Contacts of the helix formed by residues 37 - 52 (chain C) in PDB entry 2KO8
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 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C ASP 5.4 1.1 - - - +
7C ASP 2.9 30.0 + - - +
8C LEU* 3.0 13.3 + - - +
9C GLU 4.5 0.4 - - - +
10C VAL* 4.4 18.8 - - + -
36C LEU* 1.3 77.7 - - - +
38C ALA* 1.3 54.2 + - - +
39C GLN* 3.6 4.4 + - - +
40C GLY 3.2 13.5 + - - -
41C TYR* 2.6 41.8 + - - -
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Residues in contact with ALA 38 (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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1B FME 3.6 40.3 - - + +
37C THR* 1.3 74.5 - - - +
39C GLN* 1.3 58.1 + - - +
41C TYR* 3.2 9.5 + - - +
42C THR* 2.9 32.7 + - - -
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Residues in contact with GLN 39 (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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1B FME 4.4 17.8 - - - +
2B VAL* 4.5 17.7 - - - +
3B ILE* 3.6 29.0 - - + +
3C ILE* 4.7 8.5 - - - +
7C ASP* 4.1 10.4 - - - +
8C LEU* 3.7 34.8 - - + +
37C THR* 3.2 7.7 + - - +
38C ALA* 1.3 79.4 - - - +
40C GLY* 1.3 62.3 - - - +
42C THR* 3.1 6.3 + - - -
43C LEU* 3.1 25.0 + - + +
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Residues in contact with GLY 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.0 30.4 - - - -
8C LEU* 3.8 19.5 - - - +
36C LEU* 3.7 5.6 - - - -
37C THR* 3.0 12.0 + - - -
39C GLN* 1.3 79.3 - - - +
41C TYR* 1.3 57.2 + - - +
43C LEU 3.2 0.2 + - - -
44C LEU* 2.8 26.9 + - - +
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Residues in contact with TYR 41 (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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1B FME 6.1 0.7 - - + -
28C ALA* 4.7 15.8 + - - +
35C ILE* 6.0 1.4 - - + +
36C LEU* 3.6 33.3 - - + +
37C THR 2.6 31.7 + - - +
38C ALA* 3.4 9.2 - - - +
39C GLN 3.2 0.2 - - - -
40C GLY* 1.3 72.4 - - - +
42C THR* 1.3 62.5 + - - +
44C LEU* 3.5 24.0 - - + +
45C ASP* 3.2 26.2 + - + +
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Residues in contact with THR 42 (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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1B FME 3.1 21.7 - - - +
3B ILE* 3.2 26.4 + - + +
4B ALA 3.6 7.2 - - - -
5B THR* 3.5 44.2 + - - +
8B LEU* 5.5 1.3 - - + -
38C ALA 2.9 15.2 + - - -
39C GLN 3.1 8.7 + - - -
41C TYR* 1.3 76.8 - - - +
43C LEU* 1.3 60.4 + - - +
45C ASP* 4.4 2.2 - - - +
46C PHE* 3.3 21.2 + - + +
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Residues in contact with LEU 43 (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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43A LEU* 4.7 22.9 - - + -
46A PHE* 3.4 24.0 - - + -
3B ILE* 3.7 34.5 - - + -
8B LEU* 5.9 0.4 - - + -
43B LEU* 4.8 15.5 - - + -
3C ILE* 5.1 2.0 - - + -
8C LEU* 3.5 24.9 - - + -
39C GLN* 3.1 21.0 + - + +
40C GLY 3.7 2.5 - - - +
41C TYR 3.2 0.2 - - - -
42C THR* 1.3 80.3 - - - +
44C LEU* 1.3 58.1 + - - +
46C PHE* 3.6 5.1 + - - +
47C ILE* 3.0 37.4 + - + +
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Residues in contact with LEU 44 (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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46A PHE* 4.1 2.0 - - + -
50A HIS* 4.7 10.3 - - + +
36C LEU* 3.5 38.4 - - + -
40C GLY 2.8 10.9 + - - +
41C TYR* 3.4 40.8 + - + +
42C THR 3.4 0.2 - - - -
43C LEU* 1.3 76.3 - - - +
45C ASP* 1.3 68.5 + - + +
46C PHE 3.1 0.2 - - - -
47C ILE* 3.0 14.2 - - + +
48C GLN* 2.8 52.3 + - + +
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Residues in contact with ASP 45 (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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5B THR* 4.8 9.4 + - + +
