Contacts of the helix formed by residues 10 - 25 (chain B) in PDB entry 2VOO
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 MET 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B LYS* 1.3 85.6 - - - +
11B ALA* 1.3 54.8 + - - +
12B ALA 3.4 2.7 - - - -
13B LEU* 3.3 39.5 + - + -
14B GLU* 2.7 56.6 + - + +
62B THR* 5.9 0.7 - - - +
67B VAL* 3.7 32.8 - - + -
70B GLU* 5.6 2.7 - - - +
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Residues in contact with ALA 11 (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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9B LYS* 3.5 31.9 - - + +
10B MET* 1.3 77.1 - - - +
12B ALA* 1.3 58.1 + - - +
14B GLU* 3.3 7.9 + - - +
15B ALA* 2.8 30.6 + - - +
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Residues in contact with ALA 12 (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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10B MET 3.4 0.6 - - - -
11B ALA* 1.3 78.1 - - - +
13B LEU* 1.3 64.4 + - - +
15B ALA* 3.1 8.5 + - - +
16B LYS* 3.0 38.8 + - - +
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Residues in contact with LEU 13 (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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10B MET* 3.3 43.3 + - + +
12B ALA* 1.3 78.3 - - - +
14B GLU* 1.3 64.9 + - - +
16B LYS* 3.0 12.3 + - + +
17B ILE* 2.9 31.6 + - + +
61B LEU* 3.8 47.8 - - + +
62B THR* 4.8 3.8 - - - -
67B VAL* 4.4 7.2 - - + -
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Residues in contact with GLU 14 (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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9B LYS* 5.9 1.2 + - - -
10B MET* 2.7 44.8 + - + +
11B ALA* 3.7 6.9 - - - +
13B LEU* 1.3 72.3 - - - +
15B ALA* 1.3 60.9 + - - +
17B ILE* 3.4 5.8 + - - +
18B CYS* 3.0 29.1 + - - -
67B VAL* 3.8 18.5 - - + +
70B GLU* 2.7 46.8 - - - +
71B ALA* 3.6 23.1 - - + +
74B LYS* 4.1 15.8 + - - +
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Residues in contact with ALA 15 (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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11B ALA 2.8 17.4 + - - +
12B ALA* 3.4 9.0 - - - +
13B LEU 3.1 0.2 - - - -
14B GLU* 1.3 77.9 - - - +
16B LYS* 1.3 61.2 + - + +
18B CYS* 3.3 6.9 + - - +
19B HIS* 3.1 44.4 + - + +
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Residues in contact with LYS 16 (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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12B ALA* 3.0 27.2 + - - +
13B LEU* 3.0 13.5 + - + +
15B ALA* 1.3 74.2 - - + +
17B ILE* 1.3 60.0 + - - +
19B HIS* 3.5 9.0 + - - +
20B GLN* 2.9 31.2 + - - +
61B LEU* 3.9 29.1 - - + +
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Residues in contact with ILE 17 (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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13B LEU* 2.9 24.9 + - + +
14B GLU* 3.6 10.1 - - - +
15B ALA 3.3 0.2 - - - -
16B LYS* 1.3 77.0 - - - +
18B CYS* 1.3 63.0 + - - +
20B GLN* 3.7 1.4 - - - +
21B ILE* 2.9 45.8 + - + +
58B LEU* 4.1 8.7 - - + -
61B LEU* 4.0 24.9 - - + -
62B THR* 3.4 29.4 - - + -
67B VAL* 3.7 21.5 - - + -
68B ILE* 4.2 10.5 - - + +
71B ALA* 3.9 15.7 - - + -
72B LEU* 5.3 0.7 - - + -
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Residues in contact with CYS 18 (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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14B GLU 3.0 15.1 + - - +
15B ALA* 3.6 9.4 - - - +
17B ILE* 1.3 77.4 - - - +
19B HIS* 1.3 57.4 + - + +
21B ILE* 3.7 0.3 - - - +
22B GLU* 2.7 52.6 + - - +
71B ALA* 3.1 37.2 - - - -
72B LEU* 3.9 13.0 - - - -
