Contacts of the helix formed by residues 39 - 47 (chain A) in PDB entry 2H0D
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 CYS 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A CYS* 3.6 12.8 - - - +
21A CYS* 3.7 5.4 - - - -
24A TYR 3.8 6.1 - - - -
25A PHE* 4.1 0.9 - - - -
26A ILE 3.4 30.1 - - - +
27A ASP 4.5 0.2 - - - -
28A ALA* 4.6 0.2 - - - +
29A THR* 4.4 0.2 - - - -
38A PHE* 1.3 77.4 - - - +
40A LYS* 1.3 64.9 + - - +
41A THR 4.3 0.2 - - - +
42A CYS* 3.7 4.9 - - - +
43A ILE* 3.1 21.8 + - - +
201A ZN 2.4 35.7 - - - -
26B ARG* 3.4 26.0 - - - +
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Residues in contact with LYS 40 (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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26A ILE 3.3 2.8 + - - +
27A ASP* 2.9 41.3 + - + +
29A THR* 3.5 16.4 - - - +
39A CYS* 1.3 73.1 - - - +
41A THR* 1.3 65.3 + - + +
43A ILE* 3.6 0.9 - - - +
44A VAL* 3.1 29.8 + - + +
71A SER* 5.9 0.7 - - - +
15B LYS* 4.8 16.4 - - - +
17B TRP* 4.1 24.9 - - + +
18B GLU 4.4 8.6 + - - +
19B LEU* 3.7 22.9 - - + -
23B GLU* 2.5 35.2 + - - +
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Residues in contact with THR 41 (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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26A ILE 5.1 0.4 + - - -
39A CYS* 4.3 0.2 - - - +
40A LYS* 1.3 76.1 - - + +
42A CYS* 1.3 62.6 + - - +
44A VAL* 4.2 0.3 - - - +
45A ARG* 3.0 36.0 + - - +
19B LEU* 4.1 17.5 - - + -
23B GLU* 3.5 52.3 - - + +
26B ARG* 3.0 41.5 + - - +
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Residues in contact with CYS 42 (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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18A CYS* 4.0 2.5 - - - -
20A LEU* 3.7 24.9 - - + +
21A CYS* 3.7 17.0 - - - -
39A CYS* 3.4 10.7 + - - +
40A LYS 3.3 0.8 - - - -
41A THR* 1.3 84.0 + - - +
43A ILE* 1.3 57.0 + - - +
45A ARG* 4.1 2.7 - - - +
46A TYR* 3.1 28.2 + - - +
201A ZN 2.3 36.8 - - - -
26B ARG* 4.0 7.9 - - - -
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Residues in contact with ILE 43 (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* 4.1 2.9 - - + -
29A THR* 4.0 28.3 - - + +
31A ILE* 4.5 8.3 - - + -
38A PHE* 3.8 33.9 - - + -
39A CYS 3.1 18.9 + - - +
40A LYS* 3.6 4.7 - - - +
42A CYS* 1.3 74.0 - - - +
44A VAL* 1.3 63.9 + - + +
46A TYR* 3.9 6.3 - - + -
47A LEU* 2.9 54.7 + - + +
54A PRO* 3.9 27.8 - - + -
69A ILE* 4.5 9.2 - - + -
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Residues in contact with VAL 44 (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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40A LYS* 3.1 30.8 + - + +
41A THR 4.2 2.5 - - - +
43A ILE* 1.3 83.2 - - + +
45A ARG* 1.3 61.7 + - - +
47A LEU* 3.5 2.9 + - - +
48A GLU* 3.4 31.8 + - + +
66A LEU* 4.6 15.1 - - + +
69A ILE* 4.5 6.1 - - + -
17B TRP* 3.8 44.6 - - + +
19B LEU* 4.0 19.5 - - + -
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Residues in contact with ARG 45 (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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41A THR* 3.0 23.1 + - - +
42A CYS* 4.2 2.7 - - - +
44A VAL* 1.3 72.8 - - - +
46A TYR* 1.3 66.4 + - - +
48A GLU* 3.2 34.8 + - - +
49A THR* 4.1 4.2 + - - +
19B LEU* 3.9 16.4 - - + -
23B GLU 5.2 1.1 + - - -
24B LEU* 3.2 48.8 + - - +
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Residues in contact with TYR 46 (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* 4.0 22.4 - - + -
42A CYS 3.1 19.3 + - - +
43A ILE* 3.7 10.1 - - + +
45A ARG* 1.3 77.1 - - - +
47A LEU* 1.3 66.9 + - + +
48A GLU 3.0 5.0 + - - -
49A THR* 3.1 21.7 + - - -
50A SER* 3.4 30.6 + - - -
52A TYR* 3.1 30.0 + - - +
53A CYS 4.2 1.0 + - - -
54A PRO* 3.5 38.3 - - + +
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Residues in contact with LEU 47 (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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31A ILE* 5.5 0.7 - - + -
43A ILE* 2.9 36.0 + - + +
44A VAL 3.9 4.0 - - - +
45A ARG 3.4 0.4 - - - -
46A TYR* 1.3 87.6 - - + +
48A GLU* 1.3 62.2 + - - +
49A THR 3.4 0.4 - - - -
50A SER 3.2 26.3 + - - +
51A LYS* 4.5 1.6 - - - -
52A TYR 4.6 0.9 - - - +
60A VAL* 4.2 21.3 - - + -
65A PRO* 3.9 34.8 - - + +
66A LEU* 4.4 16.9 - - + +
69A ILE* 3.7 30.5 - - + -
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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