Contacts of the helix formed by residues 37 - 57 (chain F) in PDB entry 1B06
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 HIS 37 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173E GLU* 3.8 10.8 - - - -
177E TYR* 2.7 30.9 + + - -
182E ASN* 3.5 24.2 - - + +
32F VAL 3.0 17.8 + - - -
33F HIS* 3.4 22.9 - - + +
36F GLY* 1.3 68.5 - - - +
38F HIS* 1.3 66.2 + - - +
40F GLY* 3.0 11.3 + - - -
41F TYR* 3.1 36.6 + - + -
174F HIS* 3.5 35.4 + + + +
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Residues in contact with HIS 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F PHE* 3.7 11.6 - + + -
12F PRO* 3.6 28.7 - - + +
33F HIS 3.1 11.1 + - - +
34F TYR* 3.4 15.9 + - - +
37F HIS* 1.3 78.1 - - - +
39F LYS* 1.3 64.8 + - - +
41F TYR* 3.0 19.8 + - - +
42F VAL* 3.2 9.3 + - + +
81F HIS* 3.0 43.5 + - - -
84F HIS* 3.6 12.2 - - + +
85F ALA* 3.8 18.6 - - - -
88F TRP* 3.0 26.9 + + - +
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Residues in contact with LYS 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 5.5 6.0 - - - -
35A ASN* 3.8 24.9 - - - +
39A LYS* 4.0 23.6 - - - +
11F PHE* 3.3 45.7 - - + -
34F TYR 3.3 4.0 + - - -
35F ASN* 3.4 39.3 + - - +
36F GLY 4.1 0.2 - - - +
37F HIS 3.3 0.2 - - - -
38F HIS* 1.3 78.8 - - - +
40F GLY* 1.3 61.7 + - - +
42F VAL* 3.3 3.8 + - - +
43F ASN* 3.0 36.8 + - - +
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Residues in contact with GLY 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F GLY 3.1 11.9 + - - -
37F HIS 3.0 9.5 + - - -
39F LYS* 1.3 79.9 - - - +
41F TYR* 1.3 58.2 + - - +
43F ASN* 3.4 7.0 + - - +
44F GLY* 2.8 27.5 + - - -
77F ASN* 4.1 1.8 - - - +
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Residues in contact with TYR 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F HIS* 3.1 31.4 + - + -
38F HIS* 3.0 11.4 + - - +
40F GLY* 1.3 74.6 - - - +
42F VAL* 1.3 61.1 + - - +
45F ALA* 3.0 31.2 + - - +
76F PHE* 4.0 21.0 - + - -
77F ASN* 3.5 37.0 - - - +
80F GLY* 3.7 21.5 - - - -
81F HIS* 3.8 8.5 - - - +
84F HIS* 3.3 26.2 - + - -
155F HIS* 3.0 27.5 + + - -
172F PHE* 4.5 3.8 - - - -
174F HIS* 3.9 16.5 - - - -
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Residues in contact with VAL 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F TYR* 3.7 32.1 - - + +
11F PHE* 3.9 37.0 - - + +
38F HIS* 3.2 14.2 + - + +
39F LYS* 3.3 6.5 + - + +
41F TYR* 1.3 79.1 - - - +
43F ASN* 1.3 68.3 + - - +
45F ALA* 3.4 4.7 + - - +
46F ASN* 3.0 29.9 + - - +
81F HIS* 3.7 31.0 - - + +
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Residues in contact with ASN 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LYS* 4.6 13.6 + - - -
39F LYS* 3.0 34.6 + - - +
40F GLY* 3.8 6.8 - - - +
42F VAL* 1.3 84.4 - - - +
44F GLY* 1.3 56.9 + - - +
46F ASN* 3.4 7.8 + - - +
47F SER* 2.9 31.4 + - - -
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Residues in contact with GLY 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F GLY 2.8 18.0 + - - -
43F ASN* 1.3 78.5 - - - +
45F ALA* 1.3 61.0 + - - +
47F SER* 3.3 9.6 + - - -
48F LEU* 3.2 27.2 + - - +
77F ASN* 3.8 18.6 - - - -
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Residues in contact with ALA 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F TYR* 4.2 14.8 - - + -
41F TYR 3.0 18.4 + - - +
42F VAL* 3.7 5.4 - - - +
44F GLY* 1.3 76.3 - - - +
46F ASN* 1.3 59.2 + - - +
48F LEU* 3.2 4.6 + - - +
49F LEU* 2.9 32.4 + - - +
74F LEU* 3.8 7.3 - - + +
77F ASN* 3.6 17.1 - - + +
78F ILE* 4.1 23.3 - - + +
81F HIS* 5.9 1.3 - - + -
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Residues in contact with ASN 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ARG* 3.4 24.0 + - + +
9F TYR* 2.8 55.8 + - - +
42F VAL* 3.0 27.2 + - - +
43F ASN* 3.9 8.9 - - - +
45F ALA* 1.3 74.4 - - - +
47F SER* 1.3 63.0 + - - +
49F LEU* 3.2 4.2 + - - +
50F ASP* 3.1 28.9 + - - +
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Residues in contact with SER 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F ASN 2.9 17.6 + - - -
44F GLY* 3.3 10.6 + - - -
46F ASN* 1.3 78.2 - - - +
48F LEU* 1.3 67.6 + - - +
50F ASP* 3.5 23.1 - - - +
51F ARG* 3.6 12.3 + - - +
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Residues in contact with LEU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ASP* 5.0 3.1 - - - +
