Contacts of the helix formed by residues 45 - 64 (chain E) in PDB entry 3UF2
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 ASP 45 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E LEU* 3.5 2.7 - - + +
44E LYS* 1.3 85.7 - - + +
46E PRO* 1.3 75.1 - - - +
47E VAL* 3.2 19.1 + - - +
48E CYS* 3.4 19.5 + - + +
49E TYR* 3.0 24.0 + - - +
137E LYS* 2.9 34.1 + - - -
142E SER* 4.2 12.3 - - - +
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Residues in contact with PRO 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LYS 3.1 10.3 - - - +
45E ASP* 1.3 89.3 - - - +
47E VAL* 1.3 64.6 + - + +
49E TYR* 3.6 8.1 - - + +
50E LEU* 3.4 29.4 + - + +
123E GLU* 6.1 0.9 - - - +
127E LEU* 5.8 2.0 - - + -
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Residues in contact with VAL 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E ASP* 3.2 11.2 + - - +
46E PRO* 1.3 78.1 - - + +
48E CYS* 1.3 67.4 + - - +
50E LEU* 3.0 16.7 + - - +
51E LYS* 3.1 15.9 + - + +
127E LEU* 4.9 7.0 - - + -
134E ILE* 3.7 46.0 - - + +
135E PHE* 3.8 16.0 - - + -
137E LYS* 3.9 24.2 - - + +
139E CYS* 4.7 0.7 - - - -
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Residues in contact with CYS 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E LEU* 3.6 13.0 - - + +
45E ASP* 3.2 11.6 + - + +
47E VAL* 1.3 79.0 - - - +
49E TYR* 1.3 61.6 + - - +
51E LYS* 3.7 2.0 - - - +
52E LYS 3.3 17.3 + - - -
137E LYS* 3.9 17.5 - - - -
139E CYS* 2.0 60.3 - - + -
142E SER* 3.5 23.1 - - - -
143E PHE* 3.7 11.5 - - + -
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Residues in contact with TYR 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E PHE* 3.3 25.6 - + - -
38E VAL* 3.5 38.1 + - + +
40E GLN* 3.8 52.2 + - + +
43E LEU* 3.7 21.3 - - + +
44E LYS 5.5 0.2 - - - +
45E ASP 3.0 17.1 + - - +
46E PRO* 3.6 9.2 - - + +
48E CYS* 1.3 79.1 - - - +
50E LEU* 1.3 73.4 + - + +
52E LYS* 3.7 1.2 + - - +
53E ALA* 3.0 38.7 + - + +
120E VAL* 4.9 6.2 - - + +
123E GLU* 5.3 6.1 - - - -
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Residues in contact with LEU 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E PRO* 3.5 14.8 - - + +
47E VAL 3.0 7.6 + - - +
49E TYR* 1.3 88.8 - - + +
51E LYS* 1.3 59.0 + - - +
53E ALA* 3.9 2.4 - - - +
54E PHE* 2.9 32.4 + - - +
91E PHE* 4.1 3.3 - - - -
120E VAL* 4.1 22.8 - - + +
123E GLU* 4.1 32.8 - - + +
124E THR* 4.0 15.1 + - - +
127E LEU* 3.3 34.1 - - + -
135E PHE* 3.5 19.1 - - + -
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Residues in contact with LYS 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E VAL* 3.1 20.5 + - + +
48E CYS* 3.7 8.1 - - - +
49E TYR 3.4 0.2 - - - -
50E LEU* 1.3 77.9 - - - +
52E LYS* 1.3 60.0 + - - +
54E PHE* 3.5 7.6 - - - +
55E LEU* 3.5 19.7 - - - +
91E PHE* 3.7 22.7 - - + +
92E THR* 2.8 31.2 + - - +
94E ASP* 2.8 23.7 + - - +
135E PHE* 3.3 37.2 - - + +
137E LYS 3.1 18.6 + - - +
139E CYS* 3.6 21.8 - - - -
143E PHE* 4.7 5.2 - - + -
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Residues in contact with LYS 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E VAL* 4.2 12.8 - - + -
43E LEU* 4.4 7.4 - - + -
48E CYS 3.3 12.9 + - - +
49E TYR 4.2 1.6 - - - +
50E LEU 3.3 0.2 - - - -
51E LYS* 1.3 75.2 - - - +
53E ALA* 1.3 66.8 + - - +
54E PHE 3.1 1.8 - - - -
55E LEU* 2.8 27.3 + - + +
56E LEU* 3.0 18.3 + - + +
99E ASP 3.1 24.2 + - - -
101E ALA* 3.0 32.4 + - - +
102E CYS* 3.9 16.2 - - + +
103E VAL* 3.9 10.8 - - + +
143E PHE* 4.0 30.7 - - + -
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Residues in contact with ALA 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E PHE* 4.4 6.0 - - + -
38E VAL* 3.5 19.6 - - + +
49E TYR* 3.0 30.2 + - + +
50E LEU* 3.9 5.2 - - - +
52E LYS* 1.3 75.6 - - - +
54E PHE* 1.3 57.6 + - - +
56E LEU* 3.1 4.6 + - - +
57E VAL* 2.8 35.2 + - - +
120E VAL* 3.9 25.1 - - + -
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Residues in contact with PHE 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E LEU 2.9 19.3 + - - +
51E LYS 3.5 4.9 - - - +
53E ALA* 1.3 77.9 - - - +
55E LEU* 1.3 77.3 + - + +
57E VAL* 3.5 10.0 + - + +
