Contacts of the helix formed by residues 30 - 44 (chain C) in PDB entry 4LLL
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 30 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C ASP* 3.8 10.8 - - - -
24C LEU* 3.8 5.1 - - - +
29C ILE* 1.3 78.1 - - - +
31C ASN* 1.3 59.6 + - - +
32C GLU* 3.2 15.4 + - - -
33C GLN* 2.9 19.4 + - - +
34C GLY 2.9 24.3 + - - -
12F T 3.2 34.3 - - - +
13F A 2.7 19.4 + - - -
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Residues in contact with ASN 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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16C MET 5.5 0.3 - - - -
17C LYS* 4.3 18.1 - - + +
20C ALA* 3.6 26.6 - - + +
21C ASP* 3.1 18.4 + - - +
24C LEU* 3.7 13.0 - - - +
30C THR* 1.3 73.1 - - - +
32C GLU* 1.3 90.5 + - - +
34C GLY* 3.1 3.1 + - - -
35C HIS* 3.1 50.1 + - - -
108C PHE* 3.9 3.6 - - - -
111C MET* 5.7 0.7 - - - +
10D ARG* 4.8 7.1 - - - +
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Residues in contact with GLU 32 (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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17C LYS* 4.6 8.5 - - - +
21C ASP* 4.5 3.3 - - - +
30C THR* 3.2 14.3 + - - +
31C ASN* 1.3 102.0 + - - +
33C GLN* 1.3 54.8 + - - +
35C HIS* 3.5 7.3 + - - +
36C THR* 2.7 32.9 + - - -
67C LEU* 3.9 11.7 - - + +
10D ARG* 5.6 6.2 - - - -
13F A 3.4 43.3 - - - +
14F T 3.7 9.0 - - - +
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Residues in contact with GLN 33 (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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29C ILE* 3.4 13.7 - - + +
30C THR* 2.9 34.8 + - - +
32C GLU* 1.3 75.9 - - - +
34C GLY* 1.3 64.7 + - - +
36C THR* 3.3 4.5 + - - -
37C LEU* 3.0 31.7 + - - +
67C LEU* 4.2 10.4 + - + -
70C ASN* 3.5 30.9 - - - +
71C LEU* 3.8 27.0 - - + +
74C LYS* 3.8 15.8 - - - +
12F T 4.4 1.6 + - - -
13F A 3.0 27.1 + - - +
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Residues in contact with GLY 34 (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 LEU* 4.7 0.2 - - - -
29C ILE* 3.8 13.1 - - - +
30C THR 2.9 11.4 + - - -
31C ASN 3.1 5.3 + - - -
33C GLN* 1.3 76.7 - - - +
35C HIS* 1.3 55.7 + - - +
38C GLY* 2.9 23.2 + - - -
104C PHE* 3.2 28.5 - - - -
108C PHE* 3.6 15.6 - - - -
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Residues in contact with HIS 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 ASN* 3.1 31.9 + - - +
32C GLU* 3.9 6.7 - - - +
33C GLN 3.2 0.2 - - - -
34C GLY* 1.3 74.5 - - - +
36C THR* 1.3 61.8 + - - +
38C GLY* 3.6 1.6 - - - +
39C TYR* 2.8 27.0 + - - +
57C LEU* 4.9 6.9 - - + +
108C PHE* 3.4 43.1 - + + -
111C MET* 5.9 0.8 - - + +
6D SER* 3.2 15.6 + - - -
10D ARG* 3.1 53.4 + - - +
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Residues in contact with THR 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 GLU 2.7 17.8 + - - -
33C GLN 3.3 2.7 + - - -
35C HIS* 1.3 75.1 - - - +
37C LEU* 1.3 54.9 + - - +
38C GLY 3.1 0.2 - - - -
39C TYR* 3.1 2.8 + - - +
40C LEU* 2.7 41.0 + - + +
53C ILE* 4.1 14.6 - - + -
57C LEU* 3.6 31.5 - - + +
64C VAL* 5.9 0.4 - - + -
67C LEU* 3.2 31.4 - - + +
68C LEU* 4.3 13.0 - - + -
71C LEU* 4.5 2.7 - - + -
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Residues in contact with LEU 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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29C ILE* 4.6 3.8 - - + -
33C GLN 3.0 23.5 + - - +
34C GLY 3.9 2.2 - - - +
36C THR* 1.3 72.8 - - - +
