Contacts of the helix formed by residues 30 - 48 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24O LEU* 3.9 4.5 - - - +
29O ILE* 1.3 79.4 - - - +
31O ASN* 1.3 54.8 + - - +
32O GLU* 3.5 8.4 + - - +
33O GLN* 2.5 48.9 + - - +
34O GLY* 2.6 32.6 + - - -
67O LEU* 4.7 0.7 - - - +
70O ASN* 5.9 0.2 - - - +
74O LYS* 5.4 2.9 - - - +
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Residues in contact with ASN 31 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24O LEU* 4.5 22.6 - - + +
30O THR* 1.3 74.0 - - - +
32O GLU* 1.3 62.3 + - - +
34O GLY* 2.9 16.0 + - - -
35O HIS* 3.0 51.8 + - - -
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Residues in contact with GLU 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O THR* 3.3 8.3 + - - +
31O ASN* 1.3 79.7 + - - +
33O GLN* 1.3 54.5 + - - +
35O HIS* 3.6 7.5 + - - +
36O THR* 2.3 35.8 + - - -
57O LEU* 4.8 13.9 - - + +
63O THR* 5.8 6.1 - - + -
67O LEU* 4.0 24.5 - - + -
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Residues in contact with GLN 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O ILE* 3.2 14.3 - - + -
30O THR* 2.5 61.3 + - - +
32O GLU* 1.3 72.9 - - - +
34O GLY* 1.3 64.9 + - - +
36O THR* 3.6 4.4 - - - -
37O LEU* 3.4 26.4 + - - +
67O LEU* 3.6 20.7 - - + +
70O ASN* 2.9 45.7 + - - +
71O LEU* 3.5 26.0 - - + +
74O LYS* 3.7 11.0 + - - +
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Residues in contact with GLY 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24O LEU* 5.0 3.8 - - - -
29O ILE* 3.9 16.8 - - - -
30O THR 2.6 19.9 + - - -
31O ASN* 2.9 7.4 + - - -
33O GLN* 1.3 73.4 - - - +
35O HIS* 1.3 61.3 + - - -
37O LEU* 3.1 17.1 + - - +
38O GLY* 3.2 8.1 + - - -
100O LEU* 5.9 1.1 - - - +
104O PHE* 6.1 0.7 - - - -
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Residues in contact with HIS 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O ASN* 3.0 59.4 + - - +
32O GLU* 4.3 7.2 + - - +
34O GLY* 1.3 71.4 - - - -
36O THR* 1.3 52.8 + - - +
38O GLY* 2.7 8.1 + - - +
39O TYR* 2.7 35.8 + - - +
57O LEU* 4.7 15.7 - - + -
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Residues in contact with THR 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32O GLU 2.3 28.9 + - - -
33O GLN* 3.6 7.1 - - - -
34O GLY 3.2 0.2 - - - -
35O HIS* 1.3 77.0 - - - +
37O LEU* 1.3 56.9 + - - +
39O TYR* 3.8 6.4 + - - +
40O LEU* 3.2 32.4 + - + +
53O ILE* 4.1 16.9 - - + +
57O LEU* 3.3 29.0 - - + +
64O VAL* 6.1 0.2 - - + -
67O LEU* 3.8 14.1 - - + +
68O LEU* 5.3 7.0 - - + -
71O LEU* 4.1 19.7 - - + -
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Residues in contact with LEU 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O ILE* 4.4 5.8 - - + -
33O GLN 3.5 15.0 - - - +
34O GLY 3.1 8.4 + - - +
36O THR* 1.3 75.2 - - - +
38O GLY* 1.3 61.8 + - - +
40O LEU* 3.3 1.9 + - - -
41O TYR* 2.9 25.3 + - - +
71O LEU* 4.1 11.0 - - + -
76O LEU* 4.0 25.1 - - + +
77O ILE* 3.7 25.6 - - + -
93O LEU* 3.5 34.3 - - + +
97O GLY* 4.8 0.9 - - - -
100O LEU* 4.0 38.6 - - + -
101O VAL* 3.9 8.8 - - + +
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Residues in contact with GLY 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34O GLY 3.2 7.1 + - - -
35O HIS* 2.7 16.2 + - - -
37O LEU* 1.3 70.2 - - - +
39O TYR* 1.3 63.4 + - - -
41O TYR* 2.9 22.6 + - - +
42O ALA* 3.3 9.0 + - - +
101O VAL* 4.3 11.1 - - - +
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Residues in contact with TYR 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O HIS 2.7 17.0 + - - +
36O THR* 3.8 10.8 - - + +
38O GLY* 1.3 73.4 - - - +
40O LEU* 1.3 57.0 + - + +
