Contacts of the helix formed by residues 42 - 61 (chain A) in PDB entry 3AA6
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 ASN 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ASP* 4.2 12.5 + - - -
37A ARG 4.5 2.6 + - - -
40A LEU* 3.3 12.7 - - + +
41A ASN* 1.3 79.0 - - - +
43A ASP* 1.3 66.2 + - - +
44A ASN* 3.4 13.0 + - - +
45A LEU* 3.0 43.1 + - + +
46A LEU* 3.0 22.0 + - - +
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Residues in contact with ASP 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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37A ARG* 2.5 57.2 + - - +
41A ASN* 5.7 0.2 - - - -
42A ASN* 1.3 78.5 + - - +
44A ASN* 1.3 58.3 + - - +
46A LEU* 3.5 9.2 + - - +
47A ARG* 2.9 34.3 + - - +
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Residues in contact with ASN 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASN* 3.2 9.3 + - - +
43A ASP* 1.3 75.8 - - - +
45A LEU* 1.3 67.4 + - - +
47A ARG* 2.6 46.1 + - - +
48A GLU* 3.0 30.7 + - - +
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Residues in contact with LEU 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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10A ASP* 3.6 54.1 - - + +
11A GLU* 4.7 2.0 - - + +
13A LYS* 4.9 0.9 - - + -
14A VAL* 3.5 25.8 - - + +
40A LEU* 3.7 25.1 - - + -
42A ASN* 3.0 30.8 + - + +
44A ASN* 1.3 75.3 - - - +
46A LEU* 1.3 55.1 + - - +
48A GLU* 3.8 5.9 - - + +
49A GLY* 2.8 31.8 + - - +
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Residues in contact with LEU 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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14A VAL* 4.1 2.5 - - - -
17A ALA* 4.2 7.9 - - + -
21A ILE* 4.0 16.8 - - + -
33A PHE* 3.6 32.5 - - + -
36A VAL* 4.3 3.6 - - + -
37A ARG* 4.1 29.6 - - + +
40A LEU* 3.6 24.1 - - + +
42A ASN 3.0 12.7 + - - +
43A ASP* 3.7 10.5 - - - +
45A LEU* 1.3 73.8 - - - +
47A ARG* 1.3 65.4 + - - +
50A ALA* 3.1 50.3 + - + +
54A PHE* 4.7 5.5 - - + -
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Residues in contact with ARG 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 ASP* 2.9 22.6 + - - +
44A ASN* 2.6 51.2 + - - +
46A LEU* 1.3 77.8 - - - +
48A GLU* 1.3 78.3 + - + +
51A ALA* 3.4 25.7 - - + +
54A PHE* 5.8 4.5 - - - -
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Residues in contact with GLU 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 ASN* 3.0 20.2 + - - +
45A LEU* 3.9 5.6 - - + +
47A ARG* 1.3 97.5 + - - +
49A GLY* 1.3 62.1 + - - +
50A ALA 3.5 0.7 + - - -
51A ALA* 4.2 4.3 + - - +
52A HIS* 5.4 1.6 - - - -
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Residues in contact with GLY 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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14A VAL* 3.6 25.4 - - - +
15A ARG* 5.4 1.0 - - - -
18A ALA* 4.0 4.0 - - - +
45A LEU* 2.8 18.1 + - - -
48A GLU* 1.3 74.1 - - - +
50A ALA* 1.3 58.6 + - - +
51A ALA 4.0 0.4 - - - -
52A HIS* 3.2 19.1 + - - -
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Residues in contact with ALA 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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14A VAL* 4.1 5.2 - - + -
18A ALA* 3.9 20.4 - - + -
21A ILE* 4.7 4.3 - - + -
46A LEU* 3.1 39.3 + - + +
49A GLY* 1.3 80.3 - - - +
51A ALA* 1.3 60.9 + - - +
52A HIS* 3.3 9.0 - - - -
53A ALA* 3.0 23.1 + - - +
54A PHE* 3.7 11.2 - - + -
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Residues in contact with ALA 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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46A LEU 4.0 0.2 + - - -
47A ARG* 3.4 21.3 + - + +
48A GLU 4.2 4.3 + - - +
49A GLY 4.0 0.8 - - - -
50A ALA* 1.3 74.6 - - - +
52A HIS* 1.3 64.5 + - - +
53A ALA 3.2 0.5 + - - -
54A PHE* 3.4 29.9 + - + -
55A ALA* 3.7 9.9 + - - +
100A HIS* 5.8 0.3 - - - +
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Residues in contact with HIS 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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18A ALA* 3.5 22.9 - - + +
22A THR* 5.6 2.9 - - + +
48A GLU 5.4 1.5 + - - -
49A GLY 3.2 27.9 + - - -
50A ALA* 3.8 4.3 - - - -
51A ALA* 1.3 79.8 - - - +
