Contacts of the helix formed by residues 51 - 68 (chain T) in PDB entry 2BTO
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 CYS 51 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A VAL* 3.9 12.1 - - + -
48T ALA 3.7 8.7 - - - +
49T GLU 3.1 2.7 - - - -
50T TRP* 1.3 79.5 - - + +
52T GLY* 1.3 69.6 + - - +
53T PRO* 4.0 2.2 - - - -
54T CYS* 2.1 65.9 + - - +
55T LYS* 3.5 13.2 + - - +
94T ILE* 3.2 37.0 - - + -
95T PRO* 3.9 2.0 - - - -
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Residues in contact with GLY 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A VAL* 4.7 1.4 - - - +
50T TRP 3.8 3.8 + - - -
51T CYS* 1.3 74.7 - - - +
53T PRO* 1.3 69.7 - - - +
54T CYS 3.1 0.5 + - - -
55T LYS* 3.1 16.9 + - - +
56T MET* 3.4 9.0 + - - +
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Residues in contact with PRO 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL 3.6 19.1 - - - +
180A SER* 3.1 30.5 - - - +
181A SER* 3.9 8.5 - - - +
182A VAL* 4.2 7.6 - - + -
51T CYS* 3.7 5.8 - - - -
52T GLY* 1.3 88.7 - - - +
54T CYS* 1.3 60.3 + - - +
55T LYS 3.4 0.2 - - - -
56T MET* 3.2 28.2 - - + +
57T ILE* 3.6 5.9 + - - +
95T PRO* 3.8 12.5 - - + +
112T ALA* 3.4 16.1 - - + +
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Residues in contact with CYS 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45T ASP* 5.0 3.1 - - - +
47T TRP* 3.9 19.8 - - + -
48T ALA 3.7 17.7 - - - +
51T CYS* 2.1 54.6 - - + +
52T GLY 3.1 0.4 + - - -
53T PRO* 1.3 73.2 - - - +
55T LYS* 1.3 66.7 + - - +
57T ILE* 3.4 18.4 + - - +
58T ALA* 3.4 8.8 + - - +
94T ILE* 3.8 9.4 - - - -
95T PRO* 3.5 31.4 - - + -
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Residues in contact with LYS 55 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47T TRP* 5.4 6.7 - - + -
48T ALA 5.1 3.4 - - - +
49T GLU* 3.8 50.8 + - - +
51T CYS 3.5 7.8 + - - +
52T GLY* 3.1 12.0 + - - +
54T CYS* 1.3 77.4 - - - +
56T MET* 1.3 62.5 + - - +
57T ILE 3.3 0.5 + - - -
58T ALA* 3.4 9.6 + - - +
59T PRO* 3.3 18.9 - - - +
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Residues in contact with MET 56 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL 5.6 1.3 - - - +
180A SER* 5.5 5.8 - - - -
52T GLY 3.4 4.4 + - - +
53T PRO* 3.2 28.7 + - + +
55T LYS* 1.3 79.4 - - - +
57T ILE* 1.3 57.0 + - + +
59T PRO* 3.6 11.8 - - - +
60T ILE* 3.9 10.0 - - - +
112T ALA* 3.5 31.2 - - + -
113T LEU 5.4 0.9 - - - +
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Residues in contact with ILE 57 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45T ASP* 4.0 12.6 - - - +
53T PRO 3.7 6.3 - - - +
54T CYS 3.4 13.5 - - - +
56T MET* 1.3 78.1 - - + +
58T ALA* 1.3 60.2 + - - +
59T PRO* 3.3 2.2 - - - -
60T ILE* 3.0 13.4 + - + +
61T LEU* 2.8 46.3 + - + +
95T PRO* 3.8 29.8 - - + -
97T LEU* 4.5 15.5 - - + -
111T GLY 5.2 1.6 - - - +
112T ALA* 3.8 12.3 - - + -
113T LEU* 3.7 42.4 - - + +
118T LEU* 6.3 0.9 - - + -
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Residues in contact with ALA 58 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47T TRP* 6.2 4.5 - - + -
54T CYS 3.4 11.1 + - - +
55T LYS* 3.4 12.5 + - - +
57T ILE* 1.3 78.5 - - - +
59T PRO* 1.4 67.3 - - + +
60T ILE 3.4 0.2 + - - -
61T LEU* 3.5 9.9 + - - +
62T ASP* 3.0 21.2 + - - +
76T LYS* 3.8 25.8 + - - +
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Residues in contact with PRO 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55T LYS 3.3 16.2 - - - +
56T MET 3.6 8.7 - - - +
57T ILE 3.5 2.7 - - - -
58T ALA* 1.4 91.4 - - + +
60T ILE* 1.3 63.0 + - + +
62T ASP* 3.6 21.7 + - - +
63T GLU* 3.9 11.5 + - - +
