Contacts of the helix formed by residues 50 - 66 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A SER* 5.1 1.4 + - - -
29A ILE 5.0 0.9 + - - -
30A ASP* 2.8 37.9 + - + -
31A VAL 4.7 1.6 + - - -
69A TYR* 3.6 32.8 - + - -
43B PHE* 3.6 39.5 - + + -
44B PRO* 5.5 1.3 - - + +
45B VAL* 3.4 28.4 - - - +
46B TRP* 4.5 2.5 - + - +
47B LYS* 3.0 47.9 + - + +
49B LYS* 1.3 85.9 - - + +
51B GLU* 1.3 59.8 + - - +
52B GLU 3.2 2.9 - - - -
53B PHE* 2.8 26.3 + - - +
54B ILE* 3.0 25.2 + - + -
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ARG* 2.7 39.6 + - - -
46B TRP* 2.7 33.8 + - + +
48B GLU* 3.3 30.6 + - - +
50B TYR* 1.3 76.1 - - - +
52B GLU* 1.3 56.0 + - - +
54B ILE* 3.7 9.0 - - - +
55B LYS* 3.0 31.7 + - - +
75D C 3.2 29.3 - - - +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B GLU 4.8 0.4 + - - -
49B LYS 4.5 7.6 + - - +
50B TYR 2.9 3.2 + - - -
51B GLU* 1.3 73.4 - - - +
53B PHE* 1.3 64.5 + - - +
55B LYS* 4.1 3.3 - - - +
56B LYS* 3.1 31.2 + - + +
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Residues in contact with PHE 53 (chain B).
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 15.3 - - + -
34A LEU* 5.6 0.4 - - + -
61A LEU* 4.3 7.2 - - + -
64A SER* 3.3 36.1 - - - -
65A ALA* 3.6 24.7 - - + -
68A ASN* 5.1 6.3 - - - +
69A TYR* 3.9 30.5 - + + +
39B ILE* 4.0 17.7 - - + -
43B PHE* 3.9 12.3 - + - -
49B LYS 5.1 0.4 + - - +
50B TYR 2.8 9.0 + - - +
52B GLU* 1.3 76.6 - - - +
54B ILE* 1.3 58.6 + - - +
56B LYS* 3.4 4.0 + - + -
57B SER* 2.6 62.7 + - - -
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Residues in contact with ILE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B SER* 3.6 29.2 - - - +
39B ILE* 4.3 9.8 - - + +
40B ARG* 3.4 55.0 - - + +
43B PHE* 4.0 18.2 - - + -
46B TRP* 5.2 1.6 - - + +
50B TYR* 3.0 30.6 + - + +
51B GLU* 3.7 22.0 - - - +
53B PHE* 1.3 77.7 - - - +
55B LYS* 1.3 56.5 + - - +
57B SER* 3.9 1.0 - - - -
58B THR* 2.9 35.3 + - - +
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Residues in contact with LYS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B SER* 5.6 2.7 - - - -
40B ARG* 6.4 0.2 - - - +
51B GLU* 3.0 19.0 + - - +
52B GLU* 4.1 3.6 - - - +
54B ILE* 1.3 79.3 - - - +
56B LYS* 1.3 63.0 + - - +
58B THR* 3.5 3.0 + - - -
59B TYR* 3.1 73.1 + - + -
82B MSE 5.6 1.1 - - - -
85B ASP* 4.0 6.7 + - - -
74D C 2.7 49.5 + - - +
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Residues in contact with LYS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLU* 3.1 25.8 + - + +
53B PHE* 3.9 4.5 - - + +
55B LYS* 1.3 77.7 - - - +
57B SER* 1.3 62.9 + - - +
59B TYR* 3.4 8.3 + - + +
60B ARG* 3.2 54.7 + - + +
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Residues in contact with SER 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 4.1 12.3 - - - +
64A SER* 4.5 2.5 + - - -
39B ILE* 3.2 24.2 - - - -
53B PHE* 2.6 55.8 + - - -
54B ILE 3.9 0.4 - - - -
56B LYS* 1.3 72.8 - - - +
58B THR* 1.3 63.7 + - - +
60B ARG* 3.3 10.8 + - - +
61B LEU* 3.3 25.1 + - - +
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Residues in contact with THR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 5.6 0.9 - - + -
35B GLY* 3.8 9.9 + - - +
36B SER* 3.1 43.7 + - - +
39B ILE* 3.7 14.2 - - - +
54B ILE 2.9 22.0 + - - -
55B LYS* 3.9 4.9 - - - -
57B SER* 1.3 76.9 - - - +
59B TYR* 1.3 67.6 + - + +
61B LEU* 3.7 6.6 + - - +
62B ILE* 3.1 41.0 + - + +
73B VAL* 6.0 0.2 - - + -
75B ASP* 4.6 3.4 - - - +
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Residues in contact with TYR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LYS* 3.1 60.8 + - + +
56B LYS* 3.8 7.0 - - - +
57B SER 3.2 0.2 - - - -
58B THR* 1.3 86.6 - - + +
60B ARG* 1.3 59.9 + - - +
62B ILE* 3.4 7.4 + - + +
63B ASP* 2.8 30.5 + - - +
77B ASN* 5.7 0.5 + - - -
82B MSE 4.4 12.6 + - - +
85B ASP* 4.1 27.6 + - + +
86B LEU* 3.9 27.9 - - + +
89B ILE* 4.2 11.6 - - + +
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Residues in contact with ARG 60 (chain B).
