Contacts of the helix formed by residues 26 - 39 (chain C) in PDB entry 1L9W
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 26 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLY 3.2 0.8 - - - -
25C ARG* 1.3 86.2 - - - +
27C ILE* 1.3 62.7 + - + +
28C ASN* 3.2 13.8 + - - +
29C SER* 2.4 43.5 + - - -
30C VAL* 2.9 28.6 + - - +
52C PHE* 3.6 15.9 - - - -
53C MET* 6.0 4.5 - - + -
54C ASP 6.0 0.4 - - - +
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Residues in contact with ILE 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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26C ASP* 1.3 77.6 - - + +
28C ASN* 1.3 66.5 + - - +
30C VAL* 4.3 6.1 - - - -
31C LYS* 3.2 24.7 + - + +
52C PHE* 4.1 20.0 - - + -
54C ASP* 6.0 2.2 - - + +
60C SER* 4.8 17.7 - - - +
63C THR* 5.0 14.6 - - + -
64C ALA* 4.9 5.2 - - + +
67C VAL* 4.2 24.9 - - + +
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Residues in contact with ASN 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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26C ASP* 3.2 12.9 + - - +
27C ILE* 1.3 81.4 - - - +
29C SER* 1.3 62.3 + - - +
31C LYS* 3.7 6.9 - - - +
32C ALA* 3.0 21.8 + - - +
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Residues in contact with SER 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLY* 3.8 19.1 - - - -
25C ARG* 3.7 9.1 + - - +
26C ASP* 2.4 24.7 + - - -
28C ASN* 1.3 70.1 - - - +
30C VAL* 1.3 65.5 + - - +
32C ALA* 4.0 7.2 - - - -
33C GLU* 2.8 37.5 + - - +
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 4.2 9.3 - - + +
24C GLY* 3.9 22.9 - - - +
26C ASP 2.9 26.7 + - - +
27C ILE* 4.1 6.5 - - - +
28C ASN 3.3 0.4 - - - -
29C SER* 1.3 70.2 - - - +
31C LYS* 1.3 59.1 + - - +
33C GLU* 3.4 2.1 + - - +
34C ALA* 2.9 28.2 + - - +
47C TRP* 4.1 18.2 - - + +
52C PHE* 4.4 8.7 - - + -
64C ALA* 3.8 16.6 - - + +
67C VAL* 4.6 4.5 - - + -
68C ILE* 3.5 34.8 - - + -
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Residues in contact with LYS 31 (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 ILE* 3.2 18.6 + - + +
28C ASN* 3.7 7.0 - - - +
30C VAL* 1.3 77.6 - - - +
32C ALA* 1.3 67.7 + - - +
34C ALA* 4.1 3.0 - - - +
35C LEU* 3.4 40.6 + - + +
67C VAL* 3.5 31.6 - - + +
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Residues in contact with ALA 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ASN 3.0 15.7 + - - +
29C SER* 3.4 12.6 - - - +
31C LYS* 1.3 75.3 - - - +
33C GLU* 1.4 73.3 + - + +
35C LEU* 3.2 8.6 + - - +
36C ALA* 3.1 20.7 + - - +
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Residues in contact with GLU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 4.1 19.5 - - + -
23C MET 4.6 13.6 + - - +
29C SER* 2.8 26.4 + - - +
30C VAL* 4.0 2.9 - - - +
32C ALA* 1.4 84.3 - - + +
34C ALA* 1.3 56.6 + - - +
36C ALA* 3.3 5.9 + - - +
37C TYR* 2.8 39.4 + - + -
229C LYS* 3.0 35.8 + - - +
230C GLN* 3.9 9.2 - - - +
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Residues in contact with ALA 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 3.8 11.8 - - + +
30C VAL 2.9 17.5 + - - +
31C LYS* 3.5 4.5 + - - +
32C ALA 3.3 0.4 - - - -
33C GLU* 1.3 74.9 - - - +
35C LEU* 1.3 62.3 + - - +
37C TYR* 4.5 0.4 - - - +
38C ARG* 3.1 19.2 + - - +
67C VAL 4.6 1.1 - - - +
68C ILE* 4.3 14.1 - - + -
71C ALA* 4.0 15.4 - - + +
72C MET* 3.3 35.5 - - + +
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Residues in contact with LEU 35 (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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31C LYS* 3.4 40.7 + - + +
32C ALA* 3.2 11.1 + - - +
34C ALA* 1.3 76.3 - - - +
36C ALA* 1.3 57.5 + - - +
38C ARG* 2.9 62.7 + - - +
39C GLU* 3.8 5.7 + - - +
67C VAL* 6.4 0.2 - - + -
71C ALA* 4.6 14.6 - - + -
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Residues in contact with ALA 36 (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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32C ALA 3.1 12.7 + - - +
33C GLU* 3.7 10.1 - - - +
35C LEU* 1.3 71.8 - - - +
37C TYR* 1.4 60.7 + - + +
39C GLU* 2.5 42.0 + - - +
40C ALA* 3.7 1.7 + - - +
228C VAL* 5.6 3.4 - - + +
229C LYS* 4.6 14.8 - - - +
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Residues in contact with TYR 37 (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 VAL* 3.7 24.2 - - + -
21C SER 2.8 28.8 + - - -
22C LEU* 3.7 17.6 - - + -
23C MET* 4.3 5.7 + - - +
33C GLU* 2.8 41.6 + - + +
34C ALA* 4.0 5.2 - - - +
35C LEU 3.3 0.2 - - - -
36C ALA* 1.4 73.5 - - - +
38C ARG* 1.3 57.1 + - - +
40C ALA* 2.8 23.5 + - - +
42C PHE* 3.3 19.8 - - + -
45C LEU* 3.6 19.7 - - + -
72C MET* 4.2 12.3 - - - -
228C VAL* 3.9 24.1 + - + +
229C LYS* 3.6 42.9 + - + +
230C GLN* 4.7 2.3 + - - +
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Residues in contact with ARG 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ALA 3.1 11.5 + - - +
35C LEU* 2.9 48.5 + - - +
37C TYR* 1.3 77.6 - - - +
39C GLU* 1.3 73.4 + - - +
40C ALA 3.4 6.2 + - - +
71C ALA* 3.7 24.2 - - - +
72C MET* 4.1 13.2 - - + -
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Residues in contact with GLU 39 (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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35C LEU 4.5 8.4 - - - +
36C ALA* 2.5 27.7 + - - +
38C ARG* 1.3 90.8 + - - +
40C ALA* 1.3 59.1 + - - -
41C THR* 5.3 0.7 + - - -
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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