Contacts of the helix formed by residues 48 - 69 (chain T) in PDB entry 1I94
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 LYS 48 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43T LEU* 3.6 13.8 + - + +
44T ALA* 4.8 0.7 - - - -
46T GLU* 3.9 4.2 - - + +
47T GLY* 1.3 73.1 - - - +
49T ALA* 1.3 71.3 + - - +
50T GLU 3.8 0.4 - - - -
51T GLU* 4.3 17.7 - - + -
52T ALA* 3.6 16.8 + - - +
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Residues in contact with ALA 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47T GLY 2.5 11.9 + - - +
48T LYS* 1.3 77.4 - - - +
50T GLU* 1.3 68.5 + - + +
52T ALA* 3.1 10.6 + - - +
53T LEU* 3.6 4.9 + - - +
96T GLY* 4.2 22.0 - - - +
97T ALA 4.6 6.7 - - - +
98T PRO* 5.7 2.0 - - + -
99T LEU* 5.3 8.5 - - + +
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Residues in contact with GLU 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49T ALA* 1.3 76.5 - - + +
51T GLU* 1.3 54.9 + - - +
52T ALA 2.5 1.9 + - - -
53T LEU* 2.5 34.7 + - - +
54T LYS* 2.9 13.7 + - + -
99T LEU* 5.6 6.8 - - + +
100T ILE* 5.1 17.4 - - + +
1013T WO2 5.6 6.7 - - - +
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Residues in contact with GLU 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43T LEU* 4.8 6.3 - - + +
48T LYS* 4.1 19.9 + - + -
49T ALA 3.4 0.4 + - - -
50T GLU* 1.3 76.2 - - - +
52T ALA* 1.3 58.1 + - - +
54T LYS* 4.2 9.1 - - - +
55T ILE* 3.6 20.3 + - - +
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Residues in contact with ALA 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40T ALA* 3.7 13.3 - - - +
43T LEU* 3.4 26.9 - - + -
44T ALA* 3.4 22.2 - - + +
48T LYS 3.6 4.6 + - - +
49T ALA 3.1 10.6 + - - +
50T GLU 2.5 5.9 + - - -
51T GLU* 1.3 76.2 - - - +
53T LEU* 1.3 58.8 + - - +
55T ILE* 3.9 4.0 - - - +
56T MET* 3.1 22.9 + - - +
88T VAL* 5.7 3.9 - - + +
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Residues in contact with LEU 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49T ALA 3.6 4.8 + - - +
50T GLU* 2.5 18.6 + - - +
52T ALA* 1.3 71.7 - - - +
54T LYS* 1.3 66.5 + - - +
56T MET* 2.7 25.3 + - - +
57T ARG* 3.0 7.8 + - - +
100T ILE* 4.8 9.2 - - + -
101T GLY* 5.0 4.0 - - - +
102T GLY* 4.7 19.7 - - - +
103T GLY 5.2 5.2 + - - +
104T LEU* 6.5 1.1 - - + -
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Residues in contact with LYS 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50T GLU* 2.9 14.3 + - + +
51T GLU* 4.2 9.6 - - - +
53T LEU* 1.3 78.4 - - - +
55T ILE* 1.3 62.6 + - - +
57T ARG* 3.4 18.0 + - - +
58T LYS* 3.5 5.5 + - - +
100T ILE* 5.8 1.8 - - - +
1013T WO2 3.7 34.8 + - - +
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Residues in contact with ILE 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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36T LEU* 5.1 3.7 - - + +
39T LYS* 5.6 1.6 - - + -
40T ALA* 4.2 19.1 - - + +
51T GLU 3.6 16.5 + - - +
52T ALA 4.1 3.8 - - - +
53T LEU 3.1 0.8 - - - -
54T LYS* 1.3 76.5 - - - +
56T MET* 1.3 67.0 - - - +
58T LYS* 3.3 7.9 + - - +
59T ALA* 2.7 24.7 + - - +
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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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40T ALA* 4.2 7.8 - - + +
52T ALA 3.1 16.7 + - - +
53T LEU* 2.7 23.6 + - - +
55T ILE* 1.3 68.9 - - - +
57T ARG* 1.3 54.3 + - - +
59T ALA* 2.7 11.0 + - - +
60T GLU* 2.4 39.1 + - + -
88T VAL* 5.9 6.7 - - + -
103T GLY* 5.5 10.8 - - - +
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Residues in contact with ARG 57 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A U 4.1 22.0 - - - +
199A C 4.2 12.8 - - - +
53T LEU 3.0 5.9 + - - +
54T LYS* 3.5 11.7 - - - +
56T MET* 1.3 76.9 - - - +
58T LYS* 1.3 55.0 + - - +
60T GLU* 3.1 7.7 + - - +
61T SER* 2.6 36.9 + - - -
102T GLY* 6.2 0.9 - - - -
103T GLY* 5.4 5.8 - - - +
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Residues in contact with LYS 58 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36T LEU* 5.4 2.5 - - + -
54T LYS 3.5 7.1 + - - +
55T ILE* 3.3 10.7 + - - +
56T MET 3.2 0.6 - - - -
57T ARG* 1.3 79.4 - - - +
59T ALA* 1.3 69.8 + - - +
61T SER* 2.8 13.0 + - - -
62T LEU* 2.9 13.4 + - - +
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Residues in contact with ALA 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T ILE* 5.2 2.7 - - - +
36T LEU* 4.0 38.7 - - + +