74B LYS 5.1 0.2 - - - -
75B SER* 3.8 22.0 - - - -
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Residues in contact with HIS 19 (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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15B ALA* 3.1 31.5 + - + +
16B LYS* 3.9 7.3 - - - +
18B CYS* 1.3 79.4 - - + +
20B GLN* 1.3 57.4 + - - +
22B GLU* 3.5 15.7 + - - +
23B TYR* 2.9 29.6 + - - +
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Residues in contact with GLN 20 (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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16B LYS 2.9 19.0 + - - +
17B ILE* 3.7 3.4 - - - +
19B HIS* 1.3 76.2 - - - +
21B ILE* 1.3 64.2 + - + +
23B TYR* 3.1 12.0 + - - +
24B TYR* 3.2 54.5 + - + +
57B ARG* 2.9 42.2 + - + +
58B LEU* 4.1 14.6 - - + +
61B LEU* 4.1 11.4 - - + +
128B LYS* 3.9 5.7 + - - +
-2D U 2.9 23.6 + - - +
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Residues in contact with ILE 21 (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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17B ILE* 2.9 28.6 + - + +
18B CYS 3.9 1.8 - - - +
20B GLN* 1.3 75.2 - - - +
22B GLU* 1.3 64.1 + - - +
23B TYR 3.1 0.9 + - - -
24B TYR* 3.2 19.2 + - + +
25B PHE* 3.2 27.3 + - + -
52B MET* 5.8 1.3 - - - -
58B LEU* 4.2 26.2 - - + -
68B ILE* 3.7 30.5 - - + -
72B LEU* 3.8 17.3 - - + -
80B MET* 4.1 15.0 - - + -
89B ILE* 3.9 25.1 - - + -
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Residues in contact with GLU 22 (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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18B CYS* 2.7 37.5 + - - +
19B HIS* 4.0 17.5 + - - +
21B ILE* 1.3 72.1 - - - +
23B TYR* 1.3 57.7 + - - +
26B GLY* 3.0 24.7 + - - -
72B LEU* 4.8 3.7 - - + +
75B SER* 2.4 36.6 + - - -
77B ALA* 3.5 19.9 - - + +
78B GLU 4.6 0.7 + - - -
79B LEU* 3.7 23.9 + - + +
80B MET* 4.3 18.2 + - + +
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Residues in contact with TYR 23 (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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19B HIS 2.9 14.5 + - - +
20B GLN* 3.4 12.3 - - - +
21B ILE 3.1 0.4 - - - -
22B GLU* 1.3 75.7 - - - +
24B TYR* 1.3 72.7 + + - +
26B GLY* 3.0 12.0 + - - -
28B PHE* 3.7 7.7 - + + -
29B ASN* 3.3 33.4 + - + +
32B ARG* 2.8 19.2 + - - -
138B LEU 3.5 26.0 - - - -
139B ASN* 2.5 25.2 + - + -
-2D U 3.4 65.4 - + + +
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Residues in contact with TYR 24 (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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20B GLN* 3.2 38.8 + - + -
21B ILE* 3.2 17.2 + - + +
23B TYR* 1.3 79.8 - + - +
25B PHE* 1.3 64.2 + + + +
26B GLY 3.4 1.7 + - - -
29B ASN* 2.9 22.8 - - - +
30B LEU* 3.4 8.5 + - - -
36B LEU* 3.4 25.2 - - + +
52B MET* 5.5 3.1 - - - -
55B PHE* 3.5 34.6 - + + +
57B ARG* 3.4 5.9 - - - +
58B LEU* 3.3 28.7 + - + -
-2D U 3.3 27.6 - - - -
-1D U 2.6 33.8 + - - -
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Residues in contact with PHE 25 (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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21B ILE* 3.2 20.7 + - + +
22B GLU 3.8 1.6 - - - -
24B TYR* 1.3 83.9 - - + +
26B GLY* 1.3 60.2 + - - +
30B LEU* 3.8 8.3 - - + +
36B LEU* 3.8 29.6 - - + -
40B ILE* 4.1 20.4 - - + -
45B GLY 4.7 0.2 - - - -
47B VAL* 4.0 15.5 - - + -
52B MET* 3.8 26.9 - - - -
79B LEU* 4.0 3.5 - - + +
80B MET* 3.7 27.8 - - + -
89B ILE* 4.2 18.2 - - + -
90B ARG* 4.4 3.4 - - - -
91B ARG* 2.9 55.7 + - + -
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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