Contacts of the helix formed by residues 69 - 84 (chain C) in PDB entry 1LUA
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 ASP 69 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C THR* 4.3 6.3 + - - +
12C ASP* 4.8 3.1 + - - +
67C GLY 3.5 0.8 - - - -
68C GLY* 1.3 74.7 - - - +
70C MET* 1.3 67.9 + - - +
71C ALA* 3.2 13.1 + - - +
72C ALA* 2.7 40.5 + - + +
73C GLY* 3.0 18.4 + - - -
75C ARG* 4.7 2.1 + - - -
96C SER* 4.0 5.1 + - - -
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Residues in contact with MET 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLY 3.8 4.0 + - - -
69C ASP* 1.3 73.2 - - - +
71C ALA* 1.3 59.3 + - - +
73C GLY 3.1 1.6 + - - -
74C GLU* 2.8 67.0 + - + +
94C LEU* 3.2 33.7 - - + -
95C ASP* 6.0 0.2 - - - -
96C SER* 3.8 17.9 - - - +
97C ASN* 5.7 1.2 - - + +
99C SER* 4.2 21.3 - - - +
100C ASN* 5.1 3.6 - - - +
131C PRO* 3.8 32.0 - - + +
135C ARG* 4.0 15.9 - - - +
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Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ASP* 3.2 10.8 + - - +
70C MET* 1.3 78.2 - - - +
72C ALA* 1.3 64.1 + - - +
74C GLU* 3.3 14.7 + - - +
75C ARG* 3.1 41.5 + - - +
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Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C THR* 3.9 21.5 - - + -
39C PRO* 5.6 0.3 - - - +
69C ASP* 2.7 32.2 + - + +
71C ALA* 1.3 72.7 - - - +
73C GLY* 1.3 63.4 + - - +
75C ARG* 3.2 25.5 + - - +
76C VAL* 3.1 25.5 + - - +
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Residues in contact with GLY 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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11C THR* 4.1 8.5 - - - +
65C VAL* 3.7 12.4 - - - +
66C GLY 5.3 0.2 - - - -
69C ASP 3.0 10.3 + - - -
70C MET 3.1 4.0 + - - -
72C ALA* 1.3 75.1 - - - +
74C GLU* 1.3 59.5 + - - +
76C VAL* 3.2 3.3 + - - +
77C PHE* 2.8 30.0 + - - +
94C LEU* 3.9 6.5 - - - -
96C SER* 3.5 20.0 - - - -
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Residues in contact with GLU 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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70C MET* 2.8 40.3 + - + +
71C ALA* 3.3 16.4 + - - +
73C GLY* 1.3 72.5 - - - +
75C ARG* 1.3 64.5 + - + +
77C PHE* 3.3 7.4 + - - +
78C GLU* 2.9 32.8 + - + +
94C LEU* 3.9 7.4 - - + -
135C ARG* 2.9 32.3 + - - +
167C ARG* 5.5 5.0 + - - +
276C ASP* 6.0 0.2 - - - +
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Residues in contact with ARG 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PRO* 3.7 26.7 - - + +
69C ASP* 4.7 2.0 + - - -
71C ALA* 3.1 33.5 + - - +
72C ALA* 3.5 28.4 - - - +
73C GLY 3.2 0.2 - - - -
74C GLU* 1.3 78.5 - - + +
76C VAL* 1.3 62.4 + - - +
78C GLU* 3.4 6.8 + - - +
79C ALA* 3.1 21.5 + - - +
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Residues in contact with VAL 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PHE* 4.7 2.7 - - + +
11C THR* 4.0 8.3 - - + -
37C VAL* 3.7 42.2 - - + +
38C THR* 3.8 17.5 - - - -
39C PRO* 4.0 4.5 - - + -
42C VAL* 4.2 13.7 - - + -
65C VAL* 4.0 25.1 - - + -
72C ALA 3.1 12.4 + - - +
73C GLY 3.7 6.3 - - - +
75C ARG* 1.3 78.1 - - - +
77C PHE* 1.3 63.7 + - - +
79C ALA* 3.0 9.5 + - - +
80C VAL* 2.9 21.4 + - + +
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Residues in contact with PHE 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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65C VAL* 4.0 17.2 - - + +
73C GLY 2.8 16.8 + - - +
