Contacts of the helix formed by residues 48 - 63 (chain A) in PDB entry 2DN0
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 SER 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLY 3.5 1.7 + - - -
47A LEU* 1.3 73.9 - - - +
49A THR* 1.3 58.7 + - - +
50A ARG* 4.2 9.0 - - - -
51A GLU* 2.6 38.8 + - - +
52A VAL* 2.9 10.4 + - - -
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Residues in contact with THR 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A VAL* 3.3 25.8 - - + -
42A THR* 3.6 18.7 - - - +
47A LEU 3.6 1.8 + - - -
48A SER* 1.3 71.1 - - - +
50A ARG* 1.3 61.3 + - - +
52A VAL* 3.5 1.6 + - - +
53A ARG* 3.1 34.0 + - - +
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Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A SER* 5.6 10.1 - - - -
11A TYR* 5.5 10.7 - - - -
48A SER* 3.0 8.5 - - - -
49A THR* 1.3 77.7 - - - +
51A GLU* 1.3 80.2 + - - +
53A ARG* 4.0 5.5 - - - +
54A LYS* 2.9 36.8 + - + +
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 5.5 6.6 - - - +
15A LYS* 3.7 22.9 + - - -
47A LEU* 3.7 26.1 - - + +
48A SER* 2.6 26.4 + - - +
50A ARG* 1.3 97.7 + - - +
52A VAL* 1.3 61.7 + - - +
54A LYS* 3.4 10.7 + - - +
55A TRP* 3.2 22.3 + - - +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.8 11.3 - - + +
38A VAL* 4.8 9.2 - - + -
41A LEU* 3.5 37.9 - - + -
42A THR* 3.7 17.5 - - + +
45A THR* 3.8 17.5 - - - +
47A LEU* 3.4 31.0 - - + +
48A SER 2.9 8.7 + - - +
49A THR 3.7 6.1 - - - +
51A GLU* 1.3 77.6 - - - +
53A ARG* 1.3 65.0 + - + +
55A TRP* 3.4 12.0 + - - +
56A PHE* 3.2 19.4 - - + -
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Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SER* 5.7 6.9 - - - -
33A PRO* 4.7 21.7 + - + +
34A GLY* 4.9 13.7 + - - -
38A VAL* 4.1 24.8 - - + +
49A THR* 3.1 26.9 + - - +
50A ARG* 4.0 5.2 - - - +
52A VAL* 1.3 76.1 - - + +
54A LYS* 1.3 69.8 + - - +
56A PHE* 3.2 27.0 + - - +
57A SER* 3.6 5.5 + - - -
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Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ALA* 4.6 20.2 - - - +
9A SER 4.7 2.6 - - - +
10A ILE* 4.6 23.7 - - - +
11A TYR* 4.8 23.6 - - + +
50A ARG* 2.9 25.0 + - + +
51A GLU* 3.4 16.6 - - - +
52A VAL 3.3 0.2 - - - -
53A ARG* 1.3 75.3 - - - +
55A TRP* 1.3 67.2 + - - +
57A SER* 2.7 42.3 + - - -
58A ASP* 3.4 12.7 + - - +
61A TYR* 5.8 1.8 - - - -
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Residues in contact with TRP 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LYS* 4.6 20.6 - - + -
20A LEU* 4.3 17.8 - - + +
23A LEU* 3.5 46.2 - - + +
24A LYS* 3.6 33.0 - - + -
27A PHE* 4.2 10.8 - + + -
47A LEU* 6.3 0.7 - - + -
51A GLU 3.2 8.5 + - - +
52A VAL* 3.4 10.1 - - - +
54A LYS* 1.3 78.9 - - - +
56A PHE* 1.3 103.2 + + - +
58A ASP* 2.5 51.3 + - + +
59A ARG* 3.1 42.9 + - + +
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Residues in contact with PHE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.3 2.9 - - + -
26A SER* 4.1 10.8 - - - -
27A PHE* 3.5 42.7 - + + -
30A ASN 4.9 1.1 - - - -
31A GLN 4.3 2.5 - - - -
33A PRO* 3.5 41.3 - - + -
41A LEU* 3.6 32.1 - - + -
52A VAL* 3.2 31.2 - - + -
53A ARG* 3.2 14.9 + - + +
55A TRP* 1.3 104.5 - + - +
57A SER* 1.3 62.9 + - - +
59A ARG* 3.5 4.2 + - - +
60A ARG* 3.3 28.1 + - - +
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Residues in contact with SER 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 6.4 0.2 - - - -
53A ARG 3.9 5.5 + - - -
54A LYS* 2.7 42.1 + - - -
56A PHE* 1.3 73.1 - - - +
58A ASP* 1.3 63.8 + - - +
60A ARG* 3.3 11.7 + - - +
61A TYR* 3.0 35.5 + - - -
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Residues in contact with ASP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 3.5 30.0 - - - +
11A TYR 4.6 7.1 + - - +
15A LYS* 6.2 0.2 - - - -
54A LYS* 4.4 12.5 - - - +
55A TRP* 2.5 34.7 + - + +
57A SER* 1.3 71.9 - - - +
59A ARG* 1.3 68.7 + - - +
61A TYR* 2.7 20.4 + - - +
62A HIS* 2.9 14.0 + - - +
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Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.6 13.7 - - - +
24A LYS* 3.2 39.6 - - - +
27A PHE* 4.7 10.8 - - + -
55A TRP* 3.1 47.1 + - + +
56A PHE 3.8 8.1 - - - +
58A ASP* 1.3 78.9 - - - +
60A ARG* 1.3 62.8 + - - +
62A HIS* 3.3 16.6 + - - +
63A CYS* 3.1 28.0 + - - +
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Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 3.6 32.4 - - + -
31A GLN* 3.9 12.5 + - - +
32A PHE* 3.6 39.3 - - - +
56A PHE* 3.3 13.0 + - - +
57A SER* 3.4 12.1 - - - +
58A ASP 3.1 0.8 - - - -
59A ARG* 1.3 78.9 - - - +
61A TYR* 1.3 63.0 + - + +
63A CYS* 2.7 31.5 + - - +
64A ARG* 4.1 8.7 - - - +
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 3.7 38.8 - - + +
54A LYS* 5.8 1.8 - - - -
57A SER* 3.0 32.7 + - - -
58A ASP* 2.7 14.8 + - - +
60A ARG* 1.3 73.4 - - + +
62A HIS* 1.3 65.4 + - - +
63A CYS 3.1 0.7 + - - -
64A ARG* 3.4 40.7 + - + +
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Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASP 2.9 10.5 + - - +
59A ARG* 3.5 21.8 + - - +
61A TYR* 1.3 77.8 - - - +
63A CYS* 1.3 66.5 + - - +
64A ARG 3.5 3.6 + - - +
66A LEU* 5.9 0.5 - - - +
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Residues in contact with CYS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ARG* 3.1 17.6 + - - +
60A ARG* 2.7 19.3 + - - +
62A HIS* 1.3 85.6 - - - +
64A ARG* 1.3 60.4 + - - +
66A LEU* 3.2 37.4 - - + +
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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