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* 3.2 61.0 + - - +
63A ASP* 5.8 0.2 + - - -
64A SER* 4.0 27.6 + - - -
67A LYS* 5.7 4.4 - - - +
56B LYS* 3.2 47.2 + - + +
57B SER* 3.3 11.6 + - - +
59B TYR* 1.3 74.6 - - + +
61B LEU* 1.3 62.0 + - + +
63B ASP* 3.6 5.2 - - - +
64B SER* 2.8 34.9 + - - -
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 3.7 30.5 - - + -
53A PHE* 4.5 5.4 - - + -
57A SER* 3.9 18.4 - - - +
61A LEU* 4.3 24.2 - - + -
34B LEU* 3.6 29.6 - - + +
38B LEU* 4.9 6.7 - - + -
39B ILE* 4.4 14.4 - - + -
57B SER 3.3 13.2 + - - +
58B THR* 3.9 8.7 - - - +
60B ARG* 1.3 79.2 - - + +
62B ILE* 1.3 59.6 + - - +
64B SER* 3.5 6.4 + - - +
65B ALA* 2.9 33.1 + - - +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 4.3 15.3 - - + -
34B LEU* 3.7 28.0 - - + +
58B THR* 3.1 35.4 + - + +
59B TYR* 3.7 7.4 - - + +
60B ARG 3.2 0.2 - - - -
61B LEU* 1.3 75.8 - - - +
63B ASP* 1.3 62.8 + - - +
65B ALA* 3.7 1.4 - - - +
66B LEU* 3.0 24.2 + - + +
71B VAL* 4.2 15.8 - - + +
73B VAL* 4.0 17.0 - - + -
86B LEU* 3.9 23.3 - - + -
89B ILE* 3.8 21.1 - - + -
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Residues in contact with ASP 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B TYR 2.8 19.8 + - - +
60B ARG* 3.2 7.4 + - - +
62B ILE* 1.3 79.8 - - - +
64B SER* 1.3 65.8 + - - +
65B ALA 3.2 0.2 + - - -
66B LEU 3.4 5.0 + - - -
67B LYS* 3.8 6.2 + - - +
89B ILE* 4.0 18.8 - - + +
92B LYS* 2.9 35.9 + - - +
93B TYR* 2.5 42.8 + - - -
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Residues in contact with SER 64 (chain B).
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* 3.6 21.6 - - - -
56A LYS* 5.8 9.4 - - - -
57A SER* 4.6 4.2 + - - -
60A ARG* 5.5 8.1 - - - -
60B ARG 2.8 20.7 + - - -
61B LEU* 3.5 8.5 + - - +
63B ASP* 1.3 79.1 + - - +
65B ALA* 1.3 62.5 + - - +
67B LYS* 3.6 30.5 - - - +
68B ASN* 4.0 5.7 + - - -
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Residues in contact with ALA 65 (chain B).
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* 3.8 20.9 - - + -
32B ILE* 4.2 8.5 - - + -
34B LEU* 3.9 11.7 - - + -
61B LEU 2.9 19.5 + - - +
62B ILE 3.7 3.4 - - - +
63B ASP 3.1 0.2 - - - -
64B SER* 1.3 75.2 - - - +
66B LEU* 1.3 57.5 + - - +
67B LYS 2.9 7.9 + - - -
68B ASN 3.0 2.6 + - - -
69B TYR* 2.8 32.3 + - + +
71B VAL* 3.8 17.5 - - + -
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B HIS* 3.2 20.2 + - + -
1B MSE 3.6 28.0 - - - +
2B LEU* 3.6 22.9 - - + -
62B ILE* 3.0 17.1 + - + +
63B ASP 3.4 5.3 + - - +
65B ALA* 1.3 75.9 - - - +
67B LYS* 1.3 60.3 + - - +
68B ASN 3.3 0.7 - - - -
69B TYR 3.5 11.9 - - - +
71B VAL* 3.8 12.1 - - + +
89B ILE* 4.0 15.7 - - + +
90B ALA* 3.8 29.6 - - - -
93B TYR* 4.2 11.8 - - + -
95B LYS* 4.2 17.7 - - + -
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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