Contacts of the strand formed by residues 61 - 67 (chain F) 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 GLU 61 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57F ILE* 3.1 4.9 - - - +
58F TYR* 2.7 37.2 + - + +
59F ASN* 5.8 0.4 - - + -
60F ARG* 1.3 79.7 - - - +
62F GLU* 1.3 74.9 + - - +
63F TYR* 3.1 2.9 + - - +
77F THR* 3.0 33.1 + - + +
79F LEU* 5.0 7.4 - - - +
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Residues in contact with GLU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E TYR* 3.8 16.1 + - + -
55F ARG* 2.8 51.3 + - + +
56F TYR 3.4 2.7 - - - +
57F ILE* 3.4 21.3 - - + +
60F ARG 4.2 0.8 + - - -
61F GLU* 1.3 81.3 - - - +
63F TYR* 1.3 57.5 + - - +
64F VAL 3.8 8.1 - - - +
65F ARG* 2.6 38.7 + - - +
76F VAL* 3.1 35.3 - - + +
77F THR* 3.7 1.4 - - - +
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Residues in contact with TYR 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ASN* 4.0 9.2 + - - -
74E LEU* 3.3 39.3 - - + +
11F ALA* 4.5 0.2 - - - +
35F TYR* 2.4 42.2 + + - -
56F TYR* 3.0 39.3 + + + +
58F TYR* 4.0 11.9 - - + -
61F GLU* 3.1 6.8 + - - +
62F GLU* 1.3 71.5 - - - +
64F VAL* 1.3 85.9 + - + +
76F VAL* 2.8 22.6 + - - +
77F THR* 3.2 19.4 + - - +
79F LEU* 3.0 36.8 - - + -
80F GLY* 3.4 5.9 - - - -
83F ASP* 3.1 20.1 + - - -
87F TRP* 4.4 2.8 - - - -
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Residues in contact with VAL 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F TYR* 3.2 33.6 + - + +
62F GLU* 3.8 4.3 - - - +
63F TYR* 1.3 117.4 - - + +
65F ARG* 1.3 76.1 + - - +
73F HIS* 4.8 0.9 - - + -
74F ARG 4.1 6.1 - - - +
75F ALA* 4.5 0.4 - - - +
76F VAL* 3.4 4.5 - - - +
80F GLY* 3.5 16.8 - - - +
83F ASP* 4.0 5.6 - - + -
84F ALA* 4.5 15.5 - - + +
87F TRP* 3.5 31.2 - - + -
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Residues in contact with ARG 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F VAL* 3.9 19.1 - - + -
54F THR 3.5 13.7 - - - +
55F ARG* 4.1 7.0 - - - +
56F TYR* 4.8 2.5 - - - -
62F GLU* 2.6 39.6 + - - +
64F VAL* 1.3 82.9 - - - +
66F TYR* 1.3 74.5 + - - +
67F ASP* 4.3 13.8 + - - +
73F HIS* 3.0 9.0 - - - +
74F ARG* 2.8 40.9 + - + +
76F VAL* 3.6 23.3 - - + +
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Residues in contact with TYR 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F TYR* 4.0 21.3 - + - -
53F VAL* 3.1 6.4 - - - +
54F THR* 2.9 47.3 + - - +
56F TYR* 5.5 0.2 - - + -
65F ARG* 1.3 78.4 - - - +
67F ASP* 1.3 80.8 + - - +
68F SER* 3.7 15.5 + - - -
71F GLY* 3.5 8.5 - - - -
72F GLU* 3.1 41.7 - - - -
73F HIS* 3.5 26.5 - + + +
94F LEU* 5.3 1.6 - - + -
97F THR* 3.8 20.2 - - + -
98F ARG* 3.4 31.4 - - - -
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Residues in contact with ASP 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ARG* 2.5 43.3 + - - -
52F TYR 3.8 0.9 - - - -
53F VAL* 3.6 12.7 - - - +
65F ARG* 4.3 14.1 + - - +
66F TYR* 1.3 84.3 - - - +
68F SER* 1.3 77.5 + - - +
69F ASP* 3.0 12.1 + - - -
70F VAL* 3.4 24.5 - - + +
71F GLY 3.0 23.4 + - - -
72F GLU 3.9 5.5 + - - -
74F ARG* 6.4 0.2 - - - +
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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