Contacts of the helix formed by residues 50 - 66 (chain A) in PDB entry 3ADB
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 TYR 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A PHE* 3.5 38.9 - + + -
44A PRO* 6.1 0.6 - - + +
45A VAL* 3.6 23.6 - - + +
46A TRP* 4.7 2.7 - + - +
47A LYS* 3.0 39.8 + - + +
49A LYS* 1.3 90.8 - - + +
51A GLU* 1.3 67.8 + - - +
52A GLU 3.2 2.5 - - - -
53A PHE* 2.9 17.7 + - - +
54A ILE* 3.0 24.9 + - + +
30B ASP* 2.3 44.6 + - + +
31B VAL 4.6 1.0 + - - -
69B TYR* 3.7 34.8 - + - -
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Residues in contact with GLU 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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40A ARG* 3.0 35.5 + - - -
46A TRP* 2.6 42.4 + - + +
48A GLU* 3.3 30.6 + - - +
50A TYR* 1.3 78.9 - - - +
52A GLU* 1.3 56.7 + - - +
54A ILE* 3.7 8.2 - - - +
55A LYS* 2.9 32.1 + - - +
76C A 5.1 10.6 + - - +
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Residues in contact with GLU 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 GLU 4.8 1.0 + - - -
49A LYS 4.6 6.2 + - - +
50A TYR 3.0 1.0 + - - -
51A GLU* 1.3 78.1 - - - +
53A PHE* 1.3 59.0 + - - +
55A LYS* 3.8 6.6 - - - +
56A LYS* 3.0 37.5 + - + +
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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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39A ILE* 3.7 19.5 - - + -
43A PHE* 3.6 29.2 - + - -
49A LYS 5.1 0.6 + - - +
50A TYR 2.9 8.3 + - - +
52A GLU* 1.3 76.6 - - - +
54A ILE* 1.3 61.3 + - - +
56A LYS* 3.8 10.8 - - + +
57A SER* 2.6 58.0 + - - -
32B ILE* 3.9 7.0 - - + -
34B LEU* 5.7 1.1 - - + -
61B LEU* 4.5 5.6 - - + -
64B SER* 3.6 34.3 - - - -
65B ALA* 3.8 24.7 - - + -
68B ASN* 4.6 8.1 - - - +
69B TYR* 3.6 25.8 - + - +
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Residues in contact with ILE 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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36A SER* 3.5 30.3 - - - +
39A ILE* 4.2 10.5 - - + +
40A ARG* 3.5 50.9 - - + +
43A PHE* 4.0 18.6 - - + -
46A TRP* 5.2 1.3 - - + +
50A TYR* 3.0 27.0 + - + +
51A GLU* 3.7 22.2 - - - +
53A PHE* 1.3 76.7 - - - +
55A LYS* 1.3 58.0 + - - +
57A SER* 3.9 0.9 - - - -
58A THR* 2.8 36.7 + - - +
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Residues in contact with LYS 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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36A SER* 5.8 2.2 - - - -
51A GLU* 2.9 19.3 + - - +
52A GLU* 3.8 6.7 - - - +
54A ILE* 1.3 78.6 - - - +
56A LYS* 1.3 64.6 + - - +
58A THR* 3.8 4.1 - - - -
59A TYR* 3.0 65.2 + - + -
82A MSE 6.2 2.7 - - - -
85A ASP* 4.3 10.0 + - - -
74C C 4.2 10.5 - - - +
75C C 3.6 37.3 + - - +
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Residues in contact with LYS 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 GLU* 3.0 24.7 + - + +
53A PHE* 3.8 10.8 - - + +
55A LYS* 1.3 80.9 - - - +
57A SER* 1.3 63.6 + - - +
59A TYR* 3.3 7.8 + - - +
60A ARG* 3.1 24.6 + - + +
64B SER* 5.8 9.7 - - - -
67B LYS* 5.5 7.9 - - - +
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Residues in contact with SER 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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39A ILE* 3.1 27.4 - - - -
53A PHE* 2.6 53.6 + - - -
54A ILE 3.9 0.4 - - - -
56A LYS* 1.3 74.8 - - - +
58A THR* 1.3 60.7 + - - +
60A ARG* 3.3 7.6 + - - +
61A LEU* 3.1 25.5 + - - +
61B LEU* 3.9 12.6 - - - +
64B SER* 4.6 3.0 + - - -
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Residues in contact with THR 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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34A LEU* 5.5 1.1 - - + -
35A GLY* 3.8 11.0 + - - +
36A SER* 3.3 41.0 - - - +
39A ILE* 3.6 14.0 - - - +
54A ILE* 2.8 22.7 + - - +
55A LYS* 3.8 4.5 - - - -
57A SER* 1.3 76.3 - - - +
59A TYR* 1.3 67.4 + - + +
61A LEU* 3.4 7.7 + - + +
62A ILE* 3.1 39.7 + - + +
75A ASP* 4.6 2.9 - - - +
