Contacts of the helix formed by residues 39 - 47 (chain B) in PDB entry 2KNV
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B MET* 5.6 0.2 - - - -
33B LEU* 5.8 0.4 - - - -
36B LYS* 4.0 9.4 - - - +
37B ASN* 2.8 32.5 + - - +
38B TYR* 1.3 73.3 - - - +
40B ILE* 1.3 66.0 + - - +
41B GLY 3.3 2.7 + - - -
42B ALA* 3.1 22.7 + - + +
43B ALA* 2.9 23.3 + - - +
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Residues in contact with ILE 40 (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 SER* 4.6 18.4 - - - +
16B GLN* 3.8 33.2 - - + -
17B MET* 4.2 21.8 - - + -
20B MET* 5.7 7.0 - - + -
33B LEU* 6.2 0.9 - - + -
38B TYR 3.1 12.1 + - - +
39B ASP* 1.3 70.5 - - - +
41B GLY* 1.3 65.1 + - - +
43B ALA* 3.2 1.4 + - - +
44B LEU* 3.0 43.6 + - + +
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Residues in contact with GLY 41 (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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39B ASP* 3.3 2.2 + - - -
40B ILE* 1.3 79.4 - - - +
42B ALA* 1.3 61.0 + - - +
44B LEU* 3.6 7.9 + - - +
45B ASP* 3.4 20.6 + - - +
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Residues in contact with ALA 42 (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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36B LYS* 3.7 23.2 - - + +
39B ASP* 3.1 30.0 + - + +
41B GLY* 1.3 73.7 - - - +
43B ALA* 1.3 59.0 + - - +
45B ASP* 3.2 8.7 + - - +
46B THR* 2.8 29.8 + - - -
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Residues in contact with ALA 43 (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 MET* 3.8 23.6 - - + -
22B PHE* 5.4 7.4 - - + -
29B LEU* 6.2 0.7 - - + -
32B LEU* 4.7 16.2 - - + +
33B LEU* 5.4 5.8 - - + -
36B LYS* 4.6 6.7 - - + +
37B ASN 5.9 1.3 - - - +
39B ASP 2.9 15.9 + - - +
40B ILE 3.6 4.0 - - - +
42B ALA* 1.3 77.2 - - - +
44B LEU* 1.3 61.3 + - - +
46B THR* 3.1 25.3 + - - -
47B ILE* 3.8 8.0 + - - +
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Residues in contact with LEU 44 (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 MET* 4.5 13.9 - - + -
20B MET* 4.4 25.6 - - + -
22B PHE* 5.3 8.7 - - + -
40B ILE* 3.0 40.6 + - + +
41B GLY* 3.9 8.3 - - - +
43B ALA* 1.3 77.7 - - - +
45B ASP* 1.3 58.1 + - - +
47B ILE* 3.6 7.9 + - + +
48B GLN 3.2 16.8 + - - -
49B TYR 3.7 14.1 + - - +
50B SER* 3.0 41.0 + - - +
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Residues in contact with ASP 45 (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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49A TYR* 3.0 26.3 + - - -
41B GLY 3.4 10.0 + - - +
42B ALA* 3.2 11.8 + - - +
43B ALA 3.2 0.6 - - - -
44B LEU* 1.3 75.1 - - - +
46B THR* 1.3 64.8 + - - +
47B ILE 3.2 2.9 + - - -
48B GLN* 3.3 25.1 + - - +
50B SER* 3.9 5.9 + - - +
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Residues in contact with THR 46 (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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28A TRP* 6.2 4.9 - - + -
47A ILE* 4.4 5.2 - - + +
49A TYR* 3.1 20.1 - - - -
32B LEU* 4.9 16.1 - - + +
36B LYS* 3.2 26.5 - - + +
42B ALA 2.8 17.0 + - - -
43B ALA* 3.1 17.3 + - - -
45B ASP* 1.3 78.8 - - - +
47B ILE* 1.3 63.4 + - + +
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Residues in contact with ILE 47 (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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28A TRP* 6.1 0.9 - - + -
46A THR* 4.2 4.7 - - + +
47A ILE* 3.0 41.2 - - + +
48A GLN* 3.3 1.4 - - - +
22B PHE* 4.2 28.0 - - + -
28B TRP* 5.1 15.3 - - + -
32B LEU* 6.5 0.7 - - + -
43B ALA 4.3 5.2 - - - +
44B LEU* 3.8 9.2 - - + +
46B THR* 1.3 87.6 - - + +
48B GLN* 1.3 62.6 + - - +
49B TYR* 2.8 58.0 + - + +
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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