Contacts of the helix formed by residues 30 - 44 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21I ASP* 3.7 9.6 - - - -
24I LEU* 4.0 2.6 - - - +
29I ILE* 1.3 81.9 - - - +
31I ASN* 1.3 58.0 + - - +
32I GLU* 3.6 10.8 + - - +
33I GLN* 2.8 47.5 + - - +
34I GLY* 3.0 22.5 + - - -
74I LYS* 5.2 2.9 - - - +
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Residues in contact with ASN 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I MET 5.1 0.4 - - - -
17I LYS* 3.5 33.5 - - + +
20I ALA* 3.4 23.7 - - + +
21I ASP* 2.8 21.1 + - - +
24I LEU* 4.3 8.3 - - - +
30I THR* 1.3 71.8 - - - +
32I GLU* 1.3 73.8 + - - +
34I GLY* 2.9 16.5 + - - -
35I HIS* 3.3 34.0 + - - -
108I PHE* 3.7 4.7 - - - -
10J ARG* 5.7 7.1 - - - +
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Residues in contact with GLU 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I LYS* 4.9 7.3 - - - +
21I ASP* 4.7 1.4 - - - +
30I THR* 3.5 8.8 + - - +
31I ASN* 1.3 91.1 + - - +
33I GLN* 1.3 65.8 + - - +
35I HIS* 3.3 8.3 + - - +
36I THR* 3.2 25.8 + - - -
59I ARG* 6.3 0.9 - - - +
67I LEU* 3.8 17.7 - - + +
10J ARG* 6.5 0.7 - - - +
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Residues in contact with GLN 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I ILE* 3.6 8.8 - - + +
30I THR* 2.8 48.0 + - - +
31I ASN 3.2 0.2 - - - -
32I GLU* 1.3 77.9 - - - +
34I GLY* 1.3 64.6 + - - +
36I THR 3.4 0.2 + - - -
37I LEU* 3.1 31.0 + - - +
67I LEU* 4.2 19.7 + - + +
70I ASN* 4.0 30.1 - - - +
71I LEU* 3.7 30.3 - - + -
74I LYS* 3.5 19.3 + - - +
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Residues in contact with GLY 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I LEU* 5.0 1.1 - - - -
29I ILE* 3.8 19.7 - - - +
30I THR 3.0 9.1 + - - -
31I ASN 2.9 11.1 + - - -
33I GLN* 1.3 75.0 - - - +
35I HIS* 1.3 55.7 + - - +
38I GLY* 3.1 20.6 + - - -
104I PHE* 3.3 17.1 - - - -
108I PHE* 3.7 19.2 - - - -
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Residues in contact with HIS 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I ASN* 3.3 34.1 + - - -
32I GLU* 3.3 8.3 + - - +
33I GLN 3.2 0.4 - - - -
34I GLY* 1.3 75.7 - - - +
36I THR* 1.3 56.4 + - - +
38I GLY* 3.5 1.9 - - - +
39I TYR* 2.6 34.9 + - - +
108I PHE* 3.3 47.6 - + + -
4J THR* 5.8 0.4 - - + -
6J SER* 3.7 12.9 + - - -
10J ARG* 3.0 54.1 + - - +
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Residues in contact with THR 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I GLU 3.2 16.3 + - - -
33I GLN 4.1 2.2 - - - -
35I HIS* 1.3 73.6 - - - +
37I LEU* 1.3 56.1 + - - +
38I GLY 3.0 1.1 - - - -
39I TYR* 3.1 6.2 + - + +
40I LEU* 2.5 42.8 + - + +
53I ILE* 4.3 23.6 - - + +
57I LEU* 4.9 10.2 - - - +
67I LEU* 4.1 29.7 - - + +
68I LEU* 4.3 15.9 - - + -
71I LEU* 4.5 2.2 - - + -
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Residues in contact with LEU 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I ILE* 4.2 21.3 - - + -
33I GLN 3.1 18.3 + - - +
34I GLY 4.1 2.2 - - - +
36I THR* 1.3 78.1 - - - +
38I GLY* 1.3 57.5 + - - +
40I LEU* 3.4 7.6 - - + +
41I TYR* 2.8 29.5 + - - +
