Contacts of the helix formed by residues 37 - 57 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C GLU* 3.8 10.0 + - - -
177C TYR* 2.6 30.2 + + - -
182C ASN* 3.5 23.6 + - + +
32D VAL* 3.0 19.7 + - + -
33D HIS* 3.4 23.1 - - + +
36D GLY* 1.3 68.7 - - - +
38D HIS* 1.3 68.0 + - - +
40D GLY* 3.0 11.6 + - - -
41D TYR* 3.1 36.3 + - + -
174D HIS* 3.6 33.9 + + + +
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Residues in contact with HIS 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D PHE* 3.7 10.6 - + + -
12D PRO* 3.6 29.1 - - + +
33D HIS 3.1 10.0 + - - +
34D TYR* 3.4 17.4 + + - +
36D GLY 3.7 0.2 - - - -
37D HIS* 1.3 76.8 - - - +
39D LYS* 1.3 64.2 + - - +
41D TYR* 3.0 19.1 + - - +
42D VAL* 3.2 9.6 + - + +
81D HIS* 3.1 42.8 + - - -
84D HIS* 3.7 19.2 - - + +
85D ALA 3.8 9.2 - - - -
88D TRP* 2.9 29.5 + + - +
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Residues in contact with LYS 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D PHE* 3.4 45.5 - - + -
34D TYR 3.3 3.8 + - - +
35D ASN* 3.0 37.2 + - - +
36D GLY 3.9 0.6 + - - +
37D HIS 3.3 0.4 - - - -
38D HIS* 1.3 78.2 - - - +
40D GLY* 1.3 63.0 + - - +
42D VAL* 3.2 3.7 + - + +
43D ASN* 3.0 37.4 + - - +
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Residues in contact with GLY 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D GLY 3.2 12.8 + - - -
37D HIS 3.0 8.6 + - - -
39D LYS* 1.3 78.2 - - - +
41D TYR* 1.3 57.1 + - - +
43D ASN* 3.9 7.4 - - - +
44D GLY* 2.8 26.7 + - - -
77D ASN* 4.2 1.4 - - - +
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Residues in contact with TYR 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D HIS* 3.1 37.2 + - + +
38D HIS* 3.0 12.1 + - - +
40D GLY* 1.3 74.5 - - - +
42D VAL* 1.3 61.2 + - - +
45D ALA* 2.9 31.0 + - - +
76D PHE* 4.0 20.5 - + - -
77D ASN* 3.6 37.8 - - - +
80D GLY* 3.8 19.3 - - - -
81D HIS* 3.8 8.1 - - - +
84D HIS* 3.4 22.9 - + - -
155D HIS* 3.1 26.7 + - - -
172D PHE* 4.7 4.0 - - - -
174D HIS* 3.9 16.3 - - - -
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Residues in contact with VAL 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D TYR* 3.7 30.1 - - + +
11D PHE* 3.9 38.4 - - + +
38D HIS* 3.6 13.0 - - + +
39D LYS* 3.2 8.0 + - - +
41D TYR* 1.3 78.3 - - - +
43D ASN* 1.3 67.0 + - - +
45D ALA* 3.8 4.1 - - - +
46D ASN* 3.1 29.6 + - - +
81D HIS* 3.7 31.2 - - + +
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Residues in contact with ASN 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LYS* 3.0 38.0 + - - +
40D GLY* 3.9 6.8 - - - +
42D VAL* 1.3 83.1 - - - +
44D GLY* 1.3 61.7 + - - +
46D ASN* 3.4 9.0 + - - +
47D SER* 3.0 26.5 + - - -
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Residues in contact with GLY 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D GLY 2.8 18.2 + - - -
41D TYR 3.9 1.1 - - - -
42D VAL 3.3 0.2 - - - -
43D ASN* 1.3 77.6 - - - +
45D ALA* 1.3 61.1 + - - +
47D SER* 3.4 9.4 + - - -
48D LEU* 3.2 26.7 + - - +
77D ASN* 3.9 16.8 - - - -
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Residues in contact with ALA 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D TYR* 4.2 14.1 - - + -
41D TYR 2.9 18.4 + - - +
42D VAL* 3.8 5.8 - - - +
43D ASN 3.3 0.2 - - - -
44D GLY* 1.3 75.0 - - - +
46D ASN* 1.3 59.0 + - - +
48D LEU* 3.2 4.4 + - - +
49D LEU* 3.0 32.1 + - - +
74D LEU* 3.8 6.5 - - - +
77D ASN* 3.6 17.5 - - + +
78D ILE* 4.1 23.3 - - + +
81D HIS* 5.8 1.6 - - + -
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Residues in contact with ASN 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ARG* 3.4 21.2 + - + +
9D TYR* 2.9 54.1 + - - +
42D VAL* 3.1 25.1 + - - +
43D ASN* 3.8 9.5 - - - +
45D ALA* 1.3 73.5 - - - +
47D SER* 1.3 65.1 + - - +
49D LEU* 3.3 7.5 + - - +
50D ASP* 3.1 29.4 + - - +
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Residues in contact with SER 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D ASN 3.0 16.8 + - - -
44D GLY* 3.4 10.0 + - - -
46D ASN* 1.3 77.3 - - - +
48D LEU* 1.3 68.1 + - - +
50D ASP* 3.6 14.0 - - - +