53A ALA* 1.3 67.9 + - + +
55A ALA* 3.4 7.9 + - - +
56A GLN* 2.9 31.5 + - - +
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Residues in contact with ALA 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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18A ALA* 3.4 40.2 - - + +
21A ILE* 4.1 12.2 - - + +
22A THR* 3.5 15.8 - - + +
50A ALA* 3.0 14.8 + - + +
52A HIS* 1.3 82.4 - - + +
54A PHE* 1.3 58.7 + - - +
56A GLN* 3.9 1.5 - - - +
57A TYR* 2.9 30.8 + - - +
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Residues in contact with PHE 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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21A ILE* 3.9 20.2 - - + -
29A PHE* 3.8 24.1 - + + -
33A PHE* 3.8 32.1 - + - -
46A LEU* 4.7 11.4 - - + -
47A ARG* 5.6 3.4 - - - -
50A ALA* 3.7 16.8 - - + -
51A ALA* 3.8 27.1 - - + +
52A HIS 3.4 0.6 - - - -
53A ALA* 1.3 76.1 - - - +
55A ALA* 1.3 63.4 + - - +
57A TYR* 3.5 2.8 + - - +
58A ASN* 3.1 29.1 + - - +
100A HIS* 3.9 24.9 - - + +
101A LEU* 3.8 28.3 - - + -
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Residues in contact with ALA 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 ALA 3.7 7.6 + - - +
52A HIS* 3.4 9.6 + - - +
54A PHE* 1.3 81.4 - - - +
56A GLN* 1.3 62.2 + - - +
58A ASN* 3.3 1.7 + - - +
59A MET* 3.0 40.1 + - + +
100A HIS* 3.4 35.0 - - + +
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Residues in contact with GLN 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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22A THR* 4.3 12.1 - - + -
52A HIS* 2.9 21.8 + - - +
53A ALA* 3.9 7.2 - - - +
55A ALA* 1.3 75.0 - - - +
57A TYR* 1.3 58.5 + - - +
59A MET* 3.4 17.8 + - - +
60A ASP* 2.7 70.2 + - - +
78A GLU* 6.3 0.8 - - - +
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Residues in contact with TYR 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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21A ILE 3.5 19.1 - - - +
22A THR* 3.6 17.5 - - - +
24A ALA* 3.1 30.0 + - + -
25A PRO 3.1 22.4 + - - -
26A PRO* 3.9 7.8 - - - +
27A GLY 3.9 5.0 + - - -
29A PHE* 3.6 41.9 - + + +
53A ALA 2.9 18.0 + - - +
54A PHE 3.6 4.0 - - - +
56A GLN* 1.3 77.0 - - - +
58A ASN* 1.3 73.3 + - - +
60A ASP* 3.3 4.6 + - - +
61A GLN* 2.9 62.9 + - + +
63A THR* 4.9 1.6 - - - -
103A LYS* 5.2 2.0 - - - -
172A ARG* 4.3 3.9 + - - -
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Residues in contact with ASN 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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29A PHE* 6.1 0.4 - - - -
54A PHE 3.1 9.4 + - - +
55A ALA 3.3 0.4 + - - +
57A TYR* 1.3 84.1 - - - +
59A MET* 1.3 62.3 + - - +
62A PHE 3.2 17.0 + - - -
63A THR* 3.2 31.7 + - - +
76A ILE* 3.3 15.7 - - + +
98A PHE* 3.7 8.5 - - + -
100A HIS* 3.0 52.7 + - - +
103A LYS* 3.8 28.4 - - - +
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Residues in contact with MET 59 (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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55A ALA* 3.0 36.5 + - + +
56A GLN* 4.0 18.8 - - - +
58A ASN* 1.3 75.7 - - - +
60A ASP* 1.3 65.9 + - - +
62A PHE* 3.4 24.1 - - - -
76A ILE* 3.5 25.4 - - + +
77A THR* 3.8 9.1 - - - -
78A GLU* 3.8 32.6 + - + +
81A ASP* 3.6 24.2 - - - +
87A PHE* 3.9 16.4 - - + -
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Residues in contact with ASP 60 (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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22A THR* 5.1 9.4 - - - +
56A GLN* 2.7 60.7 + - - +
57A TYR* 3.7 5.4 + - - +
59A MET* 1.3 73.7 - - - +
61A GLN* 1.3 67.4 + - - +
62A PHE* 3.6 5.9 + - - -
174A ARG* 2.9 29.8 + - - +
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Residues in contact with GLN 61 (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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22A THR 5.1 4.0 + - - -
24A ALA 4.9 4.1 + - - -
26A PRO* 4.7 6.7 - - - +
57A TYR* 2.9 55.8 + - + +
60A ASP* 1.3 82.4 - - - +
62A PHE* 1.3 70.7 + - - +
63A THR* 3.2 10.3 + - - +
172A ARG* 3.5 53.5 + - - +
174A ARG* 3.7 29.5 + - - +
195A GLN* 4.7 11.1 + - - +
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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