38C GLY* 1.3 61.1 + - - +
40C LEU* 3.6 5.0 - - + +
41C TYR* 2.8 32.9 + - - +
71C LEU* 3.4 37.7 - - + -
76C LEU* 4.4 9.6 - - + -
77C ILE* 3.9 8.7 - - + -
93C LEU* 3.5 24.1 - - + +
97C GLY* 5.5 1.1 - - - +
100C LEU* 3.9 28.0 - - + -
101C VAL* 3.6 17.5 - - + +
104C PHE* 4.1 10.1 - - + -
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Residues in contact with GLY 38 (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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34C GLY 2.9 18.8 + - - -
35C HIS* 3.4 2.9 + - - -
36C THR 3.1 0.2 - - - -
37C LEU* 1.3 80.1 - - - +
39C TYR* 1.3 61.0 + - - +
41C TYR* 3.5 7.5 + - - +
42C ALA* 3.4 20.6 + - - +
101C VAL* 4.3 11.2 - - - +
104C PHE* 4.9 2.5 - - - -
108C PHE* 5.9 1.3 - - - -
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Residues in contact with TYR 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 HIS 2.8 18.2 + - - +
36C THR* 3.1 5.6 + - - +
38C GLY* 1.3 78.1 - - - +
40C LEU* 1.3 62.2 + - - +
42C ALA* 3.2 3.9 + - - -
43C HIS* 3.1 61.2 + + + +
48C LEU* 3.8 30.8 - - + +
52C ASP 5.1 1.1 + - - -
53C ILE* 4.9 14.1 - - + -
56C ALA* 3.3 33.5 - - + +
57C LEU* 4.0 22.0 - - + -
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Residues in contact with LEU 40 (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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36C THR* 2.7 32.6 + - + +
37C LEU* 3.6 9.0 - - + +
39C TYR* 1.3 75.6 - - + +
41C TYR* 1.3 56.5 + - - +
42C ALA 2.9 0.3 + - - -
44C GLN* 2.8 39.6 + - + +
48C LEU* 3.9 13.9 - - + -
53C ILE* 3.6 30.7 - - + -
68C LEU* 4.9 2.0 - - + -
71C LEU* 4.9 2.5 - - + -
77C ILE* 3.8 28.7 - - + -
91C ILE* 3.6 30.3 - - + +
92C GLY* 4.6 4.5 - - - -
93C LEU* 3.9 12.3 - - + -
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Residues in contact with TYR 41 (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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37C LEU 2.8 20.8 + - - +
38C GLY 3.7 6.5 - - - +
40C LEU* 1.3 72.7 - - - +
42C ALA* 1.3 62.2 + - + +
44C GLN* 4.3 10.9 + - - +
45C GLN* 5.6 0.2 - - - +
93C LEU* 3.4 18.1 - - + +
98C ILE* 3.6 31.4 - - + -
101C VAL* 3.7 30.1 - - + -
102C GLU* 3.3 32.9 + - + +
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Residues in contact with ALA 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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38C GLY 3.4 13.9 + - - +
39C TYR* 3.2 2.4 + - - +
40C LEU 3.0 1.0 - - - -
41C TYR* 1.3 85.8 - - + +
43C HIS* 1.3 83.8 + - + +
44C GLN 3.6 0.4 - - - -
45C GLN* 4.2 8.9 + - - +
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Residues in contact with HIS 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 TYR* 3.1 55.3 + + + +
40C LEU 3.7 0.7 - - - -
42C ALA* 1.3 97.6 - - + +
44C GLN* 1.3 64.2 + - - +
45C GLN* 3.2 10.0 + - - +
46C ASP* 3.2 32.6 + - - +
48C LEU* 3.5 14.4 - - + +
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Residues in contact with GLN 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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40C LEU* 2.8 20.0 + - + +
41C TYR* 4.3 11.1 + - - +
42C ALA 3.6 0.6 - - - -
43C HIS* 1.3 77.7 - - - +
45C GLN* 1.3 62.5 + - - +
46C ASP 3.1 5.4 + - - -
47C GLY* 3.4 12.3 - - - -
48C LEU* 4.1 9.2 + - - -
78C TYR* 4.7 4.5 + - - -
91C ILE 4.4 6.8 - - - +
92C GLY* 3.8 12.1 - - - -
93C LEU* 3.0 57.6 + - - +
98C ILE* 5.1 9.7 - - - +
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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