Contacts of the helix formed by residues 37 - 57 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A VAL 3.0 25.3 + - - -
33A HIS* 3.4 23.6 - - + +
36A GLY* 1.3 67.9 - - - -
38A HIS* 1.3 68.9 + - - +
40A GLY* 3.0 11.1 + - - -
41A TYR* 3.1 37.1 + - + -
174A HIS* 3.6 33.9 + + + +
173B GLU* 3.8 10.5 + - - -
176B TYR* 6.2 0.2 - - - -
177B TYR* 2.6 31.8 + + - -
182B ASN* 3.5 23.3 - - + +
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Residues in contact with HIS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.7 10.9 - + + -
12A PRO* 3.6 28.6 - - + +
33A HIS 3.1 10.0 + - - +
34A TYR* 3.4 16.0 + - - +
36A GLY 3.7 0.2 - - - -
37A HIS* 1.3 77.4 - - - +
39A LYS* 1.3 64.0 + - - +
41A TYR* 3.0 19.3 + - - +
42A VAL* 3.3 9.2 + - + +
80A GLY 4.7 0.2 - - - -
81A HIS* 3.2 43.3 + - - -
84A HIS* 3.6 13.1 - - + +
85A ALA* 3.7 17.7 - - - -
88A TRP* 2.9 28.9 + + + +
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.4 43.0 - - + -
34A TYR 3.4 3.8 + - - -
35A ASN* 3.2 39.2 + - - +
36A GLY 4.1 0.2 - - - +
37A HIS 3.3 0.4 - - - -
38A HIS* 1.3 76.9 - - - +
40A GLY* 1.3 64.3 + - - +
42A VAL* 3.2 4.0 + - - +
43A ASN* 3.0 38.2 + - - +
39F LYS* 4.0 25.5 - - - +
43F ASN* 4.6 13.6 + - - -
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLY 3.1 13.8 + - - -
37A HIS 3.0 8.4 + - - -
39A LYS* 1.3 79.8 - - - +
41A TYR* 1.3 58.0 + - - +
43A ASN* 3.4 8.1 + - - +
44A GLY* 2.8 26.3 + - - -
77A ASN* 4.1 1.4 - - - +
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Residues in contact with TYR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A HIS* 3.1 35.1 + - + -
38A HIS* 3.0 12.4 + - - +
40A GLY* 1.3 75.8 - - - +
42A VAL* 1.3 61.3 + - - +
45A ALA* 3.0 30.7 + - - +
76A PHE* 3.9 21.4 - + - -
77A ASN* 3.6 36.4 - - - +
80A GLY* 3.8 20.9 - - - -
81A HIS* 3.8 8.7 - - - +
84A HIS* 3.4 23.1 - + - -
155A HIS* 3.0 29.1 + + - -
172A PHE* 4.5 4.2 - - - -
174A HIS* 4.0 15.1 - - - -
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 3.7 28.9 - - + +
11A PHE* 4.0 36.8 - - + +
38A HIS* 3.7 12.3 - - + +
39A LYS* 3.2 9.1 + - - +
41A TYR* 1.3 75.8 - - - +
43A ASN* 1.3 69.8 + - - +
45A ALA* 3.4 4.9 + - - +
46A ASN* 3.0 30.3 + - - +
81A HIS* 3.6 32.8 - - + +
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Residues in contact with ASN 43 (chain A).
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* 3.0 37.3 + - - +
40A GLY* 3.8 6.6 - - - +
42A VAL* 1.3 84.0 - - - +
44A GLY* 1.3 61.8 + - - +
46A ASN* 3.4 7.6 + - - +
47A SER* 3.0 26.8 + - - -
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Residues in contact with GLY 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLY 2.8 17.8 + - - -
41A TYR 3.9 1.1 - - - -
43A ASN* 1.3 77.2 - - - +
45A ALA* 1.3 60.4 + - - +
47A SER* 3.3 8.9 + - - -
48A LEU* 3.2 26.7 + - - +
77A ASN* 3.9 17.5 - - - -
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 4.2 20.6 - - + -
41A TYR 3.0 19.0 + - - +
42A VAL* 3.7 6.3 - - - +
44A GLY* 1.3 76.2 - - - +
46A ASN* 1.3 57.9 + - - +
48A LEU* 3.1 5.2 + - - +
49A LEU* 2.9 32.2 + - - +
74A LEU* 3.9 6.7 - - - +
77A ASN* 3.6 16.0 - - + +
78A ILE* 4.2 16.6 - - + +
81A HIS* 5.8 1.3 - - + -
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Residues in contact with ASN 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 3.4 24.5 + - + +
9A TYR* 2.8 53.6 + - - +
42A VAL* 3.0 27.3 + - - +
43A ASN* 3.9 8.7 - - - +
45A ALA* 1.3 75.3 - - - +
47A SER* 1.3 61.7 + - - +
49A LEU* 3.2 3.9 + - - +
50A ASP* 3.1 30.1 + - - +
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ASN 3.0 17.0 + - - -
