Contacts of the helix formed by residues 39 - 48 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C LEU* 1.3 75.1 - - - +
40C GLU* 1.4 66.4 + - - +
41C ALA* 4.2 3.6 - - + +
42C PHE* 3.0 3.8 + - - +
43C VAL* 3.0 20.4 + - - +
127C LYS* 6.3 0.7 - - - +
201C SO4 3.6 17.9 - - - +
156I PHE* 2.7 48.7 + - + +
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Residues in contact with GLU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C PHE 3.5 12.5 - - - +
30C ALA* 3.1 33.5 + - - +
33C ALA* 3.9 13.5 - - + -
38C LEU 3.6 1.0 + - - -
39C ALA* 1.4 71.6 - - - +
41C ALA* 1.3 62.3 + - - +
44C THR* 2.7 40.7 + - - +
201C SO4 2.8 31.2 + - - +
111H LEU* 3.5 23.2 - - + +
114H GLU* 3.3 11.8 - - - +
115H LYS* 3.6 23.7 + - - +
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Residues in contact with ALA 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ALA* 3.2 2.8 - - + +
40C GLU* 1.3 78.1 - - - +
42C PHE* 1.4 58.8 + - - +
45C ALA* 3.1 29.3 + - - +
128C LEU* 3.9 36.8 - - + +
129C ASP* 5.1 4.9 - - + -
130C VAL* 6.3 0.9 - - + -
201C SO4 4.9 1.8 + - - -
104H TYR* 3.8 3.0 - - + -
107H THR* 3.6 9.4 - - + +
111H LEU* 4.1 20.5 - - + +
156I PHE* 4.7 5.8 - - + -
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Residues in contact with PHE 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU* 4.2 20.2 - - + -
39C ALA 3.0 8.7 + - - +
41C ALA* 1.4 77.2 - - - +
43C VAL* 1.3 68.2 + - - +
45C ALA* 3.3 5.5 + - - +
46C ALA* 3.0 19.1 + - - +
51C GLN* 3.6 39.5 - - + +
52C ALA 3.5 25.4 - - - -
53C LEU* 4.3 7.0 - - + -
54C PRO* 4.7 0.7 - - + -
104H TYR* 4.5 1.3 - - - -
153I THR* 5.2 1.1 - - + -
154I LYS 4.0 4.7 - - - -
155I PRO* 3.6 42.6 - - + -
156I PHE* 3.8 46.8 - + + +
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Residues in contact with VAL 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C PHE 5.7 0.4 - - - +
32C ILE* 4.5 8.7 - - + -
33C ALA* 3.9 23.8 - - + +
36C THR* 3.7 15.5 - - + +
38C LEU* 3.5 31.9 - - + +
39C ALA 3.0 15.2 + - - +
40C GLU 4.1 0.2 - - - +
42C PHE* 1.3 76.3 - - - +
44C THR* 1.3 64.6 + - - +
46C ALA* 3.1 3.1 + - - +
47C LEU* 2.9 28.2 + - + +
53C LEU* 4.4 11.9 - - + -
61C VAL* 4.3 22.2 - - + -
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Residues in contact with THR 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C PHE* 3.6 45.5 + - + +
40C GLU* 2.7 26.8 + - - +
43C VAL* 1.3 76.6 - - - +
45C ALA* 1.3 65.0 + - - +
47C LEU* 3.1 11.8 + - - +
48C LEU* 3.0 39.6 + - + +
107H THR* 3.9 21.5 - - + -
110H ALA* 4.2 9.0 - - + -
111H LEU* 3.8 5.0 - - + +
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Residues in contact with ALA 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ALA 3.1 21.3 + - - +
42C PHE 3.7 4.5 - - - +
44C THR* 1.3 76.9 - - - +
46C ALA* 1.3 59.7 + - - +
48C LEU* 3.2 4.9 + - - +
49C GLY 3.1 5.2 + - - -
50C GLN* 2.8 35.4 + - + +
51C GLN* 3.7 18.6 - - + -
103H VAL 4.8 0.2 - - - +
104H TYR* 3.8 15.0 - - + -
107H THR* 3.1 18.1 + - - +
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Residues in contact with ALA 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ARG* 2.9 23.2 + - - +
42C PHE* 3.0 12.2 + - + +
43C VAL 3.1 8.0 + - - +
45C ALA* 1.3 72.5 - - - +
47C LEU* 1.4 68.2 + - - +
49C GLY 3.0 4.0 + - - -
51C GLN* 3.3 30.2 - - + +
53C LEU* 3.5 36.8 - - + +
75C LEU* 3.8 4.5 - - + +
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ARG* 4.8 1.2 + - - +
14C LEU* 5.6 0.5 - - - +
15C ALA* 3.4 21.7 + - - +
18C ILE* 3.9 41.0 - - + +
29C PHE* 4.0 28.7 - - + -
32C ILE* 4.1 24.2 - - + -
43C VAL* 2.9 21.8 + - + +
44C THR* 3.1 7.6 + - - +
46C ALA* 1.4 78.1 - - - +
48C LEU* 1.3 64.1 + - + +
49C GLY* 3.2 3.0 + - - -
53C LEU* 4.8 4.3 - - + -
61C VAL* 4.1 28.5 - - + -
65C LEU* 4.4 5.6 - - + -
75C LEU* 4.3 9.6 - - + +
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 3.6 19.6 - - - +
15C ALA* 3.8 10.1 - - + +
18C ILE* 6.1 0.2 - - + -
19C LEU* 4.1 28.5 - - + -
29C PHE* 4.7 4.7 - - + -
44C THR* 3.0 25.8 + - + +
45C ALA* 3.4 6.7 - - - +
46C ALA 3.1 0.4 - - - -
47C LEU* 1.3 82.5 - - + +
49C GLY* 1.4 58.5 + - - +
50C GLN* 3.6 7.9 + - + +
6G ILE* 4.0 26.3 - - + +
106H THR* 3.6 48.2 + - - +
107H THR* 3.8 10.1 - - - +
110H ALA* 4.2 4.7 - - + -
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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