71I LEU* 3.7 31.4 - - + -
76I LEU* 4.3 21.8 - - + -
77I ILE* 3.6 31.2 - - + -
93I LEU* 3.9 10.4 - - + +
97I GLY* 5.5 1.6 - - - +
100I LEU* 4.6 3.8 - - + -
101I VAL* 3.6 18.7 - - + +
104I PHE* 4.5 6.5 - - + -
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Residues in contact with GLY 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I GLY 3.1 17.4 + - - -
35I HIS* 3.5 4.9 - - - -
36I THR 3.0 1.0 - - - -
37I LEU* 1.3 77.5 - - - +
39I TYR* 1.3 59.7 + - - +
41I TYR* 3.2 12.6 + - - +
42I ALA* 3.2 14.2 + - - +
101I VAL* 4.4 14.6 - - - +
104I PHE* 5.0 1.8 - - - -
108I PHE* 5.9 0.9 - - - -
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Residues in contact with TYR 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I HIS 2.6 19.9 + - - +
36I THR* 3.1 6.7 + - - +
38I GLY* 1.3 70.0 - - - +
40I LEU* 1.3 65.2 + - - +
42I ALA* 3.5 3.3 + - - +
43I HIS* 3.3 61.5 + + - +
48I LEU* 3.9 30.7 - - + +
52I ASP 4.9 1.3 + - - -
53I ILE* 4.6 17.3 - - + -
56I ALA* 3.3 34.3 - - + +
57I LEU* 6.0 6.1 - - + -
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Residues in contact with LEU 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I THR* 2.5 32.7 + - + +
37I LEU* 3.4 11.4 - - + +
39I TYR* 1.3 74.4 - - - +
41I TYR* 1.3 56.4 + - - +
44I GLN* 2.8 39.1 + - + +
48I LEU* 4.2 14.6 - - + -
53I ILE* 4.1 13.7 - - + -
68I LEU* 5.0 2.7 - - + -
77I ILE* 3.4 32.5 - - + -
91I ILE* 3.4 40.8 - - + +
92I GLY* 4.6 4.3 - - - +
93I LEU* 3.7 15.0 - - + -
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Residues in contact with TYR 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I LEU 2.8 17.3 + - - +
38I GLY 3.2 6.7 + - - +
40I LEU* 1.3 78.4 - - - +
42I ALA* 1.3 68.4 + - + +
44I GLN* 3.9 11.1 + - - +
45I GLN* 4.4 2.6 - - - +
93I LEU* 3.7 20.4 - - + +
98I ILE* 4.2 24.2 - - + -
101I VAL* 3.7 30.3 - - + -
102I GLU* 5.2 7.1 - - + +
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Residues in contact with ALA 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I GLY 3.2 11.8 + - - +
39I TYR* 3.9 1.8 - - - +
40I LEU 3.3 0.2 - - - -
41I TYR* 1.3 88.0 - - + +
43I HIS* 1.3 85.1 + - + +
44I GLN 3.5 0.2 - - - -
45I GLN* 3.1 19.6 + - - +
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Residues in contact with HIS 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I TYR* 3.3 53.9 + + + +
40I LEU 3.7 1.3 - - - -
42I ALA* 1.3 97.1 - - + +
44I GLN* 1.3 64.8 + - - +
45I GLN* 3.2 11.4 - - - +
46I ASP* 3.2 31.1 + - - +
48I LEU* 3.5 23.9 - - + +
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Residues in contact with GLN 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I LEU* 2.8 19.7 + - + +
41I TYR* 4.1 8.1 + - - +
42I ALA 3.5 0.2 - - - -
43I HIS* 1.3 78.5 - - - +
45I GLN* 1.3 59.8 + - - +
46I ASP 3.0 6.2 + - - -
47I GLY* 3.1 15.8 - - - -
48I LEU* 4.1 5.9 + - - +
78I TYR* 4.4 5.0 + - - -
91I ILE 4.4 4.4 - - - +
92I GLY* 3.3 20.5 - - - -
93I LEU* 2.5 55.4 + - + +
98I ILE* 4.8 9.8 - - - +
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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