44A GLY* 3.3 11.6 + - - -
46A ASN* 1.3 77.2 - - - +
48A LEU* 1.3 67.8 + - - +
50A ASP* 3.5 22.7 - - - +
51A ARG* 3.6 13.0 + - - +
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLY 3.2 16.5 + - - +
45A ALA 3.1 5.4 + - - +
47A SER* 1.3 84.8 + - - +
49A LEU* 1.3 61.5 + - - +
50A ASP 3.2 0.2 - - - -
51A ARG* 3.3 14.9 + - - +
52A LEU* 3.0 26.7 + - - +
69A GLY 4.8 3.1 - - - +
70A ILE* 4.0 30.1 - - + +
73A GLY* 3.3 41.7 - - - +
74A LEU* 3.7 16.8 - - + +
77A ASN* 3.9 7.6 - - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.1 22.2 - - + +
7A LYS 3.4 25.6 - - - +
8A ARG* 3.9 19.9 + - - +
9A TYR* 4.0 28.5 - - + -
45A ALA 2.9 16.4 + - - +
46A ASN* 3.2 9.6 + - - +
48A LEU* 1.3 77.0 - - - +
50A ASP* 1.3 59.2 + - - +
52A LEU* 3.4 13.2 + - + +
53A GLU* 2.9 31.2 + - - +
74A LEU* 4.1 17.3 - - + -
78A ILE* 5.4 3.8 - - + -
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Residues in contact with ASP 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 2.4 42.3 + - - +
46A ASN* 3.1 18.2 + - - +
47A SER* 3.5 15.6 - - - +
49A LEU* 1.3 76.9 - - - +
51A ARG* 1.3 57.6 + - + +
53A GLU* 3.3 5.4 + - - +
54A LYS* 3.0 43.5 + - - +
189E ASN* 5.9 1.3 + - - -
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Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A SER 3.6 10.9 + - - +
48A LEU* 3.3 21.6 + - - +
49A LEU 3.3 0.2 - - - -
50A ASP* 1.3 78.6 - - + +
52A LEU* 1.3 59.8 + - - +
54A LYS* 3.2 18.0 + - + +
55A LEU* 2.9 29.4 + - - +
60A LEU* 3.8 26.0 - - + +
64A GLN 3.1 24.9 + - - -
65A TYR* 3.5 18.0 - - - +
66A ASP 4.9 0.6 - - - +
70A ILE* 4.3 19.7 - - + +
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.5 11.9 - - + -
48A LEU 3.0 17.2 + - - +
49A LEU* 3.8 12.6 - - + +
50A ASP 3.3 0.2 - - - -
51A ARG* 1.3 75.8 - - - +
53A GLU* 1.3 58.2 + - - +
55A LEU* 3.3 26.8 + - + +
56A ILE* 2.9 47.6 + - + +
67A LEU* 4.7 8.3 - - + -
70A ILE* 4.3 15.8 - - + +
71A LEU* 5.1 9.6 - - + -
74A LEU* 4.0 22.4 - - + -
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 4.5 7.2 - - + +
5A GLN* 3.3 11.5 - - - +
6A LEU* 2.9 43.5 + - + +
8A ARG* 3.2 26.6 + - - -
49A LEU 2.9 19.0 + - - +
50A ASP* 3.4 5.5 - - - +
52A LEU* 1.3 77.4 - - - +
54A LYS* 1.3 64.2 + - - +
56A ILE* 3.2 7.4 + - - +
57A LYS* 2.9 53.2 + - + +
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Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASP* 3.0 29.9 + - - +
51A ARG* 3.5 18.1 - - + +
53A GLU* 1.3 76.6 - - + +
55A LEU* 1.3 58.4 + - - +
57A LYS* 3.2 7.1 + - - +
58A GLY 2.8 25.3 + - - -
59A ASP* 2.9 33.1 + - + +
60A LEU* 3.8 22.4 - - + +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ARG 2.9 12.6 + - - +
52A LEU* 3.4 20.2 - - + +
54A LYS* 1.3 77.5 - - - +
56A ILE* 1.3 73.9 + - + +
58A GLY* 3.3 11.8 + - - -
60A LEU* 3.8 19.5 - - + +
65A TYR* 3.5 50.0 - - + +
67A LEU* 3.8 21.8 - - + -
70A ILE* 4.2 10.8 - - + -
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Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.8 22.9 - - + +
6A LEU* 4.3 22.7 - - + -
52A LEU* 2.9 34.9 + - + +
53A GLU* 3.6 8.3 - - + +
55A LEU* 1.3 88.6 - - + +
57A LYS* 1.3 60.9 + - - +
58A GLY* 4.5 0.2 - - - -
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Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL 4.7 3.1 + - - +
4A ILE* 3.5 51.5 + - + +
53A GLU* 2.9 41.0 + - + +
54A LYS* 3.7 7.4 - - - +
56A ILE* 1.3 76.0 - - - +
58A GLY* 1.3 60.0 + - - +
59A ASP* 3.5 28.3 - - - +
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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