44F GLY 3.2 15.2 + - - +
45F ALA 3.2 8.1 + - - +
47F SER* 1.3 81.8 + - - +
49F LEU* 1.3 60.4 + - - +
50F ASP 3.2 0.4 - - - -
51F ARG* 3.2 15.8 + - - +
52F LEU* 3.0 27.2 + - - +
69F GLY 4.7 3.4 - - - +
70F ILE* 4.1 30.0 - - + +
73F GLY* 3.4 41.3 - - - +
74F LEU* 3.8 16.6 - - + +
77F ASN* 3.7 8.5 - - - +
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Residues in contact with LEU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ASN* 4.2 6.7 - - - +
148D GLN* 4.0 20.4 - - - +
6F LEU* 4.1 21.8 - - + +
7F LYS 3.5 24.5 - - - +
8F ARG* 3.8 22.1 + - - +
9F TYR* 3.9 25.1 - - + -
45F ALA 2.9 15.1 + - - +
46F ASN* 3.2 16.5 + - - +
48F LEU* 1.3 73.4 - - - +
50F ASP* 1.3 61.1 + - - +
52F LEU* 3.4 6.4 + - + +
53F GLU* 2.8 31.4 + - - +
74F LEU* 4.1 15.9 - - + -
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Residues in contact with ASP 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B LYS* 3.9 29.0 + - - -
186B ASP* 4.9 3.3 - - - +
8F ARG* 2.5 38.6 + - - +
46F ASN* 3.1 18.4 + - - +
47F SER* 3.5 16.3 - - - +
48F LEU 3.2 0.2 - - - -
49F LEU* 1.3 78.2 - - - +
51F ARG* 1.3 57.4 + - + +
53F GLU* 3.3 3.7 + - - +
54F LYS* 3.0 45.9 + - - +
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Residues in contact with ARG 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C GLY* 3.0 29.1 + - - -
65C TYR 3.9 6.8 + - - -
66C ASP* 2.9 40.7 + - - -
47F SER 3.6 10.5 + - - +
48F LEU* 3.2 17.3 + - - +
50F ASP* 1.3 78.3 - - + +
52F LEU* 1.3 64.9 + - - +
54F LYS* 3.3 16.9 + - + +
55F LEU* 3.0 23.8 + - - +
60F LEU* 3.6 19.3 - - + +
64F GLN 3.0 26.5 + - - -
65F TYR* 3.4 6.7 - - - +
70F ILE* 4.1 13.3 - - + +
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Residues in contact with LEU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D TYR* 6.0 1.3 - - - +
122D VAL* 5.1 7.4 - - + -
148D GLN* 4.0 14.4 - - - +
149D ILE* 6.2 2.5 - - + -
6F LEU* 4.4 12.8 - - + -
48F LEU 3.0 16.5 + - - +
49F LEU* 3.8 9.0 - - + +
51F ARG* 1.3 76.1 - - - +
53F GLU* 1.3 56.7 + - - +
55F LEU* 3.2 23.0 + - + +
56F ILE* 2.9 53.0 + - + +
67F LEU* 4.8 9.2 - - + -
70F ILE* 4.3 14.3 - - + +
71F LEU* 5.2 7.0 - - + -
74F LEU* 3.9 24.7 - - + -
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Residues in contact with GLU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F ILE* 4.6 5.2 - - + +
5F GLN* 3.5 12.0 - - - +
6F LEU* 2.8 42.7 + - + +
8F ARG* 3.3 25.9 + - - -
49F LEU 2.8 18.2 + - - +
50F ASP 3.4 6.1 - - - +
51F ARG 3.2 0.2 - - - -
52F LEU* 1.3 77.0 - - - +
54F LYS* 1.3 62.3 + - + +
56F ILE* 3.3 7.5 + - - +
57F LYS* 3.0 53.2 + - + +
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Residues in contact with LYS 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ASP* 3.6 36.5 + - - +
189B ASN* 5.5 9.5 - - - +
50F ASP* 3.0 29.9 + - - +
51F ARG* 3.6 17.1 - - + +
52F LEU 3.3 0.2 - - - -
53F GLU* 1.3 74.8 - - + +
55F LEU* 1.3 60.7 + - - +
57F LYS* 3.3 6.4 + - - +
58F GLY 2.8 25.5 + - - -
59F ASP* 2.9 34.4 + - + +
60F LEU* 3.3 21.0 + - + -
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Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ARG* 3.1 19.2 + - - +
122D VAL* 4.6 13.5 - - + -
125D GLU* 4.7 8.1 - - - +
51F ARG 3.0 12.4 + - - +
52F LEU* 3.2 18.4 - - + +
54F LYS* 1.3 77.6 - - - +
56F ILE* 1.3 72.6 + - + +
58F GLY* 3.2 10.6 + - - -
60F LEU* 3.8 17.9 - - + +
65F TYR* 3.5 52.9 - - + +
67F LEU* 4.0 19.3 - - + -
70F ILE* 4.2 11.2 - - + -
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Residues in contact with ILE 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D GLN 3.9 6.5 - - - +
113D TYR* 3.6 49.3 - - + +
118D ARG* 2.9 40.3 + - - +
122D VAL* 4.3 13.9 - - + -
4F ILE* 3.8 23.4 - - + +
6F LEU* 4.4 13.2 - - + -
52F LEU* 2.9 39.4 + - + +
53F GLU* 3.6 5.8 - - - +
55F LEU* 1.3 81.3 - - + +
57F LYS* 1.3 60.0 + - - +
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Residues in contact with LYS 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PRO* 6.1 9.0 - - + +
118D ARG* 5.0 0.2 - - - -
3F VAL 4.5 3.9 + - - +
4F ILE* 3.5 54.6 + - + +
5F GLN* 5.7 0.4 - - - +
53F GLU* 3.0 38.3 + - + +
54F LYS* 3.3 6.5 + - - +
56F ILE* 1.3 77.3 - - - +
58F GLY* 1.3 59.6 + - - +
59F ASP* 3.8 27.6 - - - +
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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