Contacts of the strand formed by residues 47 - 54 (chain A) in PDB entry 5ODS
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 GLN 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LYS* 3.9 3.1 - - - +
44A VAL* 2.6 55.0 + - - +
45A GLY 3.0 4.4 + - - +
46A GLU* 1.3 80.4 - - - +
48A ALA* 1.3 65.4 + - - +
49A GLN* 3.0 27.1 + - + +
65A PRO* 4.7 12.7 - - + +
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Residues in contact with ALA 48 (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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42A GLU 3.7 7.6 - - - +
43A LYS* 4.0 20.3 - - + +
46A GLU 4.2 0.6 + - - -
47A GLN* 1.3 75.0 - - - +
49A GLN* 1.3 60.2 + - - +
65A PRO* 4.0 4.2 - - - +
66A ILE 3.2 25.9 + - - +
67A SER* 4.3 17.2 + - - +
68A ALA 5.7 0.4 - - - +
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Residues in contact with GLN 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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41A ARG* 3.8 1.9 - - - +
42A GLU* 2.9 40.9 + - + +
44A VAL* 3.5 23.6 - - + +
47A GLN* 3.0 29.1 + - - +
48A ALA* 1.3 75.0 - - - +
50A VAL* 1.3 67.9 + - - +
51A VAL* 5.0 2.5 - - + -
63A ARG* 2.8 52.7 + - - +
64A ARG 3.4 15.7 - - - +
65A PRO* 4.0 7.0 - - + +
66A ILE 3.7 3.3 - - - +
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Residues in contact with VAL 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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39A CYS* 3.7 26.5 - - - -
40A ILE 3.5 2.7 - - - +
41A ARG* 4.2 20.2 - - + -
49A GLN* 1.3 78.9 - - - +
51A VAL* 1.3 63.7 + - - +
52A ILE* 3.8 20.4 + - + +
62A ILE 3.6 2.4 - - - +
64A ARG* 2.8 35.2 + - - +
66A ILE* 3.8 34.5 - - + +
68A ALA* 5.4 2.0 - - + +
71A ALA* 4.4 9.0 - - + -
80A ILE* 4.4 8.7 - - + -
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Residues in contact with VAL 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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20A ILE* 4.4 14.1 - - + -
38A ILE 3.5 2.1 - - - +
39A CYS* 3.3 4.2 - - - +
40A ILE* 2.8 50.3 + - + +
42A GLU* 4.4 12.1 - - + +
49A GLN* 4.6 3.8 - - + +
50A VAL* 1.3 77.8 - - - +
52A ILE* 1.3 63.9 + - - +
53A ILE* 4.1 4.9 - - + -
61A PRO* 3.9 24.9 - - + -
62A ILE 3.5 10.5 - - - +
63A ARG* 3.6 44.9 - - + +
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Residues in contact with ILE 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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37A PHE* 3.9 30.1 - - + -
38A ILE 3.6 3.6 - - - +
39A CYS* 4.5 8.3 - - - +
50A VAL* 3.8 28.9 - - + +
51A VAL* 1.3 75.2 - - - +
53A ILE* 1.3 64.2 + - - +
54A ASP 4.9 0.4 - - - +
61A PRO* 4.1 0.3 - - - +
62A ILE* 3.3 46.2 + - + +
64A ARG* 4.1 24.2 - - - +
66A ILE* 5.5 0.9 - - + -
73A MET* 4.1 26.5 - - + -
80A ILE* 4.7 3.1 - - + -
93A ILE* 4.5 16.2 - - + -
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Residues in contact with ILE 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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13A LEU* 5.1 2.5 - - + -
15A LEU* 3.8 24.2 - - + -
18A LEU* 4.2 14.6 - - + -
20A ILE* 4.5 9.2 - - + -
37A PHE* 3.3 9.6 - - - -
38A ILE* 2.9 38.3 + - + +
40A ILE* 3.7 25.4 - - + -
51A VAL* 4.5 2.2 - - + -
52A ILE* 1.3 75.7 - - - +
54A ASP* 1.3 73.8 + - - +
55A MET* 3.4 11.5 + - - +
57A ASP 5.1 0.2 - - - +
58A PRO* 4.0 24.5 - - + +
61A PRO* 4.0 19.7 - - + -
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Residues in contact with ASP 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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36A LYS 3.7 5.9 - - - +
37A PHE* 3.9 21.4 - - + -
52A ILE* 3.8 4.6 + - - +
53A ILE* 1.3 73.3 - - - +
55A MET* 1.3 68.9 + - - +
56A ASN* 3.1 30.4 + - - +
57A ASP* 2.9 44.7 + - + +
58A PRO* 3.0 6.8 - - - +
60A ASN 5.6 1.2 + - - +
62A ILE* 5.3 10.0 - - + +
78A LYS* 4.1 16.9 + - - -
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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