Contacts of the helix formed by residues 39 - 53 (chain I) in PDB entry 2DYS
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 VAL 39 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASP* 3.8 16.6 - - - +
302B TGL 5.5 9.4 - - + +
34I PHE* 6.0 2.2 - - + -
35I TYR* 2.9 54.7 + - + +
37I PHE 3.2 0.8 - - - -
38I ALA* 1.3 89.4 - - + +
40I ALA* 1.3 66.0 + - - +
41I GLU 3.6 0.4 - - - -
42I LYS* 3.8 3.4 - - - +
43I ARG* 3.0 39.0 + - - +
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Residues in contact with ALA 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B HIS* 4.9 1.1 + - - -
25B ASP* 4.2 14.8 - - + +
35I TYR* 3.1 10.6 + - + +
36I LYS* 3.7 28.0 - - + -
39I VAL* 1.3 82.1 - - - +
41I GLU* 1.3 65.1 + - + +
43I ARG* 3.5 2.9 - - - +
44I LYS* 3.1 36.9 + - - +
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Residues in contact with GLU 41 (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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36I LYS 3.5 22.3 - - - +
37I PHE* 4.0 11.0 - - + +
40I ALA* 1.3 76.2 - - + +
42I LYS* 1.3 66.4 + - - +
44I LYS* 3.2 28.3 + - - +
45I LYS* 2.9 30.5 + - - +
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Residues in contact with LYS 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D GLN* 4.6 13.2 - - - +
37I PHE 3.4 16.9 + - - +
38I ALA* 3.8 18.8 - - - +
39I VAL* 3.6 7.2 + - - +
40I ALA 3.3 0.4 - - - -
41I GLU* 1.3 76.6 - - - +
43I ARG* 1.3 57.8 + - - +
45I LYS* 3.3 4.9 + - - +
46I ALA* 2.9 32.2 + - + +
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Residues in contact with ARG 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 4.2 26.6 - - + +
22B HIS* 3.5 21.1 - - + +
24B HIS* 5.8 0.4 + - - -
25B ASP* 2.9 40.3 + - - +
302B TGL 3.7 39.6 + - - +
132D GLN* 3.2 38.4 + - - +
39I VAL* 3.0 28.4 + - - +
40I ALA 3.5 3.8 - - - +
42I LYS* 1.3 76.7 - - - +
44I LYS* 1.3 61.6 + - - +
46I ALA* 3.5 0.7 + - - +
47I TYR* 3.1 35.5 + - + -
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Residues in contact with LYS 44 (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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22B HIS* 3.6 40.8 - - + +
40I ALA* 3.1 24.8 + - - +
41I GLU* 3.2 32.1 + - - +
43I ARG* 1.3 73.3 - - - +
45I LYS* 1.3 61.6 + - - +
47I TYR* 4.0 2.5 - - - +
48I ALA* 3.0 29.3 + - - +
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Residues in contact with LYS 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I GLU* 2.9 20.1 + - - +
42I LYS* 3.9 4.3 - - - +
44I LYS* 1.3 76.1 - - - +
46I ALA* 1.3 55.3 + - - +
48I ALA* 4.3 4.7 - - + -
49I ASP* 2.7 73.3 + - - +
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Residues in contact with ALA 46 (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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131D ILE* 3.6 10.6 - - + +
132D GLN* 3.8 31.9 - - + +
42I LYS* 2.9 19.7 + - + +
43I ARG 3.8 4.5 - - - +
44I LYS 3.4 0.2 - - - -
45I LYS* 1.3 75.7 - - - +
47I TYR* 1.3 56.8 + - - +
49I ASP* 3.8 5.7 - - - +
50I PHE* 2.9 30.1 + - - +
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Residues in contact with TYR 47 (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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11B ASP* 3.6 15.2 + - - +
12B ALA* 3.1 29.3 + - + -
18B GLU* 3.7 40.6 - - + +
21B LEU* 3.3 22.2 - - + +
22B HIS* 4.7 9.9 - + - +
131D ILE* 3.8 31.9 - - + -
132D GLN* 3.8 20.3 + - - -
43I ARG* 3.1 29.0 + - + +
44I LYS* 4.0 4.5 - - - +
45I LYS 3.2 0.4 - - - -
46I ALA* 1.3 75.6 - - + +
48I ALA* 1.3 66.1 + - - +
50I PHE* 3.3 1.0 + - - +
51I TYR* 3.0 40.7 + + - +
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Residues in contact with ALA 48 (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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44I LYS 3.0 19.5 + - - +
45I LYS* 3.7 5.6 - - - +
47I TYR* 1.3 76.8 - - - +
49I ASP* 1.3 58.9 + - - +
51I TYR* 3.9 2.0 - - - +
52I ARG* 3.0 48.9 + - - +
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Residues in contact with ASP 49 (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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45I LYS* 2.7 65.5 + - - +
46I ALA* 3.8 6.0 - - - +
48I ALA* 1.3 70.2 - - - +
50I PHE* 1.3 67.4 + - - +
52I ARG* 3.1 34.4 + - - +
53I ASN 4.5 1.6 + - - -
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Residues in contact with PHE 50 (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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188B ARG* 3.7 23.6 - - - -
127D LYS* 6.5 0.7 - - + -
130D PRO* 3.9 41.7 - - + -
131D ILE* 3.8 22.9 - - + -
46I ALA 2.9 19.6 + - - +
47I TYR 3.7 3.6 - - - +
49I ASP* 1.3 81.0 - - - +
51I TYR* 1.3 77.4 + + - +
52I ARG 3.4 0.3 + - - -
53I ASN 4.2 1.6 + - - -
54I TYR* 3.5 48.1 + + - +
59I ASP* 5.4 1.3 - - - -
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Residues in contact with TYR 51 (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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12B ALA 3.9 4.7 + - - -
13B THR 4.4 0.9 + - - -
18B GLU* 3.8 29.4 + - - -
187B SER* 3.6 26.8 - - - -
188B ARG* 3.0 45.1 + - + +
131D ILE* 4.9 0.7 - - + -
47I TYR* 3.0 34.8 + + - +
48I ALA* 3.9 2.2 - - - +
50I PHE* 1.3 94.2 - + - +
52I ARG* 1.3 64.9 + - - +
53I ASN 3.4 0.8 + - - -
54I TYR* 3.6 31.5 + + + +
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Residues in contact with ARG 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I ALA* 3.0 32.5 + - - +
49I ASP* 3.1 39.7 + - - +
50I PHE 3.3 1.4 - - - -
51I TYR* 1.3 78.6 - - - +
53I ASN* 1.3 85.9 + - - +
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Residues in contact with ASN 53 (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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49I ASP 4.5 1.2 + - - -
50I PHE 4.2 4.2 + - - -
52I ARG* 1.3 103.3 - - - +
54I TYR* 1.3 63.1 + - - +
55I ASP* 3.6 5.2 + - - +
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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