4.7 - - + +
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Residues in contact with LEU 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ARG* 4.8 1.4 + - - +
14E LEU* 5.5 0.3 - - - +
15E ALA* 3.4 22.2 + - - +
18E ILE* 3.9 39.5 - - + +
29E PHE* 3.9 30.1 - - + -
32E ILE* 4.0 25.8 - - + -
43E VAL* 3.0 25.4 + - + +
44E THR* 3.1 7.2 + - - +
46E ALA* 1.4 76.0 - - - +
48E LEU* 1.3 65.1 + - + +
49E GLY* 3.4 2.3 + - - -
53E LEU* 4.9 2.5 - - + -
61E VAL* 4.1 27.8 - - + -
65E LEU* 4.3 7.9 - - + -
75E LEU* 4.4 8.1 - - + +
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Residues in contact with LEU 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E LEU* 3.5 13.0 - - - +
15E ALA* 3.8 11.3 - - + +
18E ILE* 6.1 0.2 - - + -
19E LEU* 4.1 29.6 - - + -
29E PHE* 4.8 3.8 - - + -
44E THR* 3.0 26.0 + - + +
45E ALA* 3.4 6.1 - - - +
46E ALA 3.1 0.2 - - - -
47E LEU* 1.3 81.7 - - + +
49E GLY* 1.3 57.2 + - - +
50E GLN* 3.4 17.5 + - + +
106G THR* 3.6 47.3 + - - +
107G THR* 3.8 11.0 - - - +
110G ALA* 4.3 6.5 - - + -
6H ILE* 3.9 22.6 - - + +
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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