Contacts of the helix formed by residues 70 - 80 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C GLY* 4.0 1.3 - - - -
26C VAL* 3.8 17.7 - - + +
27C ASN* 3.2 22.2 - - + +
68C GLY 3.5 1.1 + - - +
69C ALA* 1.3 76.2 - - - +
71C HIS* 1.3 65.8 + - - +
72C LYS* 3.5 6.2 + - - +
73C GLN* 2.9 41.0 + - - +
74C ALA* 2.9 21.0 + - - +
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Residues in contact with HIS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C VAL* 3.0 30.8 + - + +
23C THR* 4.0 3.1 - - - -
24C GLY 3.0 41.2 + - - +
25C GLY* 3.8 0.9 - - - -
27C ASN* 2.9 23.2 + - - +
28C THR* 4.6 4.0 - - + -
35C ILE* 5.5 1.6 - - + -
70C THR* 1.3 72.3 - - - +
72C LYS* 1.3 80.8 + - + +
74C ALA* 3.1 6.2 + - - +
75C VAL* 2.9 47.6 + - + +
102C SCN 3.5 17.0 + - - -
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Residues in contact with LYS 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ASN* 6.2 1.3 - - - +
70C THR* 3.2 6.3 + - - +
71C HIS* 1.3 96.2 + - + +
73C GLN* 1.3 64.0 + - + +
75C VAL* 3.3 33.6 + - - +
76C GLU* 2.9 35.1 + - + +
79C ARG* 4.9 7.2 - - - +
102C SCN 5.6 1.8 + - - -
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Residues in contact with GLN 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C GLY 3.7 5.2 - - - +
69C ALA* 3.4 13.3 - - + -
70C THR* 2.9 44.5 + - - +
72C LYS* 1.3 77.2 - - + +
74C ALA* 1.3 56.0 + - - +
76C GLU* 3.2 6.8 + - - +
77C THR* 2.9 35.1 + - - +
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Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C VAL* 5.3 1.8 - - + -
35C ILE* 3.6 40.2 - - + -
66C LEU* 4.6 8.8 - - + +
69C ALA* 4.2 8.0 - - + +
70C THR 2.9 16.5 + - - +
71C HIS* 3.5 8.3 - - - +
73C GLN* 1.3 72.2 - - - +
75C VAL* 1.3 64.8 + - + +
77C THR* 3.3 7.7 + - - -
78C LEU* 3.0 29.0 + - + +
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Residues in contact with VAL 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C VAL* 4.1 13.5 - - + -
71C HIS* 2.9 48.8 + - + +
72C LYS* 3.7 17.3 - - - +
74C ALA* 1.3 74.8 - - - +
76C GLU* 1.3 59.1 + - - +
78C LEU* 3.2 10.5 + - - +
79C ARG* 2.9 67.6 + - + +
102C SCN 4.3 13.9 - - - -
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Residues in contact with GLU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C LYS* 2.9 26.7 + - + +
73C GLN* 3.7 6.3 - - - +
75C VAL* 1.3 76.8 - - - +
77C THR* 1.3 57.4 + - - +
79C ARG* 3.2 34.1 + - - +
80C ASN* 2.8 56.6 + - - +
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Residues in contact with THR 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C VAL* 3.8 26.4 - - + +
64C VAL* 5.6 5.8 - - + +
66C LEU* 3.9 20.6 - - + +
73C GLN* 2.9 20.9 + - - +
74C ALA 3.6 5.4 - - - -
76C GLU* 1.3 77.5 - - - +
78C LEU* 1.3 62.6 + - - +
79C ARG 3.4 0.2 + - - -
80C ASN* 3.6 7.9 + - - +
81C THR* 3.3 17.7 - - - +
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 3.9 22.4 - - + +
20C ILE* 4.7 10.8 - - + -
22C VAL* 4.2 31.4 - - + -
35C ILE* 5.2 5.6 - - + -
58C VAL* 4.8 8.1 - - + -
61C VAL* 3.8 25.4 - - + -
66C LEU* 5.6 1.3 - - + -
74C ALA* 3.0 23.8 + - + +
75C VAL* 3.6 8.3 - - + +
77C THR* 1.3 78.2 - - - +
79C ARG* 1.3 52.7 + - + +
81C THR* 2.6 30.3 + - - +
87C LEU* 3.9 19.5 - - + -
97C IOD 4.1 14.6 - - + +
102C SCN 5.9 2.0 - - - -
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Residues in contact with ARG 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LYS* 3.8 5.4 + - - -
72C LYS* 4.9 6.7 - - - +
75C VAL* 2.9 37.5 + - + +
76C GLU* 3.4 31.3 + - - +
78C LEU* 1.3 74.9 - - + +
80C ASN* 1.3 64.0 + - - +
81C THR* 2.8 19.3 + - - +
97C IOD 4.2 20.0 - - + -
102C SCN 5.4 7.5 - - - -
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Residues in contact with ASN 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C GLU* 2.8 40.1 + - - +
77C THR* 4.0 5.3 - - - +
78C LEU 3.4 0.8 - - - -
79C ARG* 1.3 77.2 - - - +
81C THR* 1.3 65.3 + - - +
48D SER 3.8 10.2 - - - +
49D ASP 4.6 4.3 - - - +
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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