Contacts of the helix formed by residues 41 - 51 (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 ASN 41 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C ASN 3.2 22.6 + - - -
37C VAL* 3.5 9.2 - - - +
38C THR* 2.8 34.2 + - - +
40C ASP* 1.3 77.2 - - + +
42C VAL* 1.3 64.8 + - - +
43C GLY 3.3 1.7 + - - -
44C ALA* 3.7 13.4 + - - +
45C TYR* 3.7 29.5 + - + -
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Residues in contact with VAL 42 (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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9C PHE* 3.6 35.4 - - + -
37C VAL* 3.8 13.2 - - + -
38C THR 3.2 15.7 + - - +
39C PRO* 3.8 3.8 - - + +
41C ASN* 1.3 79.9 + - - +
43C GLY* 1.3 69.4 + - - +
45C TYR* 3.0 10.2 + - + -
46C VAL* 2.9 22.7 + - + +
76C VAL* 4.2 6.5 - - + +
79C ALA* 3.7 36.6 - - + +
80C VAL* 3.8 13.2 - - + -
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Residues in contact with GLY 43 (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 4.6 1.4 + - - -
40C ASP 4.3 6.0 + - - -
41C ASN 3.3 1.4 - - - -
42C VAL* 1.3 83.5 - - - +
44C ALA* 1.3 61.1 + - - +
46C VAL* 3.2 3.3 + - - +
47C ASP* 3.0 28.1 + - - +
79C ALA 5.7 0.7 - - - -
83C ARG* 3.3 37.5 + - - -
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Residues in contact with ALA 44 (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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17A VAL* 5.0 1.4 + - - +
40C ASP 5.4 0.6 + - - -
41C ASN* 3.7 10.0 + - - +
42C VAL 3.3 0.4 - - - -
43C GLY* 1.3 75.3 - - - +
45C TYR* 1.3 69.6 + - + +
47C ASP* 3.4 20.3 + - - +
48C GLY* 3.4 8.0 + - - -
83C ARG* 4.3 3.6 - - - +
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Residues in contact with TYR 45 (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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14A THR* 2.8 34.0 + - - +
15A PRO 4.8 2.5 - - - -
16A SER* 6.2 0.4 - - - -
17A VAL* 3.5 36.0 - - + +
9C PHE* 3.6 35.2 - + + -
34C TYR* 3.5 27.6 - + - +
35C GLY 5.0 2.8 + - - -
37C VAL* 4.1 20.0 - - + -
41C ASN* 3.7 35.7 + - + +
42C VAL* 3.0 15.7 + - + +
44C ALA* 1.3 82.4 - - + +
46C VAL* 1.3 63.5 + - - +
48C GLY 3.0 10.7 + - - -
49C THR* 3.6 3.3 + - - +
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Residues in contact with VAL 46 (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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9C PHE* 4.4 2.0 - - + -
42C VAL* 2.9 21.9 + - + +
43C GLY 3.2 7.2 + - - +
45C TYR* 1.3 72.3 - - - +
47C ASP* 1.3 67.7 + - - +
49C THR* 2.8 29.5 + - - +
50C ILE* 3.2 10.8 + - + +
63C ILE* 4.2 7.9 - - + -
80C VAL* 4.1 37.9 - - + +
83C ARG* 3.8 24.0 - - + -
84C PHE* 3.8 29.8 - - + -
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Residues in contact with ASP 47 (chain C).
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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18A PHE* 5.0 1.9 - - - -
43C GLY 3.0 14.6 + - - +
44C ALA* 3.5 12.5 - - - +
45C TYR 3.2 0.2 - - - -
46C VAL* 1.3 74.4 - - - +
48C GLY* 1.3 63.4 + - - +
49C THR 3.2 0.9 + - - -
50C ILE* 3.2 9.0 + - - +
51C TYR* 3.2 54.1 + - + +
83C ARG* 2.7 46.4 + - - +
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Residues in contact with GLY 48 (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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17A VAL* 3.7 17.0 - - - +
18A PHE* 3.8 24.4 - - - -
21A VAL* 3.9 7.1 - - - +
44C ALA 3.4 4.4 + - - -
45C TYR 3.0 10.5 + - - -
47C ASP* 1.3 81.2 - - - +
49C THR* 1.3 56.0 + - - +
52C THR* 2.8 28.5 + - - +
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Residues in contact with THR 49 (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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17A VAL* 3.9 11.9 - - + -
21A VAL* 5.0 0.9 - - - -
7C PHE* 3.7 33.2 - - + -
9C PHE* 5.2 1.3 - - + -
45C TYR 3.9 6.5 - - - +
46C VAL* 2.8 24.9 + - - -
48C GLY* 1.3 74.1 - - - +
50C ILE* 1.3 64.3 + - - +
51C TYR 3.7 0.2 - - - -
52C THR* 4.1 7.8 + - - -
53C ARG* 5.2 4.9 + - - +
58C LYS* 6.2 0.2 - - - -
61C THR* 3.6 21.4 + - + +
63C ILE* 3.7 27.8 - - + +
90C VAL* 3.7 19.7 - - - +
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Residues in contact with ILE 50 (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* 3.5 20.4 - - + +
47C ASP* 3.2 14.3 + - - +
49C THR* 1.3 90.7 - - - +
51C TYR* 1.3 83.2 + - + +
52C THR 3.6 1.3 - - - -
53C ARG 4.4 9.5 - - - +
58C LYS* 5.6 3.9 - - - +
83C ARG 4.3 16.4 - - - +
84C PHE* 4.1 10.3 - - + -
85C PHE* 4.7 0.7 - - + -
88C PHE* 3.5 43.1 - - + +
89C ARG* 3.7 33.4 - - - +
90C VAL* 4.4 1.8 - - + +
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Residues in contact with TYR 51 (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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18A PHE* 4.1 19.3 - + + -
257A LEU* 4.7 6.2 - - - +
47C ASP* 3.2 49.7 + - + +
50C ILE* 1.3 93.2 - - + +
52C THR* 1.3 62.2 + - - +
53C ARG 3.7 2.7 - - - -
85C PHE* 3.1 27.0 - + - -
88C PHE* 3.7 32.1 - + - -
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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