Contacts of the helix formed by residues 13 - 28 (chain C) in PDB entry 1LXF
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 13 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C GLN 3.9 6.5 + - - +
12C LEU* 1.3 74.8 - - - +
14C GLU* 1.3 60.4 + - + +
15C GLU* 2.7 31.2 + - + +
16C GLN* 3.3 6.9 + - - +
17C LYS* 2.9 24.2 + - - +
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Residues in contact with GLU 14 (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 THR* 1.3 77.7 - - + +
15C GLU* 1.3 55.3 + - + +
17C LYS* 3.6 13.9 - - + +
18C ASN* 2.6 53.4 + - - +
21C LYS* 5.9 4.4 - - - -
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Residues in contact with GLU 15 (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 THR* 2.7 17.3 + - + +
14C GLU* 1.3 76.0 - - + +
16C GLN* 1.3 62.7 + - - +
17C LYS 2.8 2.8 + - - -
18C ASN* 2.9 14.9 + - - +
19C GLU* 2.6 33.8 + - - +
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Residues in contact with GLN 16 (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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12C LEU* 2.8 61.1 - - + +
13C THR* 3.3 12.6 + - - +
15C GLU* 1.3 78.7 - - - +
17C LYS* 1.3 90.4 + - - +
19C GLU* 2.9 27.5 + - - +
20C PHE* 3.1 39.8 + - + +
78C LEU* 4.9 1.4 - - - +
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Residues in contact with LYS 17 (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 VAL* 3.2 40.6 + - - +
12C LEU* 4.2 15.5 + - + +
13C THR 2.9 16.1 + - - +
14C GLU* 3.6 15.9 - - + +
15C GLU 2.8 0.6 + - - -
16C GLN* 1.3 95.5 + - - +
18C ASN* 1.3 53.2 + - - +
20C PHE* 2.6 11.4 + - + +
21C LYS* 2.4 59.8 + - + +
74C PHE* 6.4 1.3 - - + -
78C LEU* 5.1 15.0 - - + +
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Residues in contact with ASN 18 (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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14C GLU* 2.6 38.2 + - - +
15C GLU* 2.9 12.5 + - - +
17C LYS* 1.3 75.8 - - - +
19C GLU* 1.3 69.2 + - - +
20C PHE 2.7 1.6 + - - -
21C LYS* 2.9 20.2 + - - +
22C ALA* 2.8 23.2 + - - +
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Residues in contact with GLU 19 (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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15C GLU* 2.6 35.2 - - - +
16C GLN* 2.9 28.0 + - - +
18C ASN* 1.3 79.2 - - - +
20C PHE* 1.3 55.9 + - + -
22C ALA* 3.5 3.8 - - - +
23C ALA* 4.4 0.5 - - - +
153I MET* 5.4 0.9 - - - +
154I MET* 4.6 27.1 - - + +
157I LEU* 2.9 32.0 - - - +
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Residues in contact with PHE 20 (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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12C LEU* 5.4 0.7 - - + -
16C GLN* 3.1 40.8 + - + +
17C LYS* 2.6 21.4 + - + +
19C GLU* 1.3 70.0 - - + +
21C LYS* 1.3 65.2 + - + +
22C ALA 2.9 1.3 - - - -
23C ALA* 2.6 19.3 + - + +
24C PHE* 3.0 13.1 + - + +
77C PHE* 4.2 13.7 - + - -
78C LEU* 4.9 13.5 - - + -
81C MET* 3.5 31.9 - - + -
85C MET* 3.8 18.6 - - + -
92C BEP 5.2 0.4 - + - -
148I ILE* 5.0 1.1 - - + -
150I ALA* 4.8 14.4 - - + -
153I MET* 3.6 33.7 - - + -
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Residues in contact with LYS 21 (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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14C GLU* 5.9 5.5 - - - +
17C LYS* 2.4 48.1 + - + +