37T SER* 4.2 9.0 - - - +
40T ALA* 4.6 1.8 - - + -
55T ILE 2.7 13.4 + - - +
56T MET* 2.7 17.6 + - - +
58T LYS* 1.3 75.6 - - - +
60T GLU* 1.3 65.7 + - - +
61T SER 2.9 0.2 + - - -
62T LEU* 3.0 14.6 + - - +
63T ILE* 3.2 9.9 + - - +
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Residues in contact with GLU 60 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A U 5.1 2.2 - - - +
199A C 3.9 16.6 + - - +
56T MET* 2.4 16.9 + - + +
57T ARG* 3.1 15.0 - - - +
59T ALA* 1.3 71.0 - - - +
61T SER* 1.3 66.8 + - - +
63T ILE* 2.9 20.8 - - - +
64T ASP* 3.4 3.3 + - - +
81T LYS* 6.0 9.5 - - + +
103T GLY* 6.2 2.2 - - - -
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Residues in contact with SER 61 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A C 3.2 33.1 + - - -
200A C 3.5 13.6 - - - +
57T ARG 2.6 15.0 + - - -
58T LYS* 2.8 14.3 + - - -
60T GLU* 1.3 69.2 - - - +
62T LEU* 1.3 67.0 + - - -
63T ILE 2.5 2.6 + - - -
64T ASP* 2.8 16.8 + - - +
65T LYS* 2.9 11.6 + - - -
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Residues in contact with LEU 62 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29T LYS 5.6 1.8 - - - +
32T ALA* 5.7 3.4 - - + -
33T ILE* 4.6 19.1 - - + +
36T LEU* 5.6 2.9 - - + -
58T LYS 2.9 9.2 + - - +
59T ALA* 3.2 13.7 - - - +
61T SER* 1.3 75.5 - - - +
63T ILE* 1.3 67.9 + - - +
65T LYS* 3.0 9.0 + - - +
66T ALA* 2.6 24.3 + - - +
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Residues in contact with ILE 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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33T ILE* 5.0 10.9 - - + +
59T ALA 3.2 4.4 + - - +
60T GLU* 2.9 17.9 - - - +
61T SER 2.5 3.4 + - - -
62T LEU* 1.3 82.4 - - - +
64T ASP* 1.3 53.4 + - - +
65T LYS 2.6 8.5 + - - -
66T ALA* 2.7 13.3 + - - +
67T ALA* 2.7 16.6 + - - +
72T LEU* 5.7 0.6 - - - +
77T ALA* 5.0 7.4 - - - +
80T ARG* 4.8 18.4 - - + -
81T LYS* 5.4 7.0 - - + +
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Residues in contact with ASP 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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178A G 6.1 0.9 - - - +
199A C 3.9 11.7 - - + +
200A C 3.6 32.6 + - - +
60T GLU 4.4 1.3 - - - +
61T SER 2.8 8.9 + - - +
63T ILE* 1.3 77.1 - - - +
65T LYS* 1.3 50.5 + - - +
67T ALA* 3.4 13.4 - - - +
68T LYS* 2.8 29.6 + - - +
77T ALA* 4.6 6.6 - - + +
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Residues in contact with LYS 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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170A C 5.6 1.4 + - - -
171A C 5.1 14.4 - - - +
200A C 4.6 11.8 - - - -
201A A 5.1 7.6 - - - +
61T SER* 2.9 10.9 + - - +
62T LEU* 3.2 14.8 - - - +
63T ILE 2.6 5.7 + - - -
64T ASP* 1.3 71.3 - - - +
66T ALA* 1.3 67.2 + - - +
67T ALA 2.9 0.9 - - - -
68T LYS* 3.1 20.0 + - - +
69T GLY 4.0 1.6 + - - -
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Residues in contact with ALA 66 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29T LYS* 4.0 27.1 - - + +
30T LYS* 5.1 2.5 - - - +
33T ILE* 5.9 2.9 - - + -
62T LEU 2.6 19.0 + - - +
63T ILE* 3.5 4.9 - - - +
65T LYS* 1.3 74.1 - - - +
67T ALA* 1.3 61.8 + - - +
69T GLY* 3.6 4.9 + - - -
70T SER 4.0 0.2 + - - -
71T THR* 3.0 41.6 + - - -
72T LEU* 4.4 5.4 - - + +
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Residues in contact with ALA 67 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63T ILE 2.7 15.5 + - - +
64T ASP* 3.4 8.7 - - - +
66T ALA* 1.3 74.6 - - - +
68T LYS* 1.3 66.2 + - - +
69T GLY 3.1 6.9 + - - +
72T LEU* 4.4 4.9 - - + +
73T HIS* 3.5 34.0 - - - +
77T ALA* 3.4 31.6 - - + -
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Residues in contact with LYS 68 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A C 4.5 13.7 - - - +
201A A 5.8 5.8 - - - +
202A A 5.8 3.8 - - - +
218A U 4.1 15.6 + - - -
64T ASP 2.8 17.5 + - - +
65T LYS* 3.1 16.4 + - - +
67T ALA* 1.3 73.9 - - - +
69T GLY* 1.3 61.7 + - - +
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Residues in contact with GLY 69 (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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65T LYS 4.0 1.6 + - - -
66T ALA 3.6 4.8 + - - -
67T ALA 3.1 7.5 + - - +
68T LYS* 1.3 84.5 - - - +
70T SER* 1.3 62.9 + - - +
73T HIS* 4.1 7.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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