Contacts of the strand formed by residues 45 - 53 (chain A) in PDB entry 1X60
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 LEU 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ALA* 5.0 9.4 - - + +
17A PHE* 3.9 8.7 - - - +
18A LYS* 3.4 28.9 - - + +
40A LEU 3.8 0.2 - - - +
41A LEU* 3.5 1.2 - - - +
42A LYS* 2.6 70.0 + - + +
44A GLY* 1.3 95.1 - - - +
46A TYR* 1.3 66.6 + - - +
47A LYS* 4.7 5.4 - - + +
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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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16A ALA* 2.8 3.6 - - - -
17A PHE 2.6 46.4 + - - +
18A LYS 3.7 22.2 - - - -
19A VAL 4.1 0.9 - - - +
20A LYS* 3.3 45.1 - - + +
23A ALA* 3.7 17.4 - - + +
39A VAL* 3.6 13.7 - - + -
40A LEU 3.4 2.7 - - - -
41A LEU* 3.1 50.5 - - + +
44A GLY 6.0 0.4 - - - -
45A LEU* 1.3 78.5 - - - +
47A LYS* 1.3 62.8 + - - +
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Residues in contact with LYS 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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13A GLN* 3.2 27.1 - - - +
16A ALA* 3.4 24.0 - - + -
38A ILE 3.2 1.1 - - - +
39A VAL* 3.1 27.5 - - - +
40A LEU* 2.8 38.8 + - + +
42A LYS* 3.2 44.9 - - + +
45A LEU* 4.3 3.6 - - + +
46A TYR* 1.3 77.6 - - - +
48A VAL* 1.3 63.6 + - - +
49A GLN* 4.0 1.6 - - + +
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Residues in contact with VAL 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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13A GLN* 3.2 6.4 + - - +
14A ILE* 3.1 37.4 + - + +
15A GLY 2.7 11.1 + - - +
17A PHE* 4.6 2.9 - - + -
23A ALA* 3.0 46.2 - - + +
26A LEU* 3.2 40.6 - - + -
27A ALA* 3.5 23.3 - - + +
38A ILE 3.4 2.7 - - - +
39A VAL* 4.6 0.7 - - + -
47A LYS* 1.3 71.9 - - - +
49A GLN* 1.3 59.8 + - - +
50A ILE* 4.8 2.0 - - + -
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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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11A LYS* 3.2 41.0 + - + +
12A VAL 2.7 23.1 - - - +
13A GLN* 4.0 11.2 - - + +
36A ASP 4.5 1.6 + - - -
37A SER* 3.1 2.1 - - - -
38A ILE* 2.7 68.6 + - + +
47A LYS* 4.0 1.3 - - + -
48A VAL* 1.3 73.1 - - - +
50A ILE* 1.3 62.0 + - - +
51A GLY 3.9 4.6 - - - +
52A ALA* 3.2 34.2 - - - +
78A GLU* 5.2 1.2 - - - +
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Residues in contact with ILE 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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12A VAL* 2.6 60.5 + - + +
14A ILE* 3.4 27.4 - - + -
30A ALA* 3.0 30.1 - - + -
35A PHE* 3.7 13.7 - - + -
36A ASP 3.3 2.7 - - - -
37A SER* 3.4 19.3 - - - +
48A VAL* 4.8 0.9 - - + -
49A GLN* 1.3 80.4 - - - +
51A GLY* 1.3 55.1 + - - +
62A LEU* 2.9 34.8 - - + -
66A ALA* 4.1 4.5 - - + -
73A ALA* 4.1 16.2 - - + -
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Residues in contact with GLY 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 LYS* 3.4 1.4 - - - -
12A VAL* 2.9 32.7 + - - +
36A ASP* 3.1 24.9 + - - +
49A GLN* 3.9 1.9 - - - +
50A ILE* 1.3 69.7 - - - +
52A ALA* 1.3 59.6 + - - -
53A PHE* 3.3 25.1 - - - -
62A LEU* 3.9 11.2 - - - -
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Residues in contact with ALA 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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10A TYR 3.6 4.7 - - - -
11A LYS* 3.5 26.0 - - + -
36A ASP* 5.4 3.4 - - - +
49A GLN* 3.2 23.3 - - - +
51A GLY* 1.3 72.4 - - - +
53A PHE* 1.3 72.6 + - - +
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Residues in contact with PHE 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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9A LEU* 4.2 7.5 - - - +
10A TYR* 2.9 31.7 + - - +
36A ASP* 5.4 6.7 - - - -
51A GLY* 3.3 34.8 - - - -
52A ALA* 1.3 79.1 - - - +
54A SER* 1.3 62.8 + - - +
55A SER 3.3 1.3 + - - +
58A ASN* 3.0 59.9 - - + +
59A ALA* 3.8 7.0 - - - -
62A LEU* 4.1 14.8 - - + -
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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