Contacts of the strand formed by residues 44 - 53 (chain A) in PDB entry 5LPN
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 ILE 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.4 3.8 - - + -
41A THR* 4.9 2.0 - - - +
42A ILE 3.5 3.7 + - - -
43A GLY* 1.3 75.5 - - - +
45A ASP* 1.3 68.7 + - - +
63A TRP* 3.7 23.1 - - + -
64A ASP 3.4 15.0 - - - +
65A THR* 4.0 22.9 - - + -
74A ILE* 5.1 1.3 - - + -
75A THR* 4.4 8.7 - - + +
78A TYR* 3.5 56.3 - - + -
970B TRP* 3.3 34.5 + - + -
978B VAL* 3.9 9.6 - - + +
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Residues in contact with ASP 45 (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 THR* 5.7 0.8 - - + +
44A ILE* 1.3 77.7 - - - +
46A PHE* 1.3 74.6 + - - +
47A LYS* 3.5 23.7 + - - +
63A TRP* 3.1 11.1 - - - +
64A ASP* 2.8 33.2 + - + +
978B VAL* 3.2 28.3 - - + +
981B LYS* 3.4 27.3 + - - +
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Residues in contact with PHE 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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26A LEU* 5.5 0.4 - - - -
45A ASP* 1.3 90.6 - - - +
47A LYS* 1.3 73.1 + - - +
48A ILE* 4.1 13.0 - - + -
61A GLN* 3.4 36.1 - - + -
62A ILE 3.0 24.0 - - - +
63A TRP* 3.5 39.7 - + + -
64A ASP* 4.4 0.7 - - - +
942B LEU* 6.1 0.7 - - + -
946B GLU* 4.6 6.2 - - - +
978B VAL* 3.9 17.5 - - + -
981B LYS* 3.7 31.1 + - + -
982B ASN* 3.9 7.9 - - + -
985B VAL* 4.2 13.0 - - + -
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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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26A LEU* 3.6 32.8 - - + -
27A PHE* 6.0 9.2 - - + -
30A SER* 4.8 14.1 - - - +
45A ASP* 3.5 22.9 + - - +
46A PHE* 1.3 83.1 + - - +
48A ILE* 1.3 70.2 + - - +
60A LEU 3.6 1.2 - - - +
62A ILE* 2.9 34.8 + - - +
64A ASP* 6.3 2.0 - - - -
946B GLU* 4.6 16.8 + - - +
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Residues in contact with ILE 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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30A SER* 5.2 4.9 - - - -
46A PHE* 4.1 13.9 - - + -
47A LYS* 1.3 86.1 - - - +
49A LYS* 1.3 69.4 + - - +
50A THR* 4.8 2.0 - - - +
59A LYS* 3.5 41.3 - - + +
60A LEU 3.5 1.3 - - - +
61A GLN* 3.7 33.4 - - + -
62A ILE* 6.1 0.4 - - - -
942B LEU* 6.4 1.1 - - + -
985B VAL* 4.7 10.8 - - + -
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Residues in contact with LYS 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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29A PHE* 2.1 76.5 + - + +
30A SER* 4.1 19.8 + - - +
48A ILE* 1.3 79.8 - - - +
50A THR* 1.3 76.1 + - - +
51A VAL* 4.7 3.4 - - + -
60A LEU* 2.9 40.2 + - + +
62A ILE* 5.5 2.4 - - + +
160A GLU* 4.7 8.7 + - - -
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Residues in contact with THR 50 (chain A).
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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5A THR 5.1 0.9 - - - +
6A TYR* 4.0 19.2 - - + -
48A ILE* 4.8 1.0 - - - +
49A LYS* 1.3 82.3 - - - +
51A VAL* 1.3 77.4 + - - +
57A LYS* 4.6 12.1 - - + -
58A ILE 3.4 18.2 - - - +
59A LYS* 3.8 24.0 - - - +
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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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29A PHE* 4.4 9.4 - - + -
49A LYS* 4.4 5.6 - - + +
50A THR* 1.3 81.1 - - - +
52A GLU* 1.3 64.5 + - - +
53A LEU* 4.1 16.6 - - + -
57A LYS* 3.0 9.0 - - - +
58A ILE* 2.8 52.4 + - + +
60A LEU* 3.9 30.1 - - + -
164A LEU* 3.8 28.5 - - + -
167A ALA* 4.9 0.4 - - + -
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Residues in contact with GLU 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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50A THR* 6.2 0.2 - - + -
51A VAL* 1.3 78.4 - - - +
53A LEU* 1.3 67.1 + - - +
54A GLN 3.9 2.3 + - - +
55A GLY* 5.4 8.0 + - - +
56A LYS 3.5 6.5 - - - +
57A LYS* 4.0 28.3 + - + +
164A LEU* 5.7 3.5 - - - +
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Residues in contact with LEU 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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51A VAL* 4.1 11.0 - - + -
52A GLU* 1.3 76.2 - - - +
54A GLN* 1.3 72.2 + - + +
55A GLY 3.2 0.9 - - - -
56A LYS* 2.8 27.4 + - - +
58A ILE* 3.5 27.4 - - + -
164A LEU* 4.0 33.9 - - + +
167A ALA* 3.6 31.0 - - + +
168A GLU* 3.6 29.4 - - + +
171A LEU* 4.2 16.4 - - + +
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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