Contacts of the helix formed by residues 43 - 51 (chain A) in PDB entry 2K6N
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 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ILE* 2.9 35.9 - - + +
42A LEU* 1.3 74.5 - - - +
44A ASP* 1.3 77.0 + - - +
45A GLU* 2.6 12.6 + - + +
46A ASP* 2.4 38.6 + - + +
47A PHE* 2.5 12.7 + - - -
55A ARG* 5.8 2.9 - - - +
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Residues in contact with ASP 44 (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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42A LEU 4.1 0.2 + - - -
43A THR* 1.3 93.9 + - - +
45A GLU* 1.3 69.6 + - - +
47A PHE* 3.5 13.3 - - - +
48A GLU* 2.5 47.4 + - + +
53A MET 4.5 2.7 - - - -
54A THR* 4.8 18.4 - - + +
55A ARG* 5.2 2.2 - - - +
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Residues in contact with GLU 45 (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 LEU* 4.7 1.7 - - - +
43A THR* 2.6 16.2 + - + +
44A ASP* 1.3 91.9 + - - +
46A ASP* 1.3 57.2 + - - +
48A GLU* 3.2 6.5 + - - +
49A PHE* 3.0 29.3 + - - +
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Residues in contact with ASP 46 (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* 3.7 6.9 - - + +
19A TYR 3.1 12.6 - - - +
20A PRO* 4.6 0.2 - - - +
21A LEU* 3.0 50.0 + - + +
24A LEU* 4.4 1.4 - - - +
42A LEU* 2.7 29.3 - - + +
43A THR* 2.4 23.5 + - + +
45A GLU* 1.3 73.9 - - - +
47A PHE* 1.3 51.7 + - - +
49A PHE* 3.3 0.9 + - - +
50A ALA* 2.6 47.8 + - - +
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Residues in contact with PHE 47 (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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39A GLU* 2.8 42.2 - - + -
42A LEU* 2.7 40.1 - - + +
43A THR 2.5 16.8 + - - +
44A ASP* 3.5 6.5 - - - -
46A ASP* 1.3 73.8 + - - +
48A GLU* 1.3 48.6 + - - +
51A LEU* 2.6 37.8 + - + +
52A ASP 2.6 30.5 + - - -
53A MET 3.1 25.2 + - - +
54A THR 3.9 3.8 - - - -
55A ARG* 3.0 42.2 - - + -
58A TYR* 3.8 12.6 - + + -
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Residues in contact with GLU 48 (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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44A ASP* 2.5 34.7 + - + +
45A GLU* 3.5 6.5 - - - +
46A ASP 3.2 0.2 - - - -
47A PHE* 1.3 75.1 - - - +
49A PHE* 1.3 58.2 + - - +
52A ASP* 3.0 38.8 + - - +
53A MET 4.0 8.3 - - - +
54A THR* 5.5 3.6 - - + -
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Residues in contact with PHE 49 (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 LEU* 4.1 32.3 - - + -
25A LEU* 5.5 8.0 - - + +
45A GLU 3.0 16.9 + - - +
48A GLU* 1.3 76.6 - - - +
50A ALA* 1.3 59.3 + - - +
52A ASP* 5.3 0.4 - - - -
73A LYS* 3.9 13.4 + - - +
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Residues in contact with ALA 50 (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 LEU* 4.8 7.0 - - + -
25A LEU* 5.6 3.8 - - + -
42A LEU* 4.2 3.1 - - + -
46A ASP* 2.6 36.9 + - - +
47A PHE* 4.5 0.2 - - - -
49A PHE* 1.3 75.4 - - - +
51A LEU* 1.3 56.5 + - - +
73A LYS* 2.7 37.9 - - - +
75A LEU* 3.3 34.0 - - + +
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Residues in contact with LEU 51 (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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39A GLU* 3.4 9.6 - - + -
42A LEU* 4.4 0.2 - - + -
47A PHE* 2.6 46.1 + - + +
50A ALA* 1.3 72.7 - - - +
52A ASP* 1.3 74.2 + - - +
53A MET* 3.0 4.7 + - - +
58A TYR* 3.2 38.3 + - + +
69A LEU* 3.4 12.6 - - + +
70A LYS* 2.9 63.0 - - + +
73A LYS* 4.5 0.7 - - - -
75A LEU* 3.5 17.7 - - + -
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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