Contacts of the helix formed by residues 37 - 57 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E VAL* 3.0 26.2 + - + -
33E HIS* 3.4 23.8 - - + +
36E GLY* 1.3 67.7 - - - -
38E HIS* 1.3 67.9 + - - +
40E GLY* 3.0 11.1 + - - -
41E TYR* 3.1 37.8 + - + -
174E HIS* 3.6 34.5 + + + +
173F GLU* 4.0 6.0 + - + -
177F TYR* 2.6 32.6 + + - -
182F ASN* 3.4 25.3 - - + +
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Residues in contact with HIS 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E PHE* 3.7 9.5 - + + -
12E PRO* 3.5 27.2 - - + +
33E HIS 3.1 10.9 + - - +
34E TYR* 3.4 15.8 + - - +
37E HIS* 1.3 78.1 - - - +
39E LYS* 1.3 64.1 + - - +
41E TYR* 3.0 19.8 + - - +
42E VAL* 3.2 12.7 + - + +
81E HIS* 3.0 44.3 + - - -
84E HIS* 3.6 11.3 - - + +
85E ALA 3.7 17.7 - - - -
88E TRP* 2.9 30.7 + + - +
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Residues in contact with LYS 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E PHE* 3.4 47.0 - - + -
34E TYR 3.3 3.8 + - - -
35E ASN* 3.1 41.1 + - - +
36E GLY 4.1 0.4 - - - +
37E HIS 3.3 0.6 - - - -
38E HIS* 1.3 77.7 - - - +
40E GLY* 1.3 62.0 + - - +
42E VAL* 3.3 4.1 + - + +
43E ASN* 3.1 39.0 + - - +
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Residues in contact with GLY 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E GLY 3.1 12.8 + - - -
37E HIS* 3.0 8.9 + - - -
39E LYS* 1.3 79.3 - - - +
41E TYR* 1.3 57.4 + - - +
43E ASN* 3.5 7.6 + - - +
44E GLY* 2.9 26.2 + - - -
77E ASN* 4.1 1.2 - - - +
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Residues in contact with TYR 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E HIS* 3.1 33.5 + - + +
38E HIS* 3.0 9.4 + - - +
40E GLY* 1.3 74.3 - - - +
42E VAL* 1.3 61.2 + - - +
45E ALA* 3.0 30.0 + - - +
76E PHE* 4.0 20.7 - + - -
77E ASN* 3.6 37.0 - - - +
80E GLY* 3.8 21.5 - - - -
81E HIS* 3.8 8.7 - - - +
84E HIS* 3.3 26.5 - + - -
155E HIS* 3.0 28.1 + + - -
172E PHE* 4.4 4.5 - - - -
174E HIS* 4.0 15.2 - - - -
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Residues in contact with VAL 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E TYR* 3.7 31.8 - - + +
11E PHE* 4.0 36.8 - - + +
38E HIS* 3.2 14.2 + - + +
39E LYS* 3.6 7.6 - - + +
41E TYR* 1.3 76.0 - - - +
43E ASN* 1.3 67.6 + - - +
45E ALA* 3.4 5.4 + - - +
46E ASN* 3.0 29.8 + - - +
81E HIS* 3.6 31.2 - - + +
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Residues in contact with ASN 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E LYS* 3.1 36.8 + - - +
40E GLY* 3.8 7.3 - - - +
42E VAL* 1.3 84.6 - - - +
44E GLY* 1.3 57.3 + - - +
46E ASN* 3.4 8.0 + - - +
47E SER* 3.0 31.0 + - - -
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Residues in contact with GLY 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E GLY 2.9 17.4 + - - -
43E ASN* 1.3 78.5 - - - +
45E ALA* 1.3 60.4 + - - +
47E SER* 3.4 8.2 + - - -
48E LEU* 3.2 27.7 + - - +
77E ASN* 3.8 18.8 - - - -
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Residues in contact with ALA 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E TYR* 4.2 14.8 - - + -
41E TYR 3.0 19.0 + - - +
42E VAL* 3.7 5.6 - - - +
44E GLY* 1.3 77.6 - - - +
46E ASN* 1.3 58.3 + - - +
48E LEU* 3.2 4.6 + - - +
49E LEU* 2.9 32.5 + - - +
74E LEU* 3.8 7.5 - - + +
77E ASN* 3.6 18.3 - - + +
78E ILE* 4.2 20.9 - - + -
81E HIS* 5.9 1.8 - - + -
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Residues in contact with ASN 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ARG* 3.3 27.4 + - + +
9E TYR* 2.8 51.4 + - - +
42E VAL* 3.0 25.0 + - - +
43E ASN* 3.9 9.1 - - - +
45E ALA* 1.3 74.0 - - - +
47E SER* 1.3 64.6 + - - +
49E LEU* 3.2 4.3 + - - +
50E ASP* 3.1 28.8 + - - +
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Residues in contact with SER 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E ASN 3.0 16.4 + - - -
44E GLY* 3.4 10.6 + - - -
46E ASN* 1.3 76.7 - - - +
48E LEU* 1.3 67.0 + - - +
50E ASP* 3.5 22.1 - - - +
51E ARG* 3.6 12.8 + - - +
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Residues in contact with LEU 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ASP* 4.9 7.0 - - - +
44E GLY 3.2 18.9 + - - +