58E GLN* 3.5 20.5 + - + +
84E SER* 3.4 42.6 - - - -
87E LEU* 3.6 33.9 - - + -
88E LYS* 4.3 16.2 - - + -
91E PHE* 4.0 37.5 - + + -
120E VAL* 4.3 13.9 - - + +
121E PHE* 4.9 9.6 - + - -
124E THR* 5.5 4.5 - - + +
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Residues in contact with LEU 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E LYS 3.5 15.3 - - - +
52E LYS* 2.8 22.6 + - + +
54E PHE* 1.3 92.4 - - + +
56E LEU* 1.3 61.3 + - + +
58E GLN* 3.4 21.5 - - + +
59E ASP* 3.8 10.3 + - - +
88E LYS* 5.6 10.1 - - + +
91E PHE* 5.8 4.9 - - + -
143E PHE* 6.4 1.6 - - + -
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Residues in contact with LEU 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E GLU* 4.8 16.8 - - + +
37E PHE* 3.7 31.4 - - + +
38E VAL* 3.6 27.6 - - + -
52E LYS* 3.0 17.8 + - + +
53E ALA* 3.1 7.6 + - - +
55E LEU* 1.3 74.0 - - + +
57E VAL* 1.3 60.7 + - - +
58E GLN 3.0 2.2 - - - -
59E ASP* 2.9 37.7 + - + +
60E ILE* 2.9 15.8 + - - +
100E LYS* 5.6 7.9 - - + +
103E VAL* 3.9 22.4 - - + -
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Residues in contact with VAL 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E PHE* 4.2 18.2 - - + -
53E ALA 2.8 23.1 + - - +
54E PHE* 3.7 8.5 - - + +
55E LEU 3.3 0.4 - - - -
56E LEU* 1.3 76.9 - - - +
58E GLN* 1.3 59.3 + - - +
60E ILE* 3.6 8.1 - - - +
61E MET* 2.9 38.0 + - + +
117E VAL* 4.1 21.1 - - + -
120E VAL* 4.3 20.4 - - + -
121E PHE* 3.6 33.4 - - + -
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Residues in contact with GLN 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E PHE* 3.5 22.5 - - + +
55E LEU* 3.4 14.6 - - + +
56E LEU 3.0 0.4 - - - -
57E VAL* 1.3 81.8 - - - +
59E ASP* 1.3 64.3 + - - +
61E MET* 3.0 22.4 + - - +
62E GLU* 3.4 23.6 + - - +
81E GLN* 4.2 13.0 + - - +
84E SER* 2.7 44.5 + - - -
85E LEU* 5.0 2.4 - - - +
88E LYS* 4.8 20.4 - - - +
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Residues in contact with ASP 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E LEU 3.9 10.9 - - - +
56E LEU* 2.9 28.5 + - + +
58E GLN* 1.3 80.1 - - - +
60E ILE* 1.3 58.6 + - + +
62E GLU* 4.9 1.3 - - - -
63E ASP* 3.0 47.8 + - - +
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Residues in contact with ILE 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E PHE* 4.7 4.5 - - + -
36E GLU 3.5 25.6 - - - +
37E PHE* 3.7 25.4 - - + -
56E LEU 2.9 16.5 + - - +
57E VAL* 3.6 12.3 - - - +
58E GLN 3.2 0.4 - - - -
59E ASP* 1.3 79.1 - - + +
61E MET* 1.3 60.1 + - + +
64E THR* 3.0 17.6 + - - +
65E MET* 2.9 48.4 + - + -
113E LEU* 3.9 33.2 - - + -
117E VAL* 4.3 7.0 - - + -
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Residues in contact with MET 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E VAL* 2.9 29.2 + - + +
58E GLN* 3.0 38.3 + - - +
60E ILE* 1.3 77.4 - - - +
62E GLU* 1.3 60.0 + - - +
65E MET* 3.1 41.8 - - + +
66E ARG* 5.3 0.3 - - - +
77E ILE* 4.0 17.2 - - + +
80E LEU* 3.7 32.3 - - - +
81E GLN* 3.7 31.7 + - + +
84E SER* 3.8 9.2 - - - +
117E VAL* 5.3 2.0 - - + -
121E PHE* 4.4 5.6 - - + -
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Residues in contact with GLU 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E GLN 3.4 16.3 + - - +
59E ASP* 4.3 2.2 - - - +
61E MET* 1.3 81.4 - - - +
63E ASP* 1.3 70.2 + - - +
66E ARG* 4.7 8.6 - - - +
81E GLN* 3.7 18.1 + - - +
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Residues in contact with ASP 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ASP* 3.0 29.3 + - - +
62E GLU* 1.3 95.2 - - - +
64E THR* 1.3 64.6 + - - +
66E ARG* 3.2 28.3 + - - -
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Residues in contact with THR 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ILE* 4.5 13.2 - - + -
34E THR 4.9 5.3 + - - +
35E PHE* 4.5 16.0 - - + +
60E ILE* 3.0 23.5 + - - +
63E ASP* 1.3 81.9 - - - +
65E MET* 1.3 61.7 + - - +
66E ARG* 3.0 22.6 + - - +
113E LEU* 3.7 26.0 - - + -
27F MET* 4.4 6.1 - - + +
28F GLU 3.9 7.1 - - - +
29F THR* 4.6 4.5 - - + +
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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