Contacts of the helix formed by residues 15 - 26 (chain E) in PDB entry 2OV2
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 GLY 15 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E ALA 3.4 1.0 - - - -
14E VAL* 1.3 79.9 - - - +
16E LYS* 1.3 65.5 + - - +
17E THR 3.4 2.5 - - - -
18E CYS* 3.5 1.4 + - - +
19E LEU* 3.0 26.7 + - - +
115E THR* 5.0 6.1 - - - +
159E ALA* 5.1 0.3 - - - +
200E GCP 3.0 43.4 + - - -
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Residues in contact with LYS 16 (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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8E VAL* 3.8 24.7 - - + +
9E VAL* 3.5 31.4 - - - -
10E GLY 3.1 12.6 + - - +
11E ASP 3.0 16.6 + - - -
14E VAL* 3.8 11.0 - - + -
15E GLY* 1.3 76.5 - - - +
17E THR* 1.3 63.9 + - - +
19E LEU* 3.3 6.7 + - - +
20E LEU* 3.1 26.0 + - - +
57E ASP* 3.8 8.7 - - - +
58E THR* 3.3 27.8 - - - -
60E GLY 4.0 2.0 - - - +
81E CYS* 4.3 9.4 - - + -
200E GCP 2.6 49.5 + - - +
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Residues in contact with THR 17 (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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16E LYS* 1.3 74.6 - - - +
18E CYS* 1.3 59.1 + - - +
20E LEU* 3.2 2.6 + - - +
21E ILE* 2.9 39.2 + - + +
29E PRO* 5.3 5.8 - - + -
33E ILE 5.5 3.8 - - - +
35E THR* 2.9 3.9 + - - +
40E TYR* 3.9 10.5 - - - +
57E ASP* 2.6 29.2 + - - +
200E GCP 2.9 13.6 + - - +
202E MG 2.1 30.6 - - - -
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Residues in contact with CYS 18 (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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15E GLY 3.9 0.4 - - - +
16E LYS 3.3 0.2 - - - -
17E THR* 1.3 73.3 - - - +
19E LEU* 1.3 54.3 + - - +
22E SER* 2.8 37.9 + - - -
28E PHE* 3.8 18.4 - - + -
29E PRO* 3.7 36.4 - - - +
31E GLU 5.5 2.5 - - - -
159E ALA* 3.6 2.0 - - - -
200E GCP 2.8 68.3 + - + +
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Residues in contact with LEU 19 (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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8E VAL* 5.0 6.5 - - + -
15E GLY 3.0 16.3 + - - +
16E LYS 3.4 7.4 - - - +
18E CYS* 1.3 79.0 - - - +
20E LEU* 1.3 62.5 + - + +
23E TYR* 3.1 30.1 + - - +
79E LEU* 4.5 11.2 - - + -
81E CYS* 4.5 8.3 - - - -
113E VAL* 3.9 11.4 - - + -
115E THR* 3.8 28.9 - - + -
157E CYS* 3.8 17.9 - - - -
159E ALA* 3.7 13.4 - - + +
165E LEU* 3.7 18.5 - - + +
168E VAL* 5.1 1.6 - - + -
169E PHE* 3.3 33.4 - - + -
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Residues in contact with LEU 20 (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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8E VAL* 4.0 21.5 - - + -
16E LYS 3.1 9.0 + - - +
17E THR 3.2 6.7 + - - +
19E LEU* 1.3 83.8 - - + +
21E ILE* 1.3 59.5 + - - +
23E TYR* 3.6 0.7 + - - +
24E THR* 2.8 35.8 + - - +
40E TYR* 3.9 18.4 - - + -
55E LEU* 3.8 31.2 - - + -
57E ASP* 3.4 48.0 - - + +
169E PHE* 3.8 24.7 - - + -
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Residues in contact with ILE 21 (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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17E THR* 2.9 34.0 + - + +
20E LEU* 1.3 75.5 - - - +
22E SER* 1.3 59.3 + - - +
24E THR* 3.7 11.2 - - - +
25E THR* 2.7 52.2 + - + +
27E ALA* 3.8 11.9 - - + +
29E PRO* 4.2 18.8 - - + -
40E TYR* 4.0 28.9 - - + +
17M PHE* 4.1 18.8 - - + -
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Residues in contact with SER 22 (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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18E CYS 2.8 23.9 + - - -
19E LEU 4.0 0.7 - - - -
21E ILE* 1.3 73.1 - - - +
23E TYR* 1.3 57.4 + - - +
26E ASN* 3.0 20.6 + - - +
27E ALA 3.2 21.2 + - - -
28E PHE* 5.0 2.2 + - - -
159E ALA* 2.7 30.4 + - - -
162E GLN* 3.0 32.3 + - - +
165E LEU* 3.2 10.2 - - - +
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Residues in contact with TYR 23 (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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19E LEU 3.1 20.1 + - - +
20E LEU 3.8 1.6 - - - +
22E SER* 1.3 78.9 - - - +
24E THR* 1.3 75.1 + - + +
26E ASN* 4.2 8.5 + - - +
42E ALA* 5.7 0.4 - - + -
44E VAL* 3.6 23.4 - - - +
53E LEU* 4.0 14.9 - - + +
55E LEU* 4.9 1.1 - - + -
162E GLN* 4.9 0.7 - - - +
165E LEU* 3.5 12.5 - - + +
166E LYS* 4.4 25.1 - - + -
169E PHE* 3.4 62.3 - + + +
170E ASP* 4.8 3.9 + - - -
173E ILE* 4.3 4.5 - - - +
12M SER 4.8 2.5 + - - -
14M PRO* 3.3 45.3 - - + +
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Residues in contact with THR 24 (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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20E LEU 2.8 24.9 + - - +
21E ILE* 3.7 5.4 + - - +
23E TYR* 1.3 85.7 - - + +
25E THR* 1.3 64.7 + - - +
26E ASN* 5.6 1.0 + - - -
40E TYR* 5.3 1.3 - - + +
42E ALA* 4.2 19.4 - - + +
55E LEU* 3.6 28.7 - - + -
14M PRO* 4.0 16.8 - - - +
15M SER* 5.4 1.2 + - - -
17M PHE* 3.5 40.4 + - + +
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Residues in contact with THR 25 (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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21E ILE* 2.7 41.1 + - + +
24E THR* 1.3 87.0 - - - +
26E ASN* 1.3 71.5 + - - +
27E ALA* 3.3 14.7 + - - +
17M PHE* 3.8 33.7 - - + -
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Residues in contact with ASN 26 (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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22E SER 3.0 17.4 + - - +
23E TYR 4.8 7.0 + - - +
24E THR 5.6 0.6 + - - -
25E THR* 1.3 80.8 + - - +
27E ALA* 1.3 58.3 + - - +
162E GLN* 3.0 33.1 + - - +
1208E CL 4.2 11.6 - - - +
14M PRO* 6.3 1.2 - - - +
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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