45E ALA* 3.6 4.0 - - - +
46E ASN 3.2 0.2 - - - -
47E SER* 1.3 82.9 + - - +
49E LEU* 1.3 59.0 - - - +
50E ASP 3.2 0.4 - - - -
51E ARG* 3.3 12.7 + - - +
52E LEU* 3.0 27.2 + - - +
69E GLY 4.6 3.6 - - - +
70E ILE* 4.0 31.6 - - + +
73E GLY* 3.4 39.3 - - - +
74E LEU* 3.7 17.3 - - + +
77E ASN* 3.6 8.7 - - - +
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Residues in contact with LEU 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ASN* 4.2 7.0 - - - +
148C GLN* 4.0 20.6 - - - +
6E LEU* 4.3 22.8 - - + +
7E LYS 3.5 25.1 - - - +
8E ARG* 3.9 20.5 + - - +
9E TYR* 3.9 29.6 - - + -
45E ALA 2.9 18.8 + - - +
46E ASN* 3.2 6.7 + - - +
48E LEU* 1.3 74.6 - - - +
50E ASP* 1.3 60.5 + - - +
52E LEU* 3.8 8.7 - - + +
53E GLU* 2.9 31.4 + - - +
74E LEU* 4.2 12.6 - - + -
78E ILE* 5.5 0.2 - - + -
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Residues in contact with ASP 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ARG* 2.5 39.4 + - - +
46E ASN* 3.1 18.9 + - - +
47E SER* 3.5 16.0 - - - +
49E LEU* 1.3 79.1 - - - +
51E ARG* 1.3 58.6 + - + +
53E GLU* 3.3 3.1 + - - +
54E LYS* 3.0 45.3 + - - +
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Residues in contact with ARG 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D GLY* 3.1 28.5 + - - -
65D TYR 3.9 8.0 + - - -
66D ASP* 2.9 41.1 + - - -
47E SER 3.6 10.2 + - - +
48E LEU* 3.3 16.9 + - - +
49E LEU 3.3 0.6 - - - -
50E ASP* 1.3 77.3 - - + +
52E LEU* 1.3 61.0 + - - +
54E LYS* 3.3 15.5 + - + +
55E LEU* 2.9 28.3 + - - +
60E LEU* 3.7 21.2 - - + +
64E GLN 3.0 26.7 + - - -
65E TYR* 3.5 5.1 - - - +
70E ILE* 4.2 14.4 - - + +
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Residues in contact with LEU 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C TYR* 6.1 1.1 - - - +
122C VAL* 5.2 6.7 - - + -
148C GLN* 4.1 13.9 - - - +
149C ILE* 6.2 2.9 - - + -
6E LEU* 4.4 12.3 - - + -
48E LEU 3.0 16.6 + - - +
49E LEU* 3.8 9.9 - - + +
50E ASP 3.4 0.2 - - - -
51E ARG* 1.3 76.1 - - - +
53E GLU* 1.3 57.9 + - - +
55E LEU* 3.2 23.5 + - + +
56E ILE* 2.9 52.4 + - + +
67E LEU* 4.8 8.1 - - + -
70E ILE* 4.3 15.2 - - + +
71E LEU* 5.2 7.6 - - + -
74E LEU* 3.9 23.1 - - + -
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Residues in contact with GLU 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ILE* 4.6 3.8 - - + +
5E GLN* 3.4 15.6 - - - +
6E LEU* 2.8 45.4 + - + +
8E ARG* 3.2 26.9 + - - -
49E LEU 2.9 18.0 + - - +
50E ASP* 3.5 5.1 - - - +
52E LEU* 1.3 78.4 - - - +
54E LYS* 1.3 63.1 + - + +
56E ILE* 3.2 6.3 + - - +
57E LYS* 3.0 50.6 + - + +
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Residues in contact with LYS 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E ASP* 3.0 30.9 + - - +
51E ARG* 3.5 16.4 - - + +
53E GLU* 1.3 76.5 - - - +
55E LEU* 1.3 58.1 + - - +
57E LYS* 3.3 6.7 + - - +
58E GLY 2.9 25.5 + - - -
59E ASP* 3.0 34.7 + - + +
60E LEU* 3.3 22.6 + - + +
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Residues in contact with LEU 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ARG* 3.0 15.7 + - - +
122C VAL* 4.5 19.3 - - + -
125C GLU* 4.7 7.2 - - - +
51E ARG 2.9 12.4 + - - +
52E LEU* 3.3 16.4 - - + +
54E LYS* 1.3 77.5 - - - +
56E ILE* 1.3 72.6 + - + +
58E GLY* 3.3 10.0 + - - -
60E LEU* 3.8 18.6 - - + +
65E TYR* 3.4 52.9 - - + +
67E LEU* 3.8 20.6 - - + -
70E ILE* 4.2 10.5 - - + -
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Residues in contact with ILE 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLN 3.9 5.2 - - - +
113C TYR* 3.7 52.0 - - + +
118C ARG* 2.9 41.0 + - - +
122C VAL* 4.4 10.8 - - + -
4E ILE* 3.9 22.4 - - + +
6E LEU* 4.2 17.0 - - + -
52E LEU* 2.9 39.6 + - + +
53E GLU* 3.6 5.6 - - - +
55E LEU* 1.3 81.7 - - + +
57E LYS* 1.3 60.7 + - - +
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Residues in contact with LYS 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E VAL 4.8 3.4 + - - +
4E ILE* 3.7 52.1 + - + +
53E GLU* 3.0 40.3 + - + +
54E LYS* 3.7 7.2 - - - +
55E LEU 3.3 0.2 - - - -
56E ILE* 1.3 77.1 - - - +
58E GLY* 1.3 59.1 + - - +
59E ASP* 3.5 27.0 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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