74C GLU 3.6 5.4 - - - +
76C VAL* 1.3 78.3 - - - +
78C GLU* 1.3 63.9 + - - +
80C VAL* 3.3 9.3 + - + +
81C LYS* 3.1 58.0 + - + +
92C CYS* 3.6 36.1 - - + -
93C MET* 3.6 22.2 - - - -
94C LEU* 3.9 37.9 - - + -
274C VAL* 4.1 15.3 - - + -
275C PHE 4.4 3.4 - - - -
276C ASP* 4.0 18.4 - - + -
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Residues in contact with GLU 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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74C GLU* 2.9 23.2 + - + +
75C ARG* 3.8 7.2 - - - +
77C PHE* 1.3 78.9 - - - +
79C ALA* 1.3 57.2 + - - +
81C LYS* 2.8 37.2 + - - +
82C LYS* 2.9 30.9 + - - +
167C ARG* 5.7 2.8 + - - -
276C ASP* 5.5 0.9 - - - +
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Residues in contact with ALA 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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39C PRO* 3.8 22.7 - - + +
42C VAL* 3.7 22.6 - - + +
43C GLY* 5.7 0.7 - - - -
75C ARG 3.1 12.5 + - - +
76C VAL 3.0 8.8 + - - +
78C GLU* 1.3 73.0 - - - +
80C VAL* 1.3 65.5 + - - +
82C LYS* 3.4 11.6 + - + +
83C ARG* 3.2 22.0 + - - +
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Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PHE* 4.5 4.9 - - + -
42C VAL* 3.8 24.9 - - + -
46C VAL* 4.1 13.2 - - + +
63C ILE* 4.1 20.4 - - + -
65C VAL* 4.4 13.2 - - + -
76C VAL* 2.9 23.7 + - + +
77C PHE* 3.4 10.3 - - + +
78C GLU 3.2 0.2 - - - -
79C ALA* 1.3 74.9 - - - +
81C LYS* 1.3 66.7 + - - +
83C ARG* 3.2 13.3 + - - +
84C PHE* 3.5 36.7 + - + -
92C CYS* 4.6 9.6 - - + -
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Residues in contact with LYS 81 (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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77C PHE* 3.1 36.8 + - + +
78C GLU* 2.8 42.3 + - - +
80C VAL* 1.3 80.5 - - + +
82C LYS* 1.3 61.8 + - - +
84C PHE* 3.3 32.2 + - + +
89C ARG* 5.2 1.2 + - - -
92C CYS* 4.4 17.0 - - - -
167C ARG* 5.7 3.8 - - - +
274C VAL* 4.3 19.5 - - + +
276C ASP* 5.1 4.2 + - - +
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Residues in contact with LYS 82 (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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78C GLU 2.9 17.6 + - - +
79C ALA* 3.6 11.0 - - + +
80C VAL 3.2 0.2 - - - -
81C LYS* 1.3 79.5 - - - +
83C ARG* 1.3 59.7 + - - +
84C PHE 3.4 6.8 - - - +
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Residues in contact with ARG 83 (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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43C GLY* 3.3 30.6 + - - +
44C ALA* 4.3 2.6 - - - +
46C VAL* 3.8 22.9 - - + -
47C ASP* 2.7 43.3 + - - +
50C ILE* 4.3 4.9 - - + +
79C ALA 3.2 12.4 + - - +
80C VAL 3.2 9.8 + - - +
82C LYS* 1.3 74.4 - - - +
84C PHE* 1.3 67.7 + - - +
85C PHE* 3.8 13.7 + - - +
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Residues in contact with PHE 84 (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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46C VAL* 3.8 24.7 - - + -
50C ILE* 4.1 3.6 - - + -
63C ILE* 4.4 1.8 - - + -
80C VAL* 3.7 25.8 - - + -
81C LYS* 3.5 27.9 - - + +
82C LYS 3.3 9.5 - - - +
83C ARG* 1.3 84.5 - - - +
85C PHE* 1.3 65.2 + - - +
88C PHE 3.6 8.5 - - - +
89C ARG* 3.6 43.5 + - + +
90C VAL* 3.4 46.9 - - + -
92C CYS* 4.2 14.4 - - - -
274C VAL* 6.1 1.8 - - + -
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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