Contacts of the helix formed by residues 42 - 58 (chain A) in PDB entry 3AQ8
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 ASP 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ASN 3.8 3.2 + - - -
41A THR* 1.3 69.8 - - - +
43A MET* 1.4 57.9 + - - +
44A ASP* 3.2 11.4 + - - +
45A HIS* 3.0 32.3 + - + +
46A GLU* 2.9 27.9 + - - +
144A HEM 4.8 0.8 + - - -
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Residues in contact with MET 43 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A TYR* 3.4 48.0 - - + -
29A LEU* 3.9 25.8 - - + -
38A PHE* 4.5 13.0 - - + +
41A THR* 3.1 36.6 + - - +
42A ASP* 1.4 68.8 + - - +
44A ASP* 1.3 65.4 + - - +
46A GLU* 3.8 5.8 - - + -
47A THR* 2.7 37.7 + - - +
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Residues in contact with ASP 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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42A ASP* 3.2 7.6 + - - +
43A MET* 1.3 82.4 - - - +
45A HIS* 1.3 64.5 + - - +
47A THR* 3.7 4.7 - - - -
48A LYS* 3.0 23.8 + - - +
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Residues in contact with HIS 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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42A ASP* 3.0 32.2 + - + +
44A ASP* 1.3 76.9 - - - +
46A GLU* 1.3 62.2 + - - +
48A LYS* 3.2 10.1 + - + +
49A GLN* 2.9 62.2 + - + +
144A HEM 3.6 20.0 + - - -
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Residues in contact with GLU 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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25A TYR* 2.4 39.3 + - + +
38A PHE* 4.2 9.3 - - + -
41A THR* 3.6 19.1 - - + +
42A ASP 2.9 16.9 + - - +
43A MET* 3.9 9.2 - - + +
45A HIS* 1.3 78.4 + - - +
47A THR* 1.3 60.6 + - - +
49A GLN* 3.9 2.2 - - - +
50A GLN* 2.9 37.6 + - - +
144A HEM 3.7 50.8 + - - +
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Residues in contact with THR 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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21A VAL* 3.8 15.9 - - + +
22A PRO* 4.3 23.2 - - + +
25A TYR* 3.9 22.0 - - - +
43A MET* 2.7 28.5 + - - +
44A ASP* 3.7 5.4 - - - -
46A GLU* 1.3 76.9 - - - +
48A LYS* 1.3 57.6 + - - +
51A THR* 2.8 39.0 + - - +
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Residues in contact with LYS 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 ASP 3.0 13.4 + - - +
45A HIS* 3.4 12.3 - - + +
47A THR* 1.3 78.7 - - - +
49A GLN* 1.4 90.1 + - - +
51A THR* 3.3 6.2 + - - -
52A ASP* 2.7 56.4 + - - +
63A HIS* 5.3 1.4 + - - +
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Residues in contact with GLN 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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45A HIS* 2.9 52.5 + - + +
46A GLU* 3.9 4.9 - - - +
48A LYS* 1.4 103.8 - - - +
50A GLN* 1.3 59.1 + - - +
52A ASP* 3.3 7.8 + - - +
53A PHE* 2.8 30.7 + - - +
64A TYR* 3.6 21.6 - - + -
65A LYS* 4.5 4.3 + - - +
66A GLY* 3.7 15.9 + - - -
144A HEM 3.8 29.2 - - + +
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Residues in contact with GLN 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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21A VAL* 4.0 11.2 - - + -
24A PHE* 4.4 13.5 - - + -
25A TYR* 3.1 33.7 + - + +
46A GLU* 2.9 20.2 + - - +
47A THR 4.0 1.6 - - - +
49A GLN* 1.3 74.2 - - - +
51A THR* 1.3 68.1 + - - +
53A PHE* 3.7 15.9 - - - -
54A LEU* 2.9 62.4 + - + +
144A HEM 3.4 38.5 + - - +
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Residues in contact with THR 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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17A MET* 3.9 21.4 + - + +
