Contacts of the helix formed by residues 54 - 66 (chain I) 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 PRO 54 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C PRO* 3.9 24.2 - - + -
38I LEU* 4.1 23.8 - - + -
42I PHE* 4.8 0.2 - - + -
52I ALA 3.9 5.6 - - - +
53I LEU* 1.3 89.8 - - + +
55I ALA* 1.3 67.9 - - - +
56I ASP* 4.6 4.5 - - + +
57I ALA* 3.2 8.2 + - + +
58I ALA* 3.0 16.1 + - - +
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Residues in contact with ALA 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I LEU 3.8 0.2 + - - -
54I PRO* 1.3 73.0 - - - +
56I ASP* 1.3 63.4 + - - +
58I ALA* 3.2 1.7 + - - +
59I ARG* 3.0 52.4 + - - +
76I GLN* 3.4 30.2 - - - +
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Residues in contact with ASP 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I PRO* 3.3 4.0 - - + +
55I ALA* 1.3 75.9 - - - +
57I ALA* 1.3 58.8 + - - +
59I ARG* 2.8 30.3 + - - +
60I LEU* 3.0 37.6 + - + +
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Residues in contact with ALA 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I THR* 4.3 17.9 - - + +
38I LEU* 4.0 27.1 - - + -
53I LEU* 4.3 12.8 - - + -
54I PRO* 3.2 14.0 + - + +
56I ASP* 1.3 80.9 - - - +
58I ALA* 1.3 57.3 + - - +
60I LEU* 3.7 10.4 - - - -
61I VAL* 2.9 35.2 + - - +
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Residues in contact with ALA 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I LEU* 4.0 18.8 - - + +
54I PRO 3.0 17.0 + - - +
55I ALA 3.6 3.4 - - - +
57I ALA* 1.3 76.0 - - - +
59I ARG* 1.3 60.0 + - - +
61I VAL* 3.6 2.9 - - - +
62I GLY* 2.9 26.5 + - - -
72I ILE* 3.8 19.3 - - + +
75I LEU* 4.4 7.3 - - + +
76I GLN* 3.6 28.5 - - + +
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Residues in contact with ARG 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I ALA* 3.0 37.5 + - - +
56I ASP* 2.8 33.1 + - - +
58I ALA* 1.3 78.1 - - - +
60I LEU* 1.3 54.7 + - + +
62I GLY* 3.3 0.9 + - - -
63I ALA* 3.0 28.8 + - - +
69I GLU* 5.9 2.0 - - - +
72I ILE* 4.0 25.6 - - + +
76I GLN* 5.4 3.2 + - - +
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Residues in contact with LEU 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I ASP 5.8 0.4 - - - +
35I GLY* 3.4 26.7 - - - +
36I THR* 4.0 19.7 - - + -
56I ASP* 3.0 25.0 + - + +
57I ALA* 3.3 6.5 + - - +
59I ARG* 1.3 71.1 - - + +
61I VAL* 1.4 65.9 + - - +
63I ALA* 3.4 7.2 + - + +
64I LYS* 3.3 33.6 + - - +
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Residues in contact with VAL 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I ILE* 3.8 38.1 - - + +
36I THR* 4.1 9.4 - - + -
43I VAL* 4.1 15.9 - - + -
47I LEU* 4.1 8.1 - - + -
53I LEU* 3.8 20.0 - - + -
57I ALA* 2.9 22.2 + - + +
58I ALA 3.6 5.6 - - - +
60I LEU* 1.4 73.5 - - - +
62I GLY* 1.3 68.1 + - - +
64I LYS* 3.2 7.7 + - - +
65I LEU* 3.0 30.6 + - + +
75I LEU* 3.9 15.0 - - + -
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Residues in contact with GLY 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I ALA 2.9 19.6 + - - -
59I ARG 3.7 1.8 - - - -
61I VAL* 1.3 78.4 - - - +
63I ALA* 1.3 57.1 + - - +
66I ASP* 2.9 24.3 + - - -
67I LEU* 2.9 25.8 + - - +
72I ILE* 3.9 22.4 - - - -
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Residues in contact with ALA 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ARG 3.0 17.6 + - - +
60I LEU* 3.8 6.5 - - - +
61I VAL 3.3 0.2 - - - -
62I GLY* 1.3 76.7 - - - +
64I LYS* 1.3 61.9 + - + +
66I ASP* 3.3 11.4 + - - +
72I ILE* 5.0 0.4 - - - +
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Residues in contact with LYS 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I LYS* 3.5 17.7 - - - +
27I LEU* 3.6 18.7 - - + +
31I GLU* 2.7 32.2 + - + +
32I ILE* 3.5 20.9 + - + +
34I ASP* 2.8 28.5 + - - +
36I THR* 6.3 0.2 - - - -
60I LEU* 3.3 20.9 - - - +
61I VAL* 3.2 8.5 + - - +
63I ALA* 1.3 77.0 - - + +
65I LEU* 1.3 63.0 + - + +
66I ASP 3.6 0.2 + - - -
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Residues in contact with LEU 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ILE* 4.0 25.8 - - + +
21I SER* 2.7 27.0 + - - +
22I LYS* 3.8 40.8 - - + +
25I LYS* 3.8 2.7 - - - -
27I LEU* 4.2 6.3 - - + -
32I ILE* 4.0 27.4 - - + -
47I LEU* 4.2 17.9 - - + -
61I VAL 3.0 20.6 + - - +
64I LYS* 1.3 78.3 - - - +
66I ASP* 1.4 69.7 + - - +
67I LEU* 3.4 21.6 + - + +
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Residues in contact with ASP 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I LYS* 3.8 18.8 + - - +
62I GLY 2.9 10.4 + - - -
63I ALA* 3.3 7.6 + - - +
64I LYS 3.3 4.0 - - - -
65I LEU* 1.4 81.0 - - - +
67I LEU* 1.4 61.8 + - - +
68I ASP 4.0 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