Contacts of the helix formed by residues 16 - 26 (chain A) 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 SER 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLN* 3.2 16.7 + - - +
10A ASP* 3.0 16.0 + - - -
14A THR 3.7 1.0 + - - -
15A PRO* 1.3 71.5 - - - +
17A VAL* 1.3 61.3 + - - +
18A PHE* 3.2 12.3 + - - +
19A ASP* 3.1 41.9 + - - -
20A VAL* 3.4 6.1 + - - +
67A GLY* 5.7 1.6 - - - -
34C TYR* 4.0 0.2 - - - -
45C TYR* 6.2 1.3 - - - -
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PRO 3.4 1.2 + - - -
16A SER* 1.3 68.6 + - - +
18A PHE* 1.3 66.8 + - - +
20A VAL* 3.1 15.8 + - - +
21A VAL* 3.2 12.0 + - - +
7C PHE* 3.6 23.6 - - + -
9C PHE* 4.9 1.6 - - + -
34C TYR* 3.4 33.4 - - + +
44C ALA 5.0 1.3 - - - +
45C TYR* 3.5 49.8 - - + +
48C GLY* 3.7 16.8 - - - +
49C THR* 3.9 8.7 - - + -
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Residues in contact with PHE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A SER* 3.2 8.2 + - - +
17A VAL* 1.3 80.3 - - - +
19A ASP* 1.3 73.9 + - - +
20A VAL 3.3 0.3 + - - -
21A VAL 3.4 0.7 + - - -
22A VAL* 3.3 36.9 + - + +
98A GLY* 6.3 0.7 - - - -
256A LYS* 4.1 25.8 - - - -
257A LEU* 3.9 22.0 - - + -
260A HIS* 4.5 4.7 - + - -
456A NAP 4.5 11.0 - - - -
47C ASP 5.0 1.1 - - - -
48C GLY* 3.8 19.8 - - - -
51C TYR* 4.1 20.6 - + + -
52C THR* 3.5 23.3 - - + +
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Residues in contact with ASP 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 5.6 1.7 - - - +
8A GLN* 3.7 21.5 + - - +
10A ASP* 4.8 0.5 - - - +
16A SER* 3.1 21.8 + - - +
18A PHE* 1.3 84.7 - - - +
20A VAL* 1.3 57.6 + - - +
22A VAL* 4.3 3.3 - - - +
23A GLY* 3.0 25.1 + - - -
31A ILE* 4.7 1.2 - - - +
64A PHE* 3.5 33.4 - - + -
66A GLY* 4.6 8.3 - - - -
67A GLY 4.8 2.8 + - - -
95A ASP 4.9 5.6 - - - +
97A ASN* 5.2 4.0 + - - -
98A GLY* 5.4 3.5 + - - -
260A HIS* 3.7 20.5 + - - -
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLN* 3.3 25.6 - - - +
15A PRO* 5.2 1.3 - - + -
16A SER 3.5 11.2 - - - +
17A VAL 3.1 8.8 + - - +
19A ASP* 1.3 74.7 - - - +
21A VAL* 1.3 67.1 + - - +
23A GLY 3.3 1.0 + - - -
24A TYR* 3.1 48.1 + - + -
31A ILE* 3.4 13.9 - - + +
7C PHE* 3.9 13.9 - - + -
32C THR* 3.7 31.2 - - + +
34C TYR* 4.5 5.6 - - - +
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Residues in contact with VAL 21 (chain A).
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* 3.2 8.3 + - + +
18A PHE 3.4 3.3 + - - +
20A VAL* 1.3 76.1 - - - +
22A VAL* 1.3 62.0 + - - +
24A TYR* 3.2 5.5 + - - +
25A ASP* 3.0 36.1 + - - +
5C LEU* 4.0 13.4 - - + +
7C PHE* 3.5 32.1 - - + -
48C GLY 3.9 7.6 - - - +
52C THR* 3.3 36.8 - - - +
53C ARG* 3.9 17.3 - - - +
61C THR* 4.7 5.8 - - + +
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Residues in contact with VAL 22 (chain A).
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* 3.3 41.6 + - + +
19A ASP 4.3 0.4 - - - +
21A VAL* 1.3 75.7 - - + +
23A GLY* 1.3 62.7 + - - +
25A ASP* 3.3 6.4 + - - +
26A GLY* 3.0 20.8 + - - -
257A LEU* 4.4 16.4 - - + +
260A HIS* 3.4 44.9 - - + +
261A ARG* 3.9 17.4 - - + +
264A ILE* 4.5 1.2 - - - +
52C THR* 4.0 12.6 - - + +
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Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.6 3.1 - - - -
19A ASP 3.0 18.4 + - - -
20A VAL 3.7 1.1 - - - -
21A VAL 3.2 0.4 - - - -
22A VAL* 1.3 76.7 - - - +
24A TYR* 1.3 60.8 + - - +
26A GLY 3.2 8.1 + - - -
27A GLY 3.4 0.5 + - - -
28A ALA* 3.3 18.3 + - - +
31A ILE* 3.8 14.1 - - - -
260A HIS* 5.2 0.8 + - - -
264A ILE* 3.6 26.4 - - - +
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Residues in contact with TYR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 3.1 44.3 + - + -
21A VAL 3.2 6.0 + - - +
23A GLY* 1.3 75.5 - - - +
25A ASP* 1.3 60.7 + - - +
26A GLY 3.1 0.2 - - - -
27A GLY* 3.0 18.4 + - - -
28A ALA 3.5 18.8 + - - +
29A ASP 3.7 8.7 - - - -
30A HIS* 3.9 2.1 - - - -
31A ILE* 3.0 43.5 + - + +
3C LYS* 4.1 12.2 - - + +
5C LEU* 3.7 27.4 - - + -
30C HIS* 3.4 53.3 - + + +
32C THR* 4.7 5.6 + - - -
53C ARG* 5.3 0.9 - - - +
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Residues in contact with ASP 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 3.0 20.0 + - - +
22A VAL* 3.3 4.4 + - - +
24A TYR* 1.3 77.1 - - - +
26A GLY* 1.3 59.4 + - - +
27A GLY 3.3 0.6 + - - -
261A ARG* 3.8 36.2 + - - +
2C SER* 4.2 11.7 + - - -
3C LYS* 4.8 1.0 + - - +
52C THR 4.5 0.7 - - - +
53C ARG* 3.0 54.7 + - - +
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Residues in contact with GLY 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL 3.0 14.3 + - - -
23A GLY 3.7 6.3 - - - -
24A TYR 3.1 0.8 - - - -
25A ASP* 1.3 79.5 - - - +
27A GLY* 1.3 56.7 + - - +
28A ALA 3.8 0.2 - - - -
261A ARG* 3.5 25.6 - - - -
264A ILE* 3.9 6.5 - - - +
265A ALA* 3.4 31.7 + - - +
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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