41C TYR 3.2 13.3 + - - +
42C THR* 4.6 2.9 - - - +
44C LEU* 1.3 90.1 - - + +
46C PHE* 1.3 57.1 + - - +
48C GLN* 3.6 4.3 - - - +
49C LYS* 2.6 64.7 + - - +
53C LYS* 2.6 29.3 + - - -
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Residues in contact with PHE 46 (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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5B THR* 5.4 4.4 - - + +
8B LEU* 3.7 31.2 - - + -
9B GLU* 3.9 21.5 - - + +
36B LEU* 3.4 13.9 - - + -
40B GLY* 3.0 29.8 - - - -
43B LEU* 3.4 38.6 - - + -
44B LEU* 3.8 2.9 - - - -
47B ILE* 4.3 6.1 - - + -
42C THR* 3.3 20.9 + - + +
43C LEU* 3.6 7.6 - - - +
45C ASP* 1.3 78.7 - - - +
47C ILE* 1.3 68.9 + - + +
49C LYS 3.6 0.3 + - - -
50C HIS* 2.6 52.4 + + - -
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Residues in contact with ILE 47 (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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46A PHE* 4.0 11.4 - - + +
47A ILE* 3.5 50.7 - - + +
50A HIS* 4.1 9.0 - - + -
51A LEU* 3.0 36.5 - - + +
47B ILE* 3.5 25.4 - - + +
43C LEU* 3.0 18.6 + - + +
44C LEU* 3.0 24.5 - - - +
46C PHE* 1.3 78.8 - - + +
48C GLN* 1.3 69.2 + - - +
50C HIS 3.6 0.2 + - - -
51C LEU* 3.2 13.7 + - - +
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Residues in contact with GLN 48 (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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50A HIS* 3.7 9.7 + - - +
51A LEU* 3.1 28.0 - - + +
44C LEU* 2.8 43.5 + - + +
45C ASP* 3.6 4.0 - - - +
47C ILE* 1.3 76.5 - - - +
49C LYS* 1.3 55.6 + - - +
50C HIS 3.0 2.4 + - - -
52C ASN* 2.6 21.1 + - - +
53C LYS* 2.5 62.1 + - - +
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Residues in contact with LYS 49 (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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5B THR* 4.6 2.6 - - - +
9B GLU* 2.6 42.0 + - - +
32B LYS* 3.6 36.6 + - + +
34B VAL* 4.0 16.2 - - + -
45C ASP* 2.6 49.8 + - - +
46C PHE 3.6 1.5 + - - +
47C ILE 3.4 0.4 - - - -
48C GLN* 1.3 75.4 - - - +
50C HIS* 1.3 63.3 + - - +
53C LYS* 2.9 37.7 - - + +
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Residues in contact with HIS 50 (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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9B GLU* 2.6 38.4 + - - -
32B LYS* 4.3 18.0 + - - +
34B VAL 5.7 0.4 + - - -
36B LEU* 3.3 42.8 - - + +
44B LEU* 4.7 8.1 - - + -
47B ILE* 4.0 11.7 - - + -
48B GLN* 3.6 10.1 + - - +
52B ASN* 5.0 0.2 + - - -
46C PHE* 2.6 44.0 + + - +
48C GLN 3.0 0.4 + - - -
49C LYS* 1.3 89.0 + - - +
51C LEU* 1.3 71.6 + - + +
53C LYS 5.1 1.3 - - - -
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Residues in contact with LEU 51 (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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51A LEU* 3.8 8.7 - - + -
47B ILE* 3.0 47.6 - - + +
48B GLN* 3.1 33.4 - - + +
51B LEU* 3.8 16.6 - - + -
52B ASN* 3.5 44.3 + - + +
47C ILE 3.2 7.5 + - - +
48C GLN 3.0 1.6 + - - -
49C LYS 3.7 0.2 - - - -
50C HIS* 1.3 92.9 - - + +
52C ASN* 1.3 64.7 + - - +
53C LYS* 3.7 2.2 - - - +
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Residues in contact with ASN 52 (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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51A LEU* 3.5 59.7 + - + +
52A ASN* 4.6 5.5 - - - +
52B ASN* 4.6 4.5 - - - +
48C GLN* 2.6 18.2 + - - +
51C LEU* 1.3 82.6 - - - +
53C LYS* 1.3 61.8 + - - +
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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