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Residues in contact with TYR 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 LYS* 3.0 48.7 + - + +
56A LYS* 3.8 6.3 - - - +
58A THR* 1.3 81.2 - - + +
60A ARG* 1.3 61.2 + - - +
62A ILE* 3.5 5.6 + - + +
63A ASP* 2.9 30.0 + - - +
82A MSE 4.1 14.7 + - - +
85A ASP* 3.4 39.8 + - + +
86A LEU* 3.7 29.6 - - + +
89A ILE* 3.9 17.4 - - + +
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Residues in contact with ARG 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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56A LYS* 3.1 15.2 + - + +
57A SER* 3.6 10.1 - - - +
58A THR 3.3 0.2 - - - -
59A TYR* 1.3 75.8 - - - +
61A LEU* 1.3 59.6 + - - +
63A ASP* 3.2 9.6 + - + +
64A SER* 2.9 30.4 + - - -
60B ARG* 3.2 61.2 + - - +
64B SER* 5.5 7.7 - - - -
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Residues in contact with LEU 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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34A LEU* 3.6 26.5 - - + -
35A GLY 6.0 0.4 - - - +
38A LEU* 4.9 9.2 - - + -
39A ILE* 3.9 28.3 - - + -
57A SER 3.1 11.6 + - - +
58A THR* 3.7 10.1 - - + +
59A TYR 3.3 0.2 - - - -
60A ARG* 1.3 76.5 - - - +
62A ILE* 1.3 64.1 + - + +
64A SER* 3.6 5.9 + - - +
65A ALA* 3.0 26.7 + - - +
39B ILE* 3.7 31.9 - - + -
53B PHE* 4.3 6.3 - - + -
57B SER* 4.1 15.0 - - - +
61B LEU* 4.3 17.5 - - + -
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Residues in contact with ILE 62 (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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2A LEU* 4.0 16.4 - - + -
34A LEU* 3.7 28.5 - - + +
58A THR* 3.1 33.5 + - + +
59A TYR* 3.9 7.4 - - + +
61A LEU* 1.3 76.0 - - - +
63A ASP* 1.3 56.9 + - - +
65A ALA* 3.8 1.1 - - - +
66A LEU* 2.9 30.2 + - + +
71A VAL* 3.7 18.9 - - + +
73A VAL* 4.0 16.2 - - + -
86A LEU* 3.8 25.4 - - + -
89A ILE* 4.3 17.7 - - + -
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Residues in contact with ASP 63 (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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59A TYR 2.9 19.8 + - - +
60A ARG* 3.2 12.4 + - - +
62A ILE* 1.3 80.3 - - - +
64A SER* 1.3 64.7 + - - +
65A ALA 3.3 0.3 + - - -
66A LEU* 3.4 6.8 + - - +
67A LYS* 3.7 13.2 + - - +
89A ILE* 4.0 18.9 - - + +
92A LYS* 2.7 29.9 + - - +
93A TYR* 2.9 38.5 + - - -
60B ARG* 5.8 0.3 + - - -
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Residues in contact with SER 64 (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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60A ARG 2.9 19.6 + - - -
61A LEU* 3.6 5.4 + - - +
63A ASP* 1.3 79.3 + - - +
65A ALA* 1.3 61.4 + - - +
66A LEU 3.4 0.2 - - - -
67A LYS* 3.8 27.8 + - - +
68A ASN* 3.9 8.3 + - - -
53B PHE* 3.3 26.0 - - - -
57B SER* 4.5 2.8 + - - -
60B ARG* 4.0 27.2 + - - -
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Residues in contact with ALA 65 (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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32A ILE* 4.1 9.2 - - + -
34A LEU* 4.0 11.0 - - + -
61A LEU 3.0 19.5 + - - +
62A ILE 3.8 2.9 - - - +
64A SER* 1.3 75.8 - - - +
66A LEU* 1.3 57.8 + - - +
67A LYS 3.0 7.5 + - - -
68A ASN* 3.0 2.3 + - - +
69A TYR* 2.8 34.2 + - + +
71A VAL* 3.8 15.9 - - + -
53B PHE* 3.6 22.2 - - + -
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Residues in contact with LEU 66 (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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0A HIS* 2.5 34.4 + - + +
1A MSE 3.8 16.2 - - - +
2A LEU* 3.8 29.2 - - + -
62A ILE 2.9 17.3 + - - +
63A ASP* 3.4 6.2 + - - +
65A ALA* 1.3 76.5 - - - +
67A LYS* 1.3 55.3 + - - +
68A ASN 3.2 0.7 - - - -
69A TYR 3.6 15.0 - - - +
71A VAL* 3.7 11.9 - - + +
89A ILE* 3.9 18.8 - - + +
90A ALA* 3.7 29.8 - - - -
93A TYR* 4.4 6.4 - - + -
95A LYS* 4.0 17.2 - - + +
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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
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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