Contacts of the helix formed by residues 17 - 25 (chain C) in PDB entry 2OVI
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 THR 17 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLY* 1.3 74.9 - - - -
18C LEU* 1.3 59.1 + - - +
19C GLU* 2.7 47.1 + - + +
20C VAL* 2.6 41.7 - - + +
21C VAL* 3.2 7.8 + - - +
65C HIS* 4.0 15.0 - - + -
114C PHE* 3.5 21.7 - - - -
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU* 4.3 10.5 - - + -
16C GLY 3.7 0.4 + - - -
17C THR* 1.3 73.6 - - - +
19C GLU* 1.3 60.9 + - - +
21C VAL* 3.0 13.5 + - + +
22C ALA* 2.8 30.7 + - - +
29C LEU* 3.5 20.2 - - + +
32C VAL* 3.9 21.7 - - + +
33C VAL* 4.5 15.0 - - + -
36C LEU* 4.5 7.6 - - + -
110C ILE* 3.7 21.3 - - + -
112C ARG* 3.3 48.7 - - - +
114C PHE* 5.8 0.4 - - - -
123C LEU* 5.4 2.5 - - + -
134C LYS* 5.8 1.6 - - - +
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Residues in contact with GLU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C THR* 2.7 37.2 + - + +
18C LEU* 1.3 82.3 + - - +
20C VAL* 1.3 55.4 + - - +
22C ALA* 3.5 7.7 + - - +
23C GLU* 3.0 25.5 + - - +
29C LEU* 3.9 21.4 - - + +
65C HIS* 3.5 29.7 + - + +
134C LYS* 2.4 38.4 + - - -
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Residues in contact with VAL 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ASP 5.5 0.4 - - - +
16C GLY* 4.5 3.8 - - - -
17C THR* 2.6 48.2 - - + +
19C GLU* 1.3 75.9 - - - +
21C VAL* 1.3 68.6 + - + +
22C ALA 3.1 0.2 - - - -
23C GLU* 3.0 8.6 + - + +
24C GLN* 2.8 46.6 + - + +
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Residues in contact with VAL 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 4.7 2.9 - - + -
9C PHE* 3.7 37.2 - - + -
10C LEU* 4.4 6.3 - - + -
14C PRO* 4.8 8.7 - - + -
15C ASP 4.8 7.4 - - - +
17C THR 3.5 13.0 - - - +
18C LEU* 3.0 20.3 + - + +
20C VAL* 1.3 81.2 - - + +
22C ALA* 1.3 62.9 + - - +
24C GLN* 3.3 12.6 + - - +
25C TYR* 3.1 29.3 + - + -
32C VAL* 3.8 21.8 - - + -
112C ARG* 5.3 0.4 - - - +
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Residues in contact with ALA 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU 2.8 13.6 + - - +
19C GLU* 3.7 6.3 - - - +
21C VAL* 1.3 74.6 - - - +
23C GLU* 1.3 63.7 + - - +
25C TYR 3.5 0.5 + - - -
26C ASN 3.1 3.6 + - - -
27C THR* 2.9 40.0 + - - +
28C THR 3.5 18.6 - - - +
29C LEU* 4.0 5.8 - - + +
32C VAL* 3.3 26.6 - - + +
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C GLU 3.0 15.2 + - - +
20C VAL* 3.0 14.5 + - + +
22C ALA* 1.3 75.6 - - - +
24C GLN* 1.3 62.7 + - + +
26C ASN* 3.2 14.5 + - - +
27C THR 5.1 1.6 - - - -
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Residues in contact with GLN 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C PHE* 4.1 19.9 - - - -
20C VAL* 2.8 32.4 + - + +
21C VAL* 3.5 21.4 + - - +
23C GLU* 1.3 74.9 - - + +
25C TYR* 1.3 61.7 + - + +
26C ASN* 3.0 9.3 + - - +
26D ASN* 3.3 14.7 + - - +
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Residues in contact with TYR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C SER* 3.2 20.6 + - - -
6C LEU* 3.5 40.8 - - + -
9C PHE* 3.1 47.2 - + + +
21C VAL* 3.1 25.8 + - + +
23C GLU 3.4 0.2 - - - -
24C GLN* 1.3 80.6 - - + +
26C ASN* 1.3 71.0 + - - +
27C THR* 3.1 20.4 + - + +
32C VAL* 5.7 0.2 - - + -
23D GLU 5.5 1.0 - - - +
26D ASN* 3.1 31.7 + - + +
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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