Contacts of the helix formed by residues 45 - 54 (chain D) in PDB entry 1OJ7
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 GLY 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D VAL 3.5 5.6 + - - -
42D LYS 3.9 5.3 + - - -
43D LYS 3.6 1.2 - - - -
44D THR* 1.3 78.7 + - - +
46D VAL* 1.3 66.0 + - - +
47D LEU 3.4 2.0 - - - -
48D ASP* 3.4 15.2 + - - +
49D GLN* 3.1 31.2 + - - +
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Residues in contact with VAL 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D VAL* 3.3 8.4 + - + +
44D THR* 3.6 19.7 - - - +
45D GLY* 1.3 76.1 - - - +
47D LEU* 1.3 66.4 + - - +
49D GLN* 3.1 10.6 + - - +
50D VAL* 3.1 25.0 + - + +
92D VAL* 3.8 24.5 - - + -
136D VAL* 4.6 1.1 - - + -
138D THR* 4.4 10.3 - - + -
179D TYR* 3.7 55.0 - - + +
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Residues in contact with LEU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ILE* 3.8 29.4 - - + -
36D TYR* 3.8 29.8 - - + -
41D VAL* 3.1 30.4 + - + +
42D LYS* 3.8 28.5 - - + +
46D VAL* 1.3 77.2 - - - +
48D ASP* 1.3 59.6 + - - +
50D VAL* 3.3 8.4 + - + +
51D LEU* 3.0 44.2 + - + +
61D GLU* 4.0 13.5 - - - +
92D VAL* 5.1 4.7 - - + -
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Residues in contact with ASP 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D VAL 4.8 0.2 + - - -
42D LYS* 4.8 10.3 - - - +
45D GLY* 3.4 14.6 + - - +
46D VAL 3.2 0.4 - - - -
47D LEU* 1.3 79.8 - - - +
49D GLN* 1.3 59.4 + - - +
51D LEU* 3.9 17.3 - - - +
52D ASP* 2.9 31.4 + - - +
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Residues in contact with GLN 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLY* 6.1 1.0 - - - -
19D ILE* 3.7 21.9 - - + +
45D GLY* 3.1 23.6 + - - +
46D VAL* 3.1 9.9 + - - +
48D ASP* 1.3 76.5 - - - +
50D VAL* 1.3 58.8 + - - +
52D ASP* 3.6 8.2 - - - +
53D ALA* 3.0 27.2 + - - +
179D TYR* 2.6 40.9 + - - +
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Residues in contact with VAL 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ILE* 3.7 20.0 - - + -
22D LEU* 4.2 2.2 - - + -
34D ILE* 3.9 20.0 - - + -
46D VAL* 3.1 16.7 + - + +
47D LEU* 3.5 9.2 - - + +
48D ASP 3.2 0.2 - - - -
49D GLN* 1.3 74.4 - - - +
51D LEU* 1.3 65.2 + - - +
53D ALA* 3.2 3.5 + - - +
54D LEU* 3.1 26.4 + - + +
90D LEU* 3.7 28.3 - - + -
92D VAL* 4.1 28.3 - - + -
136D VAL* 4.3 9.0 - - + -
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ILE* 3.5 27.4 - - + -
47D LEU* 3.0 33.4 + - + +
48D ASP* 3.9 19.1 - - - +
50D VAL* 1.3 72.8 - - - +
52D ASP* 1.3 64.2 + - - +
54D LEU* 3.3 7.2 + - - +
55D LYS* 3.2 26.4 + - - +
59D VAL* 4.1 17.0 - - + +
61D GLU* 3.8 28.3 - - - +
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Residues in contact with ASP 52 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D ASP 2.9 18.9 + - - +
49D GLN* 3.6 8.9 - - - +
51D LEU* 1.3 77.1 - - - +
53D ALA* 1.3 64.1 + - - +
55D LYS* 3.4 48.2 + - - +
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Residues in contact with ALA 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ILE* 4.3 16.8 - - + +
22D LEU* 4.0 22.0 - - + -
23D ARG* 3.2 32.7 + - + +
49D GLN 3.0 18.8 + - - +
50D VAL* 3.2 6.9 + - - +
52D ASP* 1.3 80.2 + - - +
54D LEU* 1.3 60.0 + - + +
55D LYS 3.4 0.4 - - - -
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 4.1 11.0 - - + -
23D ARG* 3.7 21.8 - - - +
26D ILE* 3.9 25.4 - - + -
32D VAL* 4.5 6.3 - - + -
34D ILE* 4.3 7.2 - - + -
50D VAL* 3.1 21.9 + - + +
51D LEU* 3.4 6.7 - - - +
52D ASP 3.3 0.4 - - - -
53D ALA* 1.3 81.5 - - - +
55D LYS* 1.3 63.4 + - - +
56D GLY 3.4 0.7 + - - -
57D MET* 3.3 34.9 + - - +
59D VAL* 4.1 28.7 - - + +
90D LEU* 3.9 26.2 - - + -
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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