Contacts of the helix formed by residues 15 - 28 (chain A) in PDB entry 2COB
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 ASN 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLN* 6.0 1.4 - - - +
14A TYR* 1.3 79.2 - - - +
16A SER* 1.3 58.2 + - - +
17A GLU* 3.0 23.2 + - + +
18A ILE* 2.9 41.0 + - + +
19A LEU 3.1 8.8 + - - -
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Residues in contact with SER 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 4.0 5.7 + - - -
15A ASN* 1.3 70.5 - - - +
17A GLU* 1.3 60.3 + - - +
19A LEU* 3.7 18.5 - - - +
20A GLU* 3.5 18.5 - - - +
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASN* 4.3 16.9 + - + +
16A SER* 1.3 74.7 - - - +
18A ILE* 1.3 64.8 + - + +
19A LEU 3.2 1.1 - - - -
20A GLU* 3.0 24.2 + - - +
21A GLU* 3.5 11.4 + - - +
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Residues in contact with ILE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 3.7 20.9 - - + -
15A ASN* 2.9 37.6 + - + +
17A GLU* 1.3 78.6 - - + +
19A LEU* 1.3 63.1 + - - +
21A GLU* 3.3 16.2 - - + +
22A ALA* 3.2 19.9 + - - +
40A TYR* 3.9 23.0 - - + +
42A ILE* 3.8 9.4 - - + -
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 3.7 29.2 - - + +
15A ASN 3.1 4.2 + - - +
16A SER* 3.7 15.0 - - - +
18A ILE* 1.3 78.5 - - - +
20A GLU* 1.3 62.6 + - - +
22A ALA* 3.4 2.4 + - - +
23A ILE* 3.1 47.3 + - + +
42A ILE* 3.7 35.2 - - + +
46A THR* 4.3 1.1 - - + -
47A LEU* 4.3 4.7 - - + -
50A LYS* 3.8 42.4 - - + +
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Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A SER 3.5 17.5 - - - +
17A GLU* 3.0 12.0 + - - +
19A LEU* 1.3 73.1 - - + +
21A GLU* 1.3 61.5 + - + +
23A ILE* 3.2 14.1 + - - +
24A SER* 2.9 34.8 + - - +
54A ARG* 3.9 29.8 + - - +
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Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU 3.5 16.2 - - - +
18A ILE* 3.3 19.1 - - + +
20A GLU* 1.3 75.8 - - - +
22A ALA* 1.3 56.7 - - - +
24A SER* 3.0 10.4 + - - -
25A VAL* 3.0 29.3 + - - +
40A TYR* 3.4 20.0 + - + +
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE 3.2 8.5 + - - +
19A LEU 3.4 3.8 + - - +
21A GLU* 1.3 77.6 - - - +
23A ILE* 1.3 56.4 + - - +
25A VAL* 3.3 13.4 - - - +
26A VAL* 3.2 26.5 - - - +
36A ALA* 3.7 3.5 - - + +
40A TYR* 3.2 38.1 - - + -
42A ILE* 3.7 15.3 - - + -
47A LEU* 3.6 12.9 - - + +
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Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.1 30.6 + - + +
20A GLU* 3.5 20.2 - - - +
21A GLU 3.1 0.6 - - - -
22A ALA* 1.3 76.3 - - - +
24A SER* 1.3 60.7 + - - +
26A VAL* 3.1 5.9 + - - +
27A MET* 2.8 63.0 + - + +
47A LEU* 3.9 15.5 - - + -
50A LYS* 3.6 29.2 - - + +
51A VAL* 4.0 16.6 - - + -
54A ARG* 4.2 12.6 - - + -
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Residues in contact with SER 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLU* 2.9 19.2 + - - +
21A GLU* 3.5 7.4 - - - -
23A ILE* 1.3 76.9 - - - +
25A VAL* 1.3 61.3 + - - +
27A MET* 3.7 10.1 - - - +
28A SER* 2.9 33.0 + - - -
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU 3.0 18.8 + - - +
22A ALA* 3.3 25.6 - - - +
24A SER* 1.3 71.8 - - - +
26A VAL* 1.3 55.5 + - - +
28A SER* 3.3 0.4 + - - -
29A GLY 3.1 4.3 + - - -
30A LYS* 2.7 57.3 + - + +
31A MET* 3.9 15.3 - - + -
36A ALA* 4.3 2.7 - - + -
40A TYR* 3.1 31.2 - - + +
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA 3.2 18.4 - - - +
23A ILE 3.1 8.0 + - - +
25A VAL* 1.3 75.0 - - - +
27A MET* 1.3 64.7 + - - +
29A GLY* 3.0 14.2 + - - -
31A MET* 3.5 14.7 - - + +
32A SER* 3.5 26.7 - - - +
33A VAL* 3.9 24.0 - - + +
36A ALA* 3.5 13.5 - - + -
47A LEU* 4.4 2.7 - - + -
51A VAL* 4.0 24.9 - - + -
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Residues in contact with MET 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 2.8 38.8 + - + +
24A SER* 3.7 9.9 - - - +
26A VAL* 1.3 71.0 - - - +
28A SER* 1.3 59.0 + - - +
29A GLY* 3.0 6.8 + - - -
51A VAL* 3.5 20.9 - - + +
54A ARG* 3.4 34.8 - - + +
55A LEU* 3.4 30.5 - - + +
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER* 2.9 21.7 + - - -
25A VAL 3.6 4.0 - - - -
27A MET* 1.3 73.0 - - - +
29A GLY* 1.3 59.8 + - - +
30A LYS* 3.6 20.4 + - - +
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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