18A LYS* 4.9 16.9 - - + -
21A VAL* 3.6 24.6 - - - +
22A PRO* 5.5 0.2 - - - +
47A THR* 2.8 29.8 + - - +
48A LYS* 3.3 6.5 + - - -
50A GLN* 1.3 77.7 - - - +
52A ASP* 1.3 58.2 + - - +
54A LEU* 4.4 0.2 - - - +
55A THR* 2.7 42.7 + - - +
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Residues in contact with ASP 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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48A LYS* 2.7 53.2 + - - +
49A GLN* 3.5 11.7 + - - +
51A THR* 1.3 81.4 - - - +
53A PHE* 1.3 58.8 + - - +
55A THR* 3.5 5.1 + - - -
56A MET* 2.9 30.3 + - - +
61A PRO 4.8 1.2 - - - +
63A HIS* 3.7 24.2 + - - +
64A TYR* 3.8 22.9 + - + +
65A LYS 5.1 0.9 + - - -
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Residues in contact with PHE 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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49A GLN 2.8 20.6 + - - +
50A GLN* 3.2 18.4 + - - +
52A ASP* 1.3 72.1 - - - +
54A LEU* 1.3 61.1 + - + +
56A MET* 3.2 23.3 + - + +
57A LEU* 2.8 63.3 + - + +
64A TYR* 3.5 34.5 - + + -
67A LYS 5.3 0.2 - - - -
68A ASN* 6.2 0.7 - - - -
69A MET* 3.8 31.6 - - + -
114A THR* 4.7 3.8 - - + -
144A HEM 3.6 39.5 - - + -
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Residues in contact with LEU 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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17A MET* 4.0 21.0 - - + +
21A VAL* 4.2 13.7 - - + -
24A PHE* 5.6 4.9 - - + -
50A GLN* 2.9 51.2 + - + +
51A THR 4.4 0.2 - - - +
53A PHE* 1.3 82.0 - - + +
55A THR* 1.3 64.3 + - - +
57A LEU* 4.3 5.8 - - + -
58A LEU* 3.0 34.6 + - + +
90A LEU* 4.5 24.2 - - + -
111A ILE* 4.2 25.4 - - + -
144A HEM 4.3 10.5 - - + -
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Residues in contact with THR 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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8A TYR* 3.4 32.5 + - + +
17A MET* 3.6 18.1 - - - +
51A THR* 2.7 30.0 + - - +
52A ASP* 3.7 6.1 - - - -
54A LEU* 1.3 80.4 - - - +
56A MET* 1.3 59.9 + - - +
58A LEU 3.7 0.7 + - - -
59A GLY 3.5 1.6 + - - -
60A GLY* 2.8 28.8 + - - -
61A PRO* 3.5 31.2 - - + +
63A HIS* 6.4 0.4 - - + -
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Residues in contact with MET 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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52A ASP 2.9 17.4 + - - +
53A PHE* 3.6 39.9 - - + +
55A THR* 1.3 78.7 - - - +
57A LEU* 1.3 78.6 + - + +
59A GLY* 3.3 12.3 + - - -
60A GLY 4.4 3.8 + - - +
61A PRO 3.6 11.4 + - - +
62A ASN* 3.3 39.0 - - + +
64A TYR* 4.1 13.7 - - + -
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Residues in contact with LEU 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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53A PHE* 2.8 50.6 + - + +
54A LEU* 3.3 9.4 + - + +
56A MET* 1.3 95.6 - - + +
58A LEU* 1.3 64.6 + - + +
59A GLY* 3.3 1.3 + - - -
110A VAL* 3.8 28.1 - - + +
111A ILE* 4.2 29.8 - - + -
114A THR* 4.5 9.4 - - + -
144A HEM 4.5 2.5 - - + -
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Residues in contact with LEU 58 (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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7A ILE* 3.4 23.6 + - + +
8A TYR* 2.8 39.2 + - + +
11A LEU* 3.6 27.4 - - + -
17A MET* 4.2 10.3 - - + -
54A LEU* 3.0 26.6 + - + +
57A LEU* 1.3 84.2 - - + +
59A GLY* 1.3 58.2 + - - +
60A GLY 3.5 2.5 - - - -
90A LEU* 6.1 1.3 - - + -
94A LEU* 6.2 0.4 - - + -
107A ALA* 3.9 36.6 - - + +
110A VAL* 4.2 13.7 - - + -
111A ILE* 4.7 12.8 - - + -
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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