Contacts of the helix formed by residues 70 - 80 (chain F) in PDB entry 3LNX
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 THR 70 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25F GLY* 4.1 2.0 - - - -
26F VAL* 3.4 19.7 - - + -
27F ASN* 3.6 22.4 - - + +
68F GLY 4.8 0.9 - - - +
69F ALA* 1.3 76.4 - - - +
71F HIS* 1.3 66.6 + - - +
72F LYS* 3.8 11.6 + - - +
73F GLN* 3.0 40.6 + - - +
74F ALA* 3.0 21.0 + - - +
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Residues in contact with HIS 71 (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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22F VAL* 3.2 29.8 + - + -
23F THR* 4.0 9.2 - - - -
24F GLY 3.0 30.6 + - - +
25F GLY* 3.9 0.4 - - - -
27F ASN* 3.2 17.8 + - - +
28F THR* 4.2 9.3 - - + +
38F LYS* 4.9 5.6 + - - -
70F THR* 1.3 72.6 - - - +
72F LYS* 1.3 69.0 + - + +
74F ALA* 3.0 7.0 + - - +
75F VAL* 3.0 49.1 + - + +
99F SCN 3.8 26.1 - - - +
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Residues in contact with LYS 72 (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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27F ASN* 5.1 11.7 - - - +
70F THR* 4.3 8.7 - - - +
71F HIS* 1.3 77.6 - - + +
73F GLN* 1.3 59.1 + - + +
75F VAL* 3.3 3.0 + - - +
76F GLU* 3.0 32.1 + - - +
99F SCN 3.9 33.9 - - - -
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Residues in contact with GLN 73 (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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68F GLY 4.0 3.1 - - - +
69F ALA* 3.4 14.1 - - + +
70F THR* 3.0 47.0 + - - +
71F HIS 3.1 1.2 - - - -
72F LYS* 1.3 77.7 - - + +
74F ALA* 1.3 58.0 + - - +
76F GLU* 3.6 4.9 + - - +
77F THR* 2.8 33.4 + - - +
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Residues in contact with ALA 74 (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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22F VAL* 5.3 2.2 - - + -
35F ILE* 3.8 36.8 - - + -
66F LEU* 4.5 12.5 - - + +
69F ALA* 4.4 5.3 - - + +
70F THR 3.0 13.2 + - - +
71F HIS 3.5 7.0 - - - +
73F GLN* 1.3 73.6 - - - +
75F VAL* 1.3 67.7 - - + +
77F THR* 3.2 8.1 + - - -
78F LEU* 3.1 30.8 + - + +
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Residues in contact with VAL 75 (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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22F VAL* 3.9 17.0 - - + -
71F HIS* 3.0 42.9 + - + +
72F LYS* 3.6 8.7 - - - +
74F ALA* 1.3 77.6 - - - +
76F GLU* 1.3 67.2 + - - +
78F LEU* 3.6 11.2 + - - +
79F ARG* 3.3 41.1 + - + +
99F SCN 4.6 9.4 - - - -
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Residues in contact with GLU 76 (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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72F LYS 3.0 17.4 + - - +
73F GLN* 4.1 4.7 - - - +
75F VAL* 1.3 83.5 - - - +
77F THR* 1.3 65.2 + - - +
78F LEU 3.1 1.8 - - - -
79F ARG* 3.0 25.8 + - - +
80F ASN* 3.0 50.0 + - - +
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Residues in contact with THR 77 (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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61F VAL* 3.9 21.6 - - + +
64F VAL* 5.5 6.5 - - + +
66F LEU* 3.9 24.9 - - + +
73F GLN* 2.8 25.2 + - - +
74F ALA* 3.2 7.1 + - - -
76F GLU* 1.3 77.4 - - - +
78F LEU* 1.3 61.9 + - - +
80F ASN* 3.8 7.7 + - - +
81F THR* 3.6 16.8 - - - +
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Residues in contact with LEU 78 (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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13F LYS* 4.4 0.2 + - - -
18F LEU* 4.1 21.9 - - + +
20F ILE* 5.1 14.8 - - + +
22F VAL* 4.0 33.9 - - + -
35F ILE* 5.8 2.0 - - + -
58F VAL* 4.9 8.5 - - + -
61F VAL* 3.6 31.0 - - + -
66F LEU* 5.7 2.5 - - + -
74F ALA* 3.1 20.5 + - + +
75F VAL* 3.8 7.4 - - - +
76F GLU 3.1 0.4 - - - -
77F THR* 1.3 79.6 - - - +
79F ARG* 1.3 58.9 + - + +
81F THR* 3.0 20.5 + - - +
87F LEU* 3.8 17.5 - - + -
97F IOD 4.0 10.0 - - - +
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Residues in contact with ARG 79 (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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13F LYS* 3.7 11.8 + - - +
75F VAL* 3.3 27.3 + - + +
76F GLU* 3.0 30.4 + - - +
78F LEU* 1.3 79.3 - - - +
80F ASN* 1.3 62.0 + - - +
81F THR 3.0 10.7 + - - +
97F IOD 4.3 16.8 - - + -
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Residues in contact with ASN 80 (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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48E SER 4.1 7.9 - - - +
49E ASP 4.9 3.1 - - - +
76F GLU* 3.0 43.4 + - - +
77F THR* 4.0 5.6 - - - +
78F LEU 3.5 0.2 - - - -
79F ARG* 1.3 77.0 + - - +
81F THR* 1.3 66.2 + - - +
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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