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Residues in contact with ILE 60 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56T MET 3.9 18.8 - - - +
57T ILE* 3.0 18.7 + - + +
59T PRO* 1.3 78.1 - - + +
61T LEU* 1.3 63.5 + - - +
63T GLU* 3.2 23.5 + - - +
64T ILE* 3.2 12.6 - - + +
113T LEU* 4.7 7.2 - - + +
114T SER* 4.8 1.8 - - - -
115T LYS* 3.6 54.5 - - + +
118T LEU* 4.1 18.4 - - + -
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Residues in contact with LEU 61 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43T LEU* 4.3 13.0 - - + -
45T ASP* 3.1 34.5 - - + +
57T ILE* 2.8 38.1 + - + +
58T ALA* 4.0 4.7 - - - +
59T PRO 3.4 0.2 - - - -
60T ILE* 1.3 73.1 - - - +
62T ASP* 1.3 62.5 + - - +
64T ILE* 3.5 9.6 + - + +
65T ALA* 3.2 20.4 + - - +
74T VAL* 4.2 28.7 - - + +
76T LYS* 3.8 18.2 - - - +
97T LEU* 4.0 24.9 - - + -
118T LEU* 4.8 9.2 - - + -
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Residues in contact with ASP 62 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23T ILE* 4.8 18.9 - - - +
58T ALA 3.0 17.3 - - - +
59T PRO* 3.7 14.9 - - - +
60T ILE 3.2 0.8 - - - -
61T LEU* 1.3 79.1 - - - +
63T GLU* 1.3 58.8 + - + +
65T ALA* 3.3 12.9 + - - +
66T ASP* 2.8 24.7 - - - +
76T LYS* 5.2 2.9 + - - -
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Residues in contact with GLU 63 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59T PRO 3.9 12.4 + - - +
60T ILE* 3.2 16.1 + - + +
62T ASP* 1.3 78.8 - - + +
64T ILE* 1.3 62.9 + - + +
66T ASP* 3.2 11.2 + - - +
67T GLU* 3.1 47.3 + - - +
115T LYS* 4.9 26.2 + - + +
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Residues in contact with ILE 64 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43T LEU* 5.2 4.7 - - + -
60T ILE* 3.2 25.1 - - + +
61T LEU* 3.5 9.8 + - + +
62T ASP 3.3 0.6 - - - -
63T GLU* 1.3 77.2 - - + +
65T ALA* 1.3 61.5 + - - +
66T ASP 3.1 5.4 - - - -
67T GLU* 4.8 2.5 - - - +
68T TYR* 3.1 53.2 + - + +
72T LEU* 3.8 23.8 - - + -
74T VAL* 4.1 8.6 - - + +
115T LYS* 4.8 12.1 - - + +
118T LEU* 3.9 23.8 - - + -
119T LYS* 5.0 6.1 - - + -
122T LEU* 4.0 16.4 - - + -
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Residues in contact with ALA 65 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23T ILE* 5.7 8.5 - - - +
61T LEU 3.2 13.2 + - - +
62T ASP* 3.4 14.8 - - - +
63T GLU 3.3 0.2 - - - -
64T ILE* 1.3 76.8 - - - +
66T ASP* 1.3 53.9 + - - +
68T TYR 4.6 0.8 - - - -
69T GLN* 2.8 31.0 + - - -
72T LEU 5.4 4.2 - - - +
74T VAL* 4.2 21.1 - - + +
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Residues in contact with ASP 66 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62T ASP 2.8 18.2 - - - +
63T GLU* 3.2 9.3 + - - +
64T ILE 3.1 0.4 - - - -
65T ALA* 1.3 81.8 - - - +
67T GLU* 1.3 64.9 + - + +
68T TYR 3.2 5.4 + - - -
69T GLN* 3.3 26.5 + - - +
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Residues in contact with GLU 67 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63T GLU* 3.1 36.6 + - - +
64T ILE* 3.5 2.4 + - - +
66T ASP* 1.3 80.9 - - + +
68T TYR* 1.3 75.3 + - + +
69T GLN 3.5 1.4 + - - -
71T LYS* 5.7 2.3 - - - +
119T LYS* 2.9 36.5 + - - +
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Residues in contact with TYR 68 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64T ILE* 3.1 46.8 + - + +
65T ALA 4.8 1.6 - - - -
67T GLU* 1.3 88.8 - - + +
69T GLN* 1.3 57.7 + - - +
71T LYS* 3.9 23.3 - - + -
72T LEU* 2.8 58.0 + - + +
119T LYS* 3.3 42.5 + - + +
122T LEU* 4.3 20.9 - - + -
123T ASP* 3.2 24.7 + - - -
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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