Contacts of the helix formed by residues 39 - 53 (chain E) in PDB entry 1VHA
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 39 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ASP* 2.9 23.3 + - - +
38E GLY* 1.3 72.4 - - - +
40E VAL* 1.3 58.2 + - - +
41E ALA* 3.2 11.4 + - - +
42E LEU* 3.2 39.8 + - - +
43E HIS* 3.0 32.9 + - - -
74E SER* 3.5 8.6 + - - +
113E MSE 5.3 2.6 - - - +
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Residues in contact with VAL 40 (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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9E ASP* 3.1 29.9 - - - +
10E VAL 3.8 1.8 - - - -
11E HIS* 3.6 37.2 - - + +
38E GLY 2.9 7.5 + - - +
39E ASP* 1.3 72.0 - - - +
41E ALA* 1.3 62.8 + - + +
44E ALA* 2.9 32.1 + - - +
99E ILE* 5.2 7.0 - - + -
147E ILE* 3.7 28.3 - - + +
148E ALA 4.1 8.3 - - - +
149E CYS* 3.5 19.7 - - + +
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Residues in contact with ALA 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ASP* 3.2 10.4 + - - +
40E VAL* 1.3 83.2 - - + +
42E LEU* 1.3 66.0 + - + +
44E ALA* 4.0 1.7 - - - +
45E LEU* 3.1 23.9 + - - +
97E ILE* 4.2 17.4 - - + +
99E ILE* 4.4 7.6 - - + -
113E MSE 3.9 25.6 - - + -
117E ILE* 6.0 0.2 - - + -
149E CYS* 3.6 19.5 - - - -
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Residues in contact with LEU 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ASP* 3.2 28.5 + - - +
41E ALA* 1.3 82.2 - - + +
43E HIS* 1.3 57.7 + - - +
45E LEU* 3.4 5.7 + - + +
46E THR* 2.7 38.1 + - - +
74E SER* 3.6 17.9 - - - +
75E ARG* 3.5 46.9 - - + +
78E LEU* 3.9 22.1 - - + +
113E MSE 6.2 1.8 - - + -
116E LYS* 6.5 0.4 - - + -
117E ILE* 4.1 24.9 - - + -
120E ASP* 6.1 0.2 - - - +
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Residues in contact with HIS 43 (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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9E ASP* 3.3 38.4 + - - +
35E HIS* 5.0 7.5 - + - -
36E SER* 3.4 36.7 - - - -
37E ASP* 4.7 2.2 - - - -
38E GLY* 5.1 1.0 - - - -
39E ASP 3.0 16.3 + - - +
40E VAL 3.8 0.4 - - - +
42E LEU* 1.3 79.3 - - - +
44E ALA* 1.3 62.1 + - - +
46E THR* 3.4 6.6 + - - -
47E ASP* 3.1 27.5 + - - +
58E ILE* 3.5 28.8 - - + +
71E ASN 5.3 0.2 + - - -
72E ALA 5.5 0.2 + - - -
74E SER* 3.1 30.6 + - - -
77E LEU* 4.4 7.8 - - + +
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Residues in contact with ALA 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E GLY* 3.4 24.7 - - - -
8E PHE 4.1 2.5 - - - +
9E ASP* 3.9 6.2 - - - +
40E VAL 2.9 18.8 + - - +
41E ALA 4.0 2.5 - - - +
43E HIS* 1.3 76.3 - - - +
45E LEU* 1.3 58.3 + - - +
47E ASP* 3.3 1.8 + - - -
48E ALA* 2.9 26.2 + - - +
149E CYS* 3.5 28.5 - - - +
151E ALA* 3.8 12.8 - - + -
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Residues in contact with LEU 45 (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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41E ALA 3.1 17.6 + - - +
42E LEU* 3.7 7.0 - - + +
44E ALA* 1.3 77.9 - - - +
46E THR* 1.3 62.6 + - - +
48E ALA* 3.3 0.7 + - - +
49E ILE* 3.1 36.6 + - + +
78E LEU* 4.3 15.7 - - + -
95E VAL* 3.7 33.7 - - + -
97E ILE* 3.8 22.7 - - + -
117E ILE* 3.4 34.8 - - + -
121E LEU* 4.2 6.5 - - + -
151E ALA* 3.9 10.7 - - + +
152E VAL 5.2 0.4 - - - +
153E ALA* 4.8 4.0 - - + -
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Residues in contact with THR 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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42E LEU 2.7 24.3 + - - -
43E HIS* 3.5 6.4 - - - -
45E LEU* 1.3 76.9 - - - +
47E ASP* 1.3 58.0 + - - +
49E ILE* 3.5 3.1 + - - +
50E LEU* 3.0 39.9 + - + +
58E ILE* 3.7 34.7 - - + +
61E LEU* 4.7 0.7 - - + -
74E SER 4.8 1.2 + - - -
77E LEU* 4.4 5.7 - - - +
78E LEU* 3.5 28.3 + - - +
81E ALA* 3.9 22.3 - - + +
