Contacts of the helix formed by residues 36 - 48 (chain C) in PDB entry 1KA8
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 TYR 36 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C MET* 4.6 2.0 - - - -
22C TYR* 3.0 19.5 - + + -
24C GLY* 3.4 24.2 - - - +
28C ILE* 3.5 38.7 - - + +
30C PRO 5.4 0.2 - - - -
32C ASN* 3.0 30.8 + - + +
33C TYR 4.0 0.3 - - - +
35C LYS* 1.3 110.7 + - + +
37C LEU* 1.3 67.0 + - - +
39C HIS* 2.9 36.0 + + + +
40C ALA* 2.9 21.1 + - - +
81C GLN* 5.1 2.1 + - + +
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Residues in contact with LEU 37 (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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8C PHE* 3.4 32.1 - - + -
12C LEU* 3.9 13.2 - - + -
21C MET* 4.2 20.9 - - + +
22C TYR 2.6 17.5 + - - +
23C MET* 3.8 30.7 - - + -
35C LYS 3.9 1.6 + - - -
36C TYR* 1.3 70.9 - - - +
38C TYR* 1.3 57.4 + - - +
40C ALA* 3.1 7.7 + - + +
41C TYR* 2.8 25.3 + - - +
59C PHE* 4.1 7.4 - - + -
63C LEU* 3.8 7.2 - - + -
85C THR* 4.8 6.7 - - + -
87C LEU* 3.6 28.7 - - + -
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Residues in contact with TYR 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C MET* 4.2 6.0 - - - -
24C GLY 4.1 15.3 - - - +
25C ASN* 4.1 4.0 - - - +
26C ALA* 4.0 33.6 - - + +
36C TYR 3.2 0.4 - - - -
37C LEU* 1.3 79.2 - - - +
39C HIS* 1.3 58.4 + - - +
41C TYR* 2.9 20.9 - + - +
42C LEU* 2.9 63.2 + - + +
53C VAL* 4.1 4.0 - - - +
54C LEU 2.5 28.2 + - - -
55C SER* 3.4 7.8 - - - -
56C LEU* 3.4 45.8 + - + -
59C PHE* 3.8 19.3 - + + -
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Residues in contact with HIS 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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25C ASN 2.9 37.8 + - - -
26C ALA* 5.2 0.2 - - - -
28C ILE* 3.0 29.7 + - + +
31C ARG* 3.2 46.4 + - + -
32C ASN 3.5 15.5 - - - +
33C TYR* 3.0 20.4 - - + -
36C TYR* 2.9 32.9 + + + +
38C TYR* 1.3 73.9 - + - +
40C ALA* 1.3 68.0 + - - +
42C LEU* 3.1 10.8 + - + +
43C ALA 2.9 18.7 + - - -
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Residues in contact with ALA 40 (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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8C PHE* 3.7 14.6 - - + -
21C MET* 4.8 0.2 - - - -
33C TYR* 3.4 28.4 + - - +
36C TYR 2.9 8.9 + - - +
37C LEU* 3.3 12.6 - - + +
39C HIS* 1.3 74.9 - - - +
41C TYR* 1.3 63.4 + - - +
43C ALA* 3.1 6.0 + - - +
44C TYR* 3.0 20.3 + - - +
89C LEU* 4.2 17.0 - - + -
97C TRP* 3.5 13.4 - - + -
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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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5C THR* 2.7 35.5 + - + -
8C PHE* 3.5 22.8 - + + -
37C LEU 2.8 12.3 + - - +
38C TYR* 2.9 28.3 - + - +
40C ALA* 1.3 76.2 - - - +
42C LEU* 1.3 65.6 + - + +
44C TYR* 3.1 5.2 + - - +
45C MET* 3.0 53.0 + - + +
52C ASN 5.0 0.3 + - - -
53C VAL* 3.9 10.1 - - + -
54C LEU* 3.2 40.6 + - + +
59C PHE* 3.5 37.2 - + + -
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Residues in contact with LEU 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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26C ALA* 5.5 2.5 - - + -
31C ARG* 3.7 32.8 - - - +
33C TYR* 4.9 3.4 - - + +
38C TYR* 2.9 44.9 + - + +
39C HIS* 3.1 16.1 + - + +
41C TYR* 1.3 79.1 - - + +
43C ALA* 1.3 64.8 + - - +
45C MET* 3.3 5.6 + - - +
46C GLU* 2.9 26.7 + - - +
53C VAL* 3.8 28.9 - - + -
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Residues in contact with ALA 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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33C TYR* 3.3 36.7 - - + -
39C HIS 2.9 5.7 + - - -
40C ALA 3.2 10.5 - - - +
42C LEU* 1.3 75.3 - - - +
44C TYR* 1.3 57.7 + - - +
46C GLU* 3.5 5.7 - - - +
47C ALA* 2.8 31.5 + - - +
97C TRP* 4.1 8.3 - - + +
99C PRO* 4.0 20.7 - - + +
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Residues in contact with TYR 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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4C PRO* 3.6 21.3 - - + +
7C ASP* 3.1 24.8 + - - +
8C PHE* 3.3 47.8 - + + -
11C TYR* 4.3 15.5 - + - -
40C ALA 3.0 7.4 + - - +
41C TYR 3.3 7.9 - - - +
43C ALA* 1.3 73.4 - - - +
45C MET* 1.3 76.1 + - + +
47C ALA* 2.9 4.8 + - - +
48C ASN* 2.8 53.9 + - - -
97C TRP* 3.7 43.2 - + + -
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Residues in contact with MET 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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4C PRO* 3.0 42.4 - - + -
5C THR 4.1 4.7 - - - -
41C TYR* 3.0 55.4 + - + +
42C LEU 3.8 3.1 - - - +
44C TYR* 1.3 82.9 - - + +
46C GLU* 1.3 58.6 - - - +
48C ASN* 2.9 18.4 + - - +
49C GLY 3.0 0.3 + - - -
50C TYR* 3.0 50.5 + - + +
52C ASN 5.1 3.4 - - - +
53C VAL* 3.6 27.1 - - + -
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Residues in contact with GLU 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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42C LEU 2.9 19.0 + - - +
43C ALA* 3.5 7.2 - - - +
45C MET* 1.3 77.7 - - - +
47C ALA* 1.3 66.7 + - - +
49C GLY* 3.1 13.6 + - - +
50C TYR 4.1 9.4 + - - +
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Residues in contact with ALA 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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43C ALA 2.8 22.2 + - - +
44C TYR 3.3 4.9 - - - +
46C GLU* 1.3 78.1 + - - +
48C ASN* 1.3 62.6 + - - +
49C GLY 3.7 0.5 + - - -
97C TRP* 3.7 33.2 - - + +
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Residues in contact with ASN 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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4C PRO* 5.7 0.2 - - + -
44C TYR* 2.8 64.0 + - + +
45C MET* 2.9 6.2 + - - +
47C ALA* 1.3 85.0 - - - +
49C GLY* 1.3 56.8 + - - +
50C TYR* 3.0 30.8 - - + -
97C TRP* 5.2 2.4 - - - +
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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