Contacts of the helix formed by residues 37 - 57 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLU* 3.7 21.5 - - - -
176A TYR* 6.2 0.2 - - - -
177A TYR* 2.7 31.2 + + - -
182A ASN* 3.6 23.2 - - + +
32B VAL 3.0 17.4 + - - -
33B HIS* 3.4 21.8 - - + +
36B GLY* 1.3 69.1 - - - -
38B HIS* 1.3 68.6 + - - +
40B GLY* 3.0 10.7 + - - -
41B TYR* 3.1 36.4 + - + -
174B HIS* 3.5 24.0 + + - +
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Residues in contact with HIS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.8 8.5 - + + -
12B PRO* 3.6 27.4 - - + +
33B HIS 3.1 10.2 + - - +
34B TYR* 3.4 16.6 + - - +
37B HIS* 1.3 76.5 - - - +
39B LYS* 1.3 64.6 + - - +
41B TYR* 3.0 18.8 + + - +
42B VAL* 3.3 11.7 + - + +
81B HIS* 3.0 43.7 + - - -
84B HIS* 3.7 11.3 - - + +
85B ALA* 3.7 18.2 - - - -
88B TRP* 2.9 29.4 + + + +
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Residues in contact with LYS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.4 45.3 - - + -
34B TYR 3.3 3.8 + - - -
35B ASN* 3.3 39.9 + - - +
36B GLY 4.1 0.2 - - - +
37B HIS 3.3 0.2 - - - -
38B HIS* 1.3 78.6 - - - +
40B GLY* 1.3 61.8 + - - +
42B VAL* 3.3 3.3 + - - +
43B ASN* 3.1 39.1 + - - +
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Residues in contact with GLY 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLY 3.1 13.0 + - - -
37B HIS* 3.0 9.5 + - - -
39B LYS* 1.3 78.7 - - - +
41B TYR* 1.3 58.4 + - - +
43B ASN* 3.5 8.1 + - - +
44B GLY* 2.9 24.8 + - - -
77B ASN* 4.1 1.7 - - - +
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Residues in contact with TYR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS* 3.1 38.0 + - + -
38B HIS* 3.0 13.0 + - - +
40B GLY* 1.3 74.4 - - - +
42B VAL* 1.3 62.3 + - - +
45B ALA* 3.0 30.0 + - - +
76B PHE* 4.0 19.6 - + - -
77B ASN* 3.6 37.3 - - - +
80B GLY* 3.7 22.2 - - - -
81B HIS* 3.7 8.7 - - - +
84B HIS* 3.4 23.6 - + - -
155B HIS* 3.0 28.8 + + - -
172B PHE* 4.6 4.3 - - - -
174B HIS* 4.0 15.8 - - - -
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TYR* 3.6 35.4 - - + +
11B PHE* 4.0 35.0 - - + +
38B HIS* 3.3 14.3 + - + +
39B LYS* 3.6 7.0 - - + +
41B TYR* 1.3 78.3 - - - +
43B ASN* 1.3 66.7 + - - +
45B ALA* 3.4 5.0 + - - +
46B ASN* 3.0 28.9 + - - +
81B HIS* 3.7 31.2 - - + +
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Residues in contact with ASN 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LYS* 3.1 38.4 + - - +
40B GLY* 3.9 7.0 - - - +
42B VAL* 1.3 83.4 - - - +
44B GLY* 1.3 57.7 + - - +
46B ASN* 3.4 8.4 + - - +
47B SER* 3.0 30.5 + - - -
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Residues in contact with GLY 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLY 2.9 18.0 + - - -
43B ASN* 1.3 77.8 - - - +
45B ALA* 1.3 60.5 + - - +
47B SER* 3.2 9.4 + - - -
48B LEU* 3.2 27.2 + - - +
77B ASN* 3.9 18.8 - - - -
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TYR* 4.3 14.8 - - + -
41B TYR 3.0 19.2 + - - +
42B VAL* 3.8 6.1 - - - +
44B GLY* 1.3 76.4 - - - +
46B ASN* 1.3 57.5 + - - +
48B LEU* 3.3 3.9 + - - +
49B LEU* 3.0 31.7 + - - +
74B LEU* 3.8 7.4 - - - +
77B ASN* 3.6 17.1 - - + +
78B ILE* 4.2 22.0 - - + -
81B HIS* 5.9 1.1 - - + -
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Residues in contact with ASN 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 3.3 20.1 + - + +
9B TYR* 2.9 50.8 + - - +
42B VAL* 3.0 28.3 + - - +
43B ASN* 3.8 9.5 - - - +
45B ALA* 1.3 73.4 - - - +
47B SER* 1.3 64.3 + - - +
49B LEU* 3.2 6.4 + - - +
50B ASP* 3.1 31.1 + - - +
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Residues in contact with SER 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ASN 3.0 16.1 + - - -
