Contacts of the strand formed by residues 51 - 58 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ILE* 4.5 23.5 - - - +
41B CYS* 3.1 1.6 - - - -
42B TYR* 2.7 56.9 + - + +
49B ARG* 5.4 3.4 - - + +
50B ILE* 1.3 79.0 - - - +
52B TYR* 1.3 60.9 + - - +
53B VAL* 4.2 14.1 - - + +
67B ASP* 2.6 41.5 + - - +
68B SER* 4.3 3.8 - - - -
69B ASP* 3.2 34.8 + - - +
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Residues in contact with TYR 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ALA* 3.2 24.4 - - + +
39B GLY* 3.6 22.9 - - - -
40B GLU 3.9 0.2 - - - -
41B CYS* 3.0 27.4 - - + -
51B ARG* 1.3 70.8 - - - +
53B VAL* 1.3 63.7 + - - +
54B THR* 3.4 21.3 - - + +
66B TYR* 3.6 14.8 - + - +
67B ASP 3.7 0.3 - - - -
68B SER* 2.9 39.1 + - - +
97B THR* 4.0 10.3 - - + -
100B GLU* 2.5 52.5 + - + +
101B LEU* 4.0 29.5 - - + +
104B VAL* 4.2 11.7 - - - +
105B CYS* 4.5 0.4 - - + -
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ILE* 5.7 2.2 - - + -
38B MET 3.7 0.9 - - - +
40B GLU* 2.8 48.8 + - + +
42B TYR* 4.2 14.8 - - + -
51B ARG* 3.9 14.8 + - + +
52B TYR* 1.3 81.8 - - - +
54B THR* 1.3 63.7 + - - +
55B ARG* 3.9 36.6 + - + +
65B ARG* 4.0 15.9 - - + -
66B TYR 3.2 10.5 - - - +
67B ASP* 4.2 20.4 - - - +
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Residues in contact with THR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LYS 5.4 0.7 - - - +
37B PHE* 3.9 25.6 - - + -
38B MET 3.6 3.4 - - - -
39B GLY* 4.2 3.1 - - - -
52B TYR* 3.4 44.2 - - + +
53B VAL* 1.3 74.1 - - - +
55B ARG* 1.3 64.2 + - - +
56B TYR* 4.2 10.4 + - - -
65B ARG* 3.5 4.5 - - - +
66B TYR* 2.9 46.0 + - - +
73B HIS* 5.2 0.2 - - - -
97B THR* 4.5 5.7 - - + +
100B GLU* 4.1 4.3 - - - +
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ILE* 4.4 13.7 - - - +
144A TYR* 3.4 27.1 + - - -
36B GLN 3.5 1.4 - - - +
37B PHE* 3.4 8.7 - - - -
38B MET* 3.4 36.1 + - + +
40B GLU* 3.1 34.3 + - - -
42B TYR* 4.2 4.4 + - - -
53B VAL* 3.9 21.9 - - + +
54B THR* 1.3 79.2 - - - +
56B TYR* 1.3 63.7 + - - +
57B ILE* 3.6 13.0 - - + -
62B GLU* 2.8 51.7 + - - +
64B VAL 4.0 3.6 - - - -
65B ARG* 3.9 9.4 - - - +
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Residues in contact with TYR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ASN* 4.3 1.3 - - - -
7B LYS 4.4 2.3 + - - -
8B ALA* 4.2 3.8 - - + -
9B ASN* 3.0 49.7 + - - -
35B TYR* 3.2 30.3 - + - +
36B GLN 3.4 4.9 - - - -
37B PHE* 3.8 30.0 - + + -
54B THR* 4.2 16.9 + - - -
55B ARG* 1.3 77.7 - - - +
57B ILE* 1.3 61.8 + - - +
62B GLU* 3.4 2.4 - - - -
63B TYR* 3.0 36.9 + - + -
64B VAL* 3.2 21.8 + - + +
65B ARG* 5.2 1.1 - - - -
73B HIS* 4.3 5.5 - - - -
87B TRP* 3.5 33.7 - + - -
97B THR* 5.4 0.7 + - - +
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Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A TYR* 3.8 38.6 - - + -
34B VAL 3.9 0.2 - - - +
35B TYR* 3.6 9.1 - - - -
36B GLN* 2.8 50.5 + - + +
38B MET* 4.4 7.6 - - - -
55B ARG* 3.6 28.3 - - + +
56B TYR* 1.3 79.3 - - - +
58B TYR* 1.3 61.2 + - - +
59B ASN 3.8 5.2 - - - +
60B ARG* 3.5 14.8 - - - +
61B GLU 3.4 24.7 - - - +
62B GLU* 3.6 16.6 - - - +
63B TYR* 4.2 2.9 - - - -
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Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 3.7 26.7 - - + -
74A LEU* 3.5 39.1 + - + -
75A THR* 3.2 21.1 + - - -
78A SER* 3.6 25.5 - - - -
81A THR* 3.7 14.8 + - - -
33B PHE* 3.8 10.4 - + - -
34B VAL 4.0 0.9 - - - -
35B TYR* 4.5 3.4 - + - -
57B ILE* 1.3 71.1 - - - +
59B ASN* 1.3 97.1 + - - +
60B ARG 2.6 17.8 + - - -
61B GLU* 2.7 28.1 + - + +
63B TYR* 3.9 21.1 - - + -
79B LEU* 4.6 7.9 - - + -
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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