Contacts of the strand formed by residues 51 - 58 (chain D) in PDB entry 1LNU
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 ARG 51 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ILE* 4.6 23.1 - - - +
41D CYS* 3.0 2.5 - - - -
42D TYR* 2.6 57.1 + - + +
49D ARG* 5.5 3.6 - - - +
50D ILE* 1.3 79.1 - - - +
52D TYR* 1.3 59.5 + - - +
53D VAL* 4.2 10.7 - - + +
67D ASP* 2.3 46.8 + - - +
68D SER* 4.4 4.9 - - - -
69D ASP* 3.8 34.4 + - - +
70D VAL* 5.7 0.4 - - - +
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Residues in contact with TYR 52 (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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6D ALA* 3.2 17.3 - - + +
39D GLY* 3.4 24.7 - - - -
40D GLU 3.7 0.9 - - - -
41D CYS* 3.0 29.4 - - + -
51D ARG* 1.3 70.5 - - - +
53D VAL* 1.3 66.7 + - - +
54D THR* 3.1 26.4 - - + +
66D TYR* 3.6 14.7 - + + +
67D ASP 3.7 0.2 - - - -
68D SER* 2.9 35.8 + - - -
97D THR* 4.0 15.0 - - + -
100D GLU* 2.2 53.1 + - + +
101D LEU* 4.1 29.4 - - + +
104D VAL* 4.3 5.3 - - - +
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Residues in contact with VAL 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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1C ILE* 5.8 1.8 - - + -
38D MET 3.7 0.9 - - - +
40D GLU* 2.8 47.2 + - + +
42D TYR* 4.3 10.3 - - + -
51D ARG* 3.9 14.3 + - + +
52D TYR* 1.3 81.3 - - - +
54D THR* 1.3 63.6 + - - +
55D ARG* 3.6 41.5 + - + +
65D ARG* 4.1 12.3 - - + -
66D TYR 3.2 9.0 - - - +
67D ASP* 3.7 25.1 - - - +
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Residues in contact with THR 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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7D LYS 5.1 0.9 - - - +
37D PHE* 3.6 30.7 - - + -
38D MET 3.5 2.2 - - - -
39D GLY* 4.0 5.2 - - - -
52D TYR* 3.1 39.9 - - + +
53D VAL* 1.3 72.9 - - - +
55D ARG* 1.3 62.1 + - - +
56D TYR* 4.2 9.8 + - - -
65D ARG* 3.4 4.2 - - - +
66D TYR* 3.0 53.3 + - - +
73D HIS* 5.1 0.3 - - - -
97D THR* 4.4 6.9 - - + +
100D GLU* 4.1 2.5 - - - +
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Residues in contact with ARG 55 (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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1C ILE* 4.2 16.6 - - - +
144C TYR* 3.6 17.7 + - - -
36D GLN 3.5 1.6 - - - +
37D PHE* 3.5 24.1 - - - -
38D MET* 3.4 27.9 + - - +
40D GLU* 2.5 32.1 + - - -
42D TYR* 3.7 7.5 + - - -
53D VAL* 3.6 25.0 - - + +
54D THR* 1.3 79.1 - - - +
56D TYR* 1.3 65.0 + - - +
57D ILE* 3.8 14.7 - - + +
62D GLU* 3.0 44.4 + - - +
64D VAL 4.0 3.8 - - - -
65D ARG* 4.0 10.5 - - - +
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Residues in contact with TYR 56 (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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70C ASN* 4.4 0.9 - - - -
7D LYS 4.1 1.9 + - - -
8D ALA* 4.0 4.7 - - + -
9D ASN* 3.0 44.9 + - - -
35D TYR* 3.6 22.7 - + + +
36D GLN 3.4 4.9 - - - -
37D PHE* 3.5 33.7 - + - -
54D THR* 4.2 17.7 + - - +
55D ARG* 1.3 77.0 - - - +
57D ILE* 1.3 62.4 + - - +
62D GLU* 3.4 2.9 - - - -
63D TYR* 2.9 46.1 + - + -
64D VAL* 3.2 28.0 + - + +
65D ARG* 5.2 0.7 - - - -
73D HIS* 4.9 4.8 - - - -
87D TRP* 3.7 29.4 - + - -
97D THR* 6.1 0.3 - - - +
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Residues in contact with ILE 57 (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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144C TYR* 3.4 50.5 - - + +
35D TYR* 3.6 8.4 - - - -
36D GLN* 2.8 56.1 + - + +
38D MET* 4.0 7.6 - - - -
55D ARG* 3.8 20.2 - - + -
56D TYR* 1.3 78.7 - - - +
58D TYR* 1.3 61.6 + - - +
59D ASN 3.8 6.0 + - - +
60D ARG* 3.5 14.1 - - - -
61D GLU 3.3 24.2 - - - +
62D GLU* 3.8 8.3 - - - -
63D TYR* 4.3 3.1 - - - -
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Residues in contact with TYR 58 (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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71C LEU* 3.8 25.1 - - + -
74C LEU* 3.8 38.4 - - + -
75C THR* 3.7 13.4 - - - -
78C SER* 3.5 27.6 - - - -
81C THR* 3.1 19.4 + - - -
33D PHE* 3.6 14.4 - - + -
34D VAL 4.1 3.8 - - - -
35D TYR* 4.7 2.7 - + - -
57D ILE* 1.3 70.1 - - - +
59D ASN* 1.3 97.8 + - - +
60D ARG 2.5 18.5 + - - -
61D GLU* 2.7 29.2 + - + +
63D TYR* 3.9 18.2 - - + -
79D LEU* 5.2 8.3 - - + -
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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