51D ARG* 3.6 21.0 + - - +
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Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLY 3.2 16.6 + - - +
45D ALA 3.6 0.2 - - - +
46D ASN 3.2 0.4 - - - -
47D SER* 1.3 84.0 + - - +
49D LEU* 1.3 61.2 + - - +
50D ASP 3.2 0.4 - - - -
51D ARG* 3.3 19.6 + - - +
52D LEU* 3.0 26.5 + - - +
69D GLY 4.8 2.9 - - - +
70D ILE* 4.1 25.7 - - + +
73D GLY* 3.4 39.9 - - - +
74D LEU* 3.6 21.8 - - + +
77D ASN* 3.8 8.7 - - - +
66E ASP* 4.9 3.6 - - - +
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 4.2 21.9 - - + +
7D LYS 3.4 24.5 - - - +
8D ARG* 3.9 20.4 + - - +
9D TYR* 3.9 29.4 - - + -
45D ALA 3.0 18.8 + - - +
46D ASN* 3.6 7.9 - - - +
48D LEU* 1.3 73.6 - - - +
50D ASP* 1.3 61.2 + - - +
52D LEU* 3.8 9.3 - - + +
53D GLU* 2.8 31.2 + - - +
74D LEU* 4.4 11.9 - - + -
78D ILE* 5.4 0.4 - - + -
146F ASN* 4.2 7.0 - - - +
148F GLN* 4.0 20.2 - - - +
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Residues in contact with ASP 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ARG* 2.5 41.1 + - - +
46D ASN* 3.1 19.1 + - - +
47D SER* 3.6 15.6 - - - +
48D LEU 3.2 0.2 - - - -
49D LEU* 1.3 77.8 - - - +
51D ARG* 1.3 56.9 + - - +
53D GLU* 3.3 3.0 + - - +
54D LYS* 3.0 48.2 + - - +
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Residues in contact with ARG 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D SER 3.6 10.8 + - - +
48D LEU* 3.3 19.6 + - - +
49D LEU 3.2 0.4 - - - -
50D ASP* 1.3 76.2 - - - +
52D LEU* 1.3 60.5 + - - +
54D LYS* 3.2 8.8 + - + +
55D LEU* 2.9 28.8 + - - +
60D LEU* 3.5 26.9 - - + +
64D GLN 3.0 24.5 + - - -
65D TYR* 3.4 5.7 - - - +
70D ILE* 4.2 11.9 - - + +
63E GLY* 3.0 28.4 + - - -
65E TYR 3.7 9.3 + - - -
66E ASP* 2.7 43.7 + - - -
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 4.4 13.2 - - + -
48D LEU 3.0 15.8 + - - +
49D LEU* 3.8 8.5 - - + +
51D ARG* 1.3 76.7 - - - +
53D GLU* 1.3 59.5 + - - +
55D LEU* 3.2 26.6 + - + +
56D ILE* 2.9 49.9 + - + +
67D LEU* 4.7 7.9 - - + -
70D ILE* 4.3 15.8 - - + +
71D LEU* 5.1 8.3 - - + -
74D LEU* 4.0 23.3 - - + -
113F TYR* 5.9 1.8 - - - +
122F VAL* 5.2 6.7 - - + -
148F GLN* 4.0 14.4 - - - +
149F ILE* 6.2 3.6 - - + -
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 4.6 4.0 - - + +
5D GLN* 3.5 15.3 - - - +
6D LEU* 2.9 43.4 + - + +
8D ARG* 3.1 29.8 + - - -
49D LEU 2.8 17.5 + - - +
50D ASP* 3.4 5.6 - - - +
51D ARG 3.2 0.2 - - - -
52D LEU* 1.3 77.1 - - - +
54D LYS* 1.3 62.9 + - - +
56D ILE* 3.3 6.1 + - - +
57D LYS* 3.0 51.5 + - + +
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Residues in contact with LYS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ASP* 3.0 34.5 + - - +
51D ARG* 3.5 13.9 - - + +
53D GLU* 1.3 77.3 - - + +
55D LEU* 1.3 58.0 + - - +
57D LYS* 3.2 7.3 + - - +
58D GLY 2.9 25.5 + - - -
59D ASP* 3.0 34.8 + - + +
60D LEU* 3.9 22.0 - - + -
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ARG 2.9 12.2 + - - +
52D LEU* 3.2 18.1 + - + +
54D LYS* 1.3 76.9 - - - +
56D ILE* 1.3 75.4 + - + +
58D GLY* 3.3 10.0 + - - -
60D LEU* 3.8 18.5 - - + +
65D TYR* 3.5 50.9 - - + +
67D LEU* 3.8 20.6 - - + -
70D ILE* 4.1 9.9 - - + -
118F ARG* 3.0 15.3 + - - +
122F VAL* 4.5 17.5 - - + -
125F GLU* 4.9 6.7 - - - +
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Residues in contact with ILE 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 4.0 13.4 - - + +
6D LEU* 4.4 13.0 - - + -
52D LEU* 2.9 40.7 + - + +
53D GLU* 3.3 5.6 + - - +
55D LEU* 1.3 87.1 - - + +
57D LYS* 1.3 58.5 + - - +
112F GLN 4.3 7.0 - - - +
113F TYR* 3.6 62.7 - - + +
118F ARG* 3.0 35.2 + - - +
122F VAL* 4.4 6.5 - - + -
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Residues in contact with LYS 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D VAL 4.5 3.7 + - - +
4D ILE* 3.5 53.3 + - + +
5D GLN* 5.8 0.2 - - - +
53D GLU* 3.0 37.5 + - + +
54D LYS* 3.7 7.0 - - - +
56D ILE* 1.3 77.0 - - - +
58D GLY* 1.3 59.8 + - - +
59D ASP* 3.5 27.6 - - - +
118F ARG* 5.0 0.2 - - - -
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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