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Residues in contact with ASP 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E HIS 4.2 1.1 - - - -
7E GLY* 4.0 11.9 - - - -
8E PHE 4.2 14.1 - - - +
9E ASP* 5.2 3.6 - - - +
43E HIS* 3.1 17.8 + - - +
44E ALA* 3.3 6.7 + - - +
46E THR* 1.3 73.4 - - - +
48E ALA* 1.3 61.2 + - - +
50E LEU* 4.0 3.1 - - - +
51E GLY* 2.8 25.5 + - - -
57E ASP* 3.5 10.9 - - - +
58E ILE* 2.6 46.7 + - - +
131F LYS* 3.3 23.2 + - + +
133F THR* 5.5 5.4 - - - +
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Residues in contact with ALA 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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5E GLY* 3.2 12.6 - - - +
6E HIS* 3.6 15.9 - - - +
7E GLY* 3.6 13.0 - - - +
44E ALA 2.9 17.0 + - - +
45E LEU* 3.6 6.3 - - + +
46E THR 3.3 0.2 - - - -
47E ASP* 1.3 77.4 - - - +
49E ILE* 1.3 57.7 + - - +
52E ALA* 3.0 23.9 + - - +
151E ALA* 3.8 17.0 - - + +
152E VAL 4.4 0.2 - - - -
153E ALA* 4.0 17.5 - - + -
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Residues in contact with ILE 49 (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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45E LEU* 3.1 37.8 + - + +
46E THR* 4.0 3.4 - - - +
48E ALA* 1.3 73.7 - - - +
50E LEU* 1.3 66.1 + - - +
51E GLY 3.1 1.1 - - - -
52E ALA* 3.4 5.5 + - - +
53E ALA* 3.2 21.1 + - - +
78E LEU* 4.6 5.2 - - + -
81E ALA* 5.0 5.6 - - + +
82E PHE* 5.1 7.0 - - + +
85E VAL* 3.3 31.2 - - + -
92E ILE* 4.0 15.3 - - + -
95E VAL* 4.5 0.7 - - + -
121E LEU* 3.9 26.2 - - + -
153E ALA* 3.7 21.1 - - + -
155E LEU* 3.9 10.1 - - + +
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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
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46E THR* 3.0 27.3 + - + +
47E ASP 4.0 2.9 - - - +
49E ILE* 1.3 77.0 - - - +
51E GLY* 1.3 58.2 + - - +
53E ALA* 3.4 3.0 + - - -
54E ALA 3.0 6.1 + - - -
55E LEU* 2.8 53.1 + - + +
56E GLY 3.8 12.3 + - - +
57E ASP* 3.3 33.2 - - - +
58E ILE* 3.4 12.6 - - - +
60E LYS 5.3 0.4 - - - +
61E LEU* 4.3 15.9 - - + -
81E ALA* 3.7 34.3 - - + +
84E GLN* 5.3 2.2 - - - +
85E VAL* 4.6 1.1 - - + -
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Residues in contact with GLY 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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3E ARG* 4.4 3.1 + - - -
4E ILE 4.5 0.2 - - - +
47E ASP 2.8 14.3 + - - -
48E ALA 3.7 0.2 - - - -
49E ILE 3.1 0.2 - - - -
50E LEU* 1.3 74.6 - - - +
52E ALA* 1.3 62.7 - - - +
53E ALA 3.0 1.8 - - - -
54E ALA 3.0 9.9 + - - -
94F ASN* 4.6 0.9 + - - -
96F ASP* 3.3 21.8 - - - +
129F ASN* 3.2 36.0 - - - +
131F LYS* 3.8 1.1 - - - +
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Residues in contact with ALA 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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3E ARG* 2.3 47.6 + - - +
4E ILE 3.2 33.4 - - - -
5E GLY* 3.5 4.8 - - - +
48E ALA 3.0 13.1 + - - +
49E ILE* 3.4 6.2 + - - +
51E GLY* 1.3 74.8 - - - +
53E ALA* 1.3 55.9 + - - +
153E ALA 4.2 3.4 - - - +
155E LEU* 3.9 20.2 - - + -
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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
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3E ARG* 4.3 3.4 - - - +
49E ILE 3.2 15.9 + - - +
50E LEU 3.9 3.6 - - - +
51E GLY 3.0 0.8 - - - -
52E ALA* 1.3 77.3 - - - +
54E ALA* 1.3 64.1 + - - +
55E LEU* 3.2 21.1 + - + +
85E VAL* 4.2 8.3 - - + -
88E LYS* 2.9 29.8 + - + -
90E TYR* 4.6 13.9 - - + -
155E LEU* 3.9 14.6 - - + -
126F GLU* 4.2 0.3 - - - +
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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
------------------------------------------------------------
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