42O ALA* 3.1 3.3 + - - -
43O HIS* 2.9 45.6 + - + +
48O LEU* 5.4 2.5 - - + -
53O ILE* 5.6 9.0 - - + -
56O ALA* 6.0 6.1 - - + -
57O LEU* 5.4 10.1 - - + -
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Residues in contact with LEU 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O THR* 3.2 23.8 + - + +
37O LEU* 3.6 12.3 - - + +
38O GLY 3.1 0.6 - - - -
39O TYR* 1.3 74.5 - - - +
41O TYR* 1.3 61.2 + - - +
42O ALA 3.1 2.0 - - - -
44O GLN* 2.9 38.9 - - + +
48O LEU* 3.5 27.4 - - + -
53O ILE* 4.4 9.0 - - + -
68O LEU* 5.6 1.1 - - + -
71O LEU* 5.3 0.2 - - + -
77O ILE* 3.7 21.8 - - + -
91O ILE* 3.6 44.9 - - + +
93O LEU* 4.1 17.5 - - + +
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Residues in contact with TYR 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O LEU 2.9 12.3 + - - +
38O GLY* 2.9 12.6 + - - +
40O LEU* 1.3 78.2 - - - +
42O ALA* 1.3 59.0 + - + +
44O GLN* 5.0 1.6 - - - -
45O GLN* 5.1 1.2 - - - +
93O LEU* 3.8 17.0 - - + -
98O ILE* 3.7 23.7 - - + +
101O VAL* 3.5 35.7 - - + -
102O GLU* 3.1 24.9 + - + -
105O THR* 5.9 2.7 - - - -
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Residues in contact with ALA 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O GLY 3.3 7.0 + - - +
39O TYR* 3.1 5.5 + - - +
41O TYR* 1.3 83.1 - - + +
43O HIS* 1.3 81.2 + - + +
44O GLN 3.5 1.1 - - - -
45O GLN* 2.4 32.1 + - - +
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Residues in contact with HIS 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O TYR* 2.9 30.5 + - + +
42O ALA* 1.3 95.0 + - + +
44O GLN* 1.3 65.7 + - - +
45O GLN* 3.2 11.0 + - - +
46O ASP* 3.2 22.7 + - - +
48O LEU* 3.2 28.7 - - + +
56O ALA* 6.2 3.8 - - + -
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Residues in contact with GLN 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O LEU* 2.9 25.0 + - + +
41O TYR* 5.0 0.9 - - - -
43O HIS* 1.3 76.4 - - - +
45O GLN* 1.3 62.3 + - - +
47O GLY* 3.0 22.5 + - - -
48O LEU* 3.9 14.0 + - - +
78O TYR* 4.2 8.3 + - - -
80O TYR* 4.4 10.6 + - + +
91O ILE 3.8 16.4 - - - +
92O GLY* 3.4 8.5 - - - -
93O LEU* 2.9 49.1 + - - +
98O ILE* 5.8 0.9 - - - +
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Residues in contact with GLN 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41O TYR 5.1 1.2 - - - +
42O ALA 2.4 32.5 + - - +
43O HIS* 3.5 10.2 + - - +
44O GLN* 1.3 79.4 + - - +
46O ASP* 1.3 76.4 + - - +
47O GLY* 3.1 1.4 + - - -
80O TYR* 5.6 1.5 + - - -
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Residues in contact with ASP 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O HIS* 3.2 23.3 + - - +
44O GLN 3.0 0.8 + - - -
45O GLN* 1.3 95.3 + - - +
47O GLY* 1.3 61.4 + - - +
48O LEU* 3.9 12.4 - - + +
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Residues in contact with GLY 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44O GLN 3.0 12.2 + - - -
45O GLN 3.1 2.1 - - - -
46O ASP* 1.3 83.1 - - - +
48O LEU* 1.3 63.0 + - - +
49O THR* 3.9 2.1 + - - -
52O ASP* 3.6 9.4 - - - +
80O TYR* 4.6 3.4 - - - -
88O ARG* 5.6 1.9 + - - -
90O ASN* 3.6 30.5 - - - +
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Residues in contact with LEU 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O TYR* 5.0 1.6 - - + +
40O LEU* 3.5 34.1 - - + -
43O HIS* 3.2 43.5 - - + +
44O GLN* 3.9 5.2 + - - +
46O ASP* 3.9 14.6 - - + +
47O GLY* 1.3 74.8 - - - +
49O THR* 1.3 60.8 + - - +
52O ASP* 3.6 16.4 - - + +
53O ILE* 3.9 23.8 - - + -
90O ASN* 3.5 7.0 + - - +
91O ILE* 3.0 34.5 + - + +
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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