44B GLY* 3.2 12.0 + - - -
45B ALA 3.3 0.2 - - - -
46B ASN* 1.3 76.7 - - - +
48B LEU* 1.3 67.0 + - - +
50B ASP* 3.5 22.8 - - - +
51B ARG* 3.5 12.0 + - - +
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLY 3.2 18.8 + - - +
45B ALA* 3.8 4.5 - - - +
47B SER* 1.3 82.9 + - - +
49B LEU* 1.3 61.0 + - - +
50B ASP 3.2 0.4 - - - -
51B ARG* 3.3 15.9 + - - +
52B LEU* 3.0 27.7 + - - +
69B GLY 4.7 2.9 - - - +
70B ILE* 4.1 30.6 - - + +
73B GLY* 3.4 42.2 - - - +
74B LEU* 3.8 16.4 - - + +
77B ASN* 3.9 7.2 - - - +
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 4.2 18.8 - - + +
7B LYS 3.3 26.2 - - - +
8B ARG* 3.8 23.1 + - - +
9B TYR* 4.0 25.6 - - + -
45B ALA 3.0 22.7 + - - +
46B ASN* 3.2 11.9 + - - +
48B LEU* 1.3 74.4 - - - +
50B ASP* 1.3 61.1 + - - +
52B LEU* 3.8 8.8 - - + +
53B GLU* 2.9 31.2 + - - +
74B LEU* 4.2 20.4 - - + -
78B ILE* 5.4 3.1 - - + -
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Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 2.4 42.1 + - - +
46B ASN* 3.1 17.8 + - - +
47B SER* 3.5 16.8 - - - +
48B LEU 3.2 0.2 - - - -
49B LEU* 1.3 76.9 - - - +
51B ARG* 1.3 57.3 + - + +
53B GLU* 3.2 4.8 + - - +
54B LYS* 3.0 44.3 + - - +
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Residues in contact with ARG 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B SER 3.5 8.4 + - - +
48B LEU* 3.3 24.1 + - - +
49B LEU 3.3 0.2 - - - -
50B ASP* 1.3 78.1 - - + +
52B LEU* 1.3 60.3 + - - +
54B LYS* 3.2 14.2 + - + +
55B LEU* 2.9 28.5 + - - +
60B LEU* 3.7 26.0 - - + +
64B GLN 3.0 25.3 + - - -
65B TYR* 3.4 17.6 - - - +
66B ASP 4.9 0.6 - - - +
70B ILE* 4.0 22.4 - - + +
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 4.5 12.1 - - + -
48B LEU 3.0 16.5 + - - +
49B LEU* 3.8 10.8 - - + +
50B ASP 3.3 0.2 - - - -
51B ARG* 1.3 76.0 - - - +
53B GLU* 1.3 58.4 + - - +
55B LEU* 3.2 25.1 + - + +
56B ILE* 2.9 49.7 + - + +
67B LEU* 4.7 9.2 - - + -
70B ILE* 4.3 15.0 - - + +
71B LEU* 5.2 8.5 - - + -
74B LEU* 4.0 22.0 - - + -
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 4.6 4.0 - - + +
5B GLN* 3.4 15.3 - - - +
6B LEU* 2.9 44.9 + - + +
8B ARG* 3.2 27.2 + - - -
49B LEU 2.9 19.4 + - - +
50B ASP 3.4 5.6 - - - +
51B ARG 3.2 0.2 - - - -
52B LEU* 1.3 77.2 - - - +
54B LYS* 1.3 62.6 + - - +
56B ILE* 3.2 6.0 + - - +
57B LYS* 3.0 51.4 + - + +
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Residues in contact with LYS 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ASP* 3.0 29.2 + - - +
51B ARG* 3.6 16.1 - - + +
53B GLU* 1.3 78.3 - - + +
55B LEU* 1.3 58.5 + - - +
57B LYS* 3.3 7.4 + - - +
58B GLY 2.9 24.3 + - - -
59B ASP* 2.9 35.4 + - + +
60B LEU* 3.3 20.8 + - + -
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ARG 2.9 12.6 + - - +
52B LEU* 3.3 20.2 - - + +
53B GLU 3.2 0.2 - - - -
54B LYS* 1.3 77.3 - - - +
56B ILE* 1.3 75.2 + - + +
58B GLY* 3.2 12.5 + - - -
60B LEU* 3.9 16.9 - - + +
65B TYR* 3.4 52.9 - - + +
67B LEU* 4.1 20.9 - - + -
70B ILE* 4.3 10.1 - - + -
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Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 3.8 24.2 - - + +
6B LEU* 4.1 24.0 - - + -
52B LEU* 2.9 39.8 + - + +
53B GLU* 3.6 5.4 - - + +
55B LEU* 1.3 87.4 - - + +
57B LYS* 1.3 61.6 + - - +
58B GLY* 4.5 0.2 - - - -
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Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL 4.7 2.5 + - - +
4B ILE* 3.7 54.3 + - + +
53B GLU* 3.0 40.9 + - + +
54B LYS* 3.7 7.4 - - - +
56B ILE* 1.3 75.5 - - - +
58B GLY* 1.3 58.5 + - - +
59B ASP* 3.4 28.2 + - - +
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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