18C ASN* 3.5 21.4 + - - +
20C PHE* 1.3 70.4 - - + +
22C ALA* 1.3 56.5 + - - +
24C PHE* 2.8 39.3 + - + +
25C ASP* 3.1 7.7 + - - +
74C PHE* 4.8 17.9 - - + -
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Residues in contact with ALA 22 (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 ASN 2.8 12.1 + - - +
19C GLU* 3.5 7.0 - - - +
20C PHE 2.8 0.4 + - - -
21C LYS* 1.3 77.3 - - - +
23C ALA* 1.3 53.1 + - - +
25C ASP* 2.7 30.0 + - - +
26C ILE* 3.0 15.6 - - - +
154I MET* 6.1 1.8 - - + -
157I LEU* 3.3 31.4 - - + +
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Residues in contact with ALA 23 (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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19C GLU 4.4 1.6 - - - +
20C PHE* 2.6 15.7 + - + +
22C ALA* 1.3 75.4 - - - +
24C PHE* 1.3 55.1 + - - +
26C ILE* 3.0 26.6 + - - +
27C PHE* 2.8 25.9 - - + -
77C PHE* 5.3 0.7 - - + -
153I MET* 3.5 35.2 - - + -
157I LEU* 3.2 22.6 - - + +
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Residues in contact with PHE 24 (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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20C PHE* 3.0 6.5 + - + -
21C LYS* 2.8 24.8 + - + +
23C ALA* 1.3 77.8 - - - +
25C ASP* 1.3 53.5 + - - +
26C ILE 3.1 1.4 + - - -
27C PHE* 4.2 3.6 - - + -
28C VAL* 2.6 46.7 + - + +
34C GLY 4.5 6.1 - - - -
36C ILE* 4.6 7.6 - - + -
73C ASP 4.2 2.5 - - - -
74C PHE* 2.9 70.2 - + + -
77C PHE* 2.8 59.7 - + + -
78C LEU* 3.6 8.7 - - + -
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Residues in contact with ASP 25 (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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21C LYS 3.1 5.5 + - - +
22C ALA* 2.7 17.2 + - - +
24C PHE* 1.3 80.1 - - - +
26C ILE* 1.3 65.2 + - + +
28C VAL* 4.8 1.8 - - - +
29C LEU* 2.8 26.7 - - - +
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Residues in contact with ILE 26 (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 ALA 3.0 19.1 - - - +
23C ALA* 3.1 21.3 - - - +
25C ASP* 1.3 85.7 - - + +
27C PHE* 1.3 59.4 + - - +
28C VAL 3.3 1.8 - - - -
29C LEU* 2.8 35.8 - - + +
40C GLU* 2.9 10.0 - - - +
43C LYS* 4.9 0.4 - - - +
44C VAL* 3.6 17.1 - - + +
47C MET* 3.2 34.3 - - + -
156I ALA* 3.8 14.4 - - + +
157I LEU* 3.6 15.5 - - + -
160I ALA* 5.4 7.0 - - + -
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Residues in contact with PHE 27 (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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23C ALA* 2.8 30.7 + - + +
24C PHE* 4.3 6.3 - + - +
26C ILE* 1.3 77.0 - - - +
28C VAL* 1.3 58.1 + - + +
36C ILE* 3.5 27.5 - - + +
40C GLU* 2.6 36.7 - - - +
41C LEU* 3.8 37.5 - - + -
44C VAL* 2.9 44.9 - - + -
77C PHE* 4.0 14.8 - + - -
92C BEP 3.6 15.7 - + - -
153I MET* 3.4 35.7 - - + -
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Residues in contact with VAL 28 (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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24C PHE* 2.6 37.5 - - + +
25C ASP* 4.5 2.2 - - - +
27C PHE* 1.3 74.3 - - - +
29C LEU* 1.3 57.6 + - - +
30C GLY 3.0 11.2 + - - +
31C ALA* 3.4 20.8 + - + +
33C ASP 4.3 5.0 - - - +
34C GLY* 3.0 50.5 - - - +
35C CYS 3.4 18.2 - - - +
36C ILE* 3.6 11.7 - - + -
40C GLU* 4.7 0.2 - - - -
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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