Contacts of the helix formed by residues 27 - 52 (chain C) in PDB entry 5XBY
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 27 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PRO* 4.1 4.8 - - - +
26C PRO* 1.3 83.2 - - + +
28C LEU* 1.3 63.5 + - - +
29C VAL* 2.9 24.6 + - - +
30C GLU* 3.2 25.2 + - + +
31C PHE* 3.1 22.9 + - - +
40D ARG* 6.0 1.2 - - - +
43D ARG* 4.9 9.8 + - - -
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TYR* 2.9 23.2 + - - +
20C VAL* 3.7 31.6 - - + -
25C PRO* 4.7 11.0 - - + +
26C PRO 4.0 1.4 + - - +
27C ASP* 1.3 73.7 + - - +
29C VAL* 1.3 58.0 + - + +
31C PHE* 3.8 4.5 - - - +
32C ALA* 2.9 23.6 + - - +
6D PRO* 4.0 14.1 - - + -
7D PRO 4.3 7.6 - - - +
8D GLY 3.9 7.2 - - - +
9D LEU* 3.7 40.2 - - + +
12D LEU* 3.6 16.2 - - + -
43D ARG* 6.1 1.7 - - - +
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASP* 2.9 8.6 + - - +
28C LEU* 1.3 72.9 - - + +
30C GLU* 1.3 67.9 + - - +
32C ALA* 3.1 7.8 + - - +
33C VAL* 3.0 23.6 + - - +
12D LEU* 3.8 15.5 - - + -
36D PHE* 3.7 11.9 - - + +
39D LEU* 4.2 12.8 - - + -
40D ARG* 3.7 39.5 - - + +
43D ARG* 3.0 43.1 - - - +
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Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASP* 3.2 27.5 + - + +
29C VAL* 1.3 80.7 - - - +
31C PHE* 1.3 58.9 + - - +
33C VAL* 3.5 3.8 + - - +
34C GLU* 2.9 35.6 + - + +
40D ARG* 2.7 44.4 + - - +
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Residues in contact with PHE 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TYR* 4.1 15.5 - + - -
19C GLU* 4.0 18.2 - - + -
20C VAL* 4.1 11.2 - - + -
23C GLN* 3.1 48.2 - - + -
25C PRO* 3.6 30.1 - - + -
27C ASP 3.1 18.7 + - - +
28C LEU* 3.9 4.0 - - - +
30C GLU* 1.3 75.1 - - - +
32C ALA* 1.3 55.3 + - - +
34C GLU* 3.5 16.1 - - + +
35C TYR* 2.6 52.3 + + + +
38C ARG* 5.6 5.4 - - - -
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Residues in contact with ALA 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TYR* 3.6 23.3 - - + +
28C LEU 2.9 16.1 + - - +
29C VAL* 3.2 10.5 - - - +
31C PHE* 1.3 72.8 - - - +
33C VAL* 1.3 59.6 + - - +
36C PHE* 2.9 39.0 + - + +
36D PHE* 3.7 36.3 - - + -
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Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL 3.0 15.1 + - - +
30C GLU* 3.7 7.9 - - - +
32C ALA* 1.3 74.1 - - - +
34C GLU* 1.3 58.9 + - - +
36C PHE* 5.2 1.1 - - - -
37C THR* 2.6 43.5 + - - +
33D VAL* 5.0 4.5 - - + +
36D PHE* 3.5 37.0 - - + +
37D THR* 3.7 17.5 - - - +
40D ARG* 3.5 37.7 - - + +
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Residues in contact with GLU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLU* 2.9 28.0 + - + +
31C PHE* 3.2 18.8 + - + +
33C VAL* 1.3 77.3 - - - +
35C TYR* 1.3 63.6 + - - +
37C THR* 3.9 3.5 - - - -
38C ARG* 3.0 69.9 + - - +
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Residues in contact with TYR 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU 4.9 1.6 + - - -
15C GLY* 3.7 21.9 + - - -
16C TYR* 3.9 26.2 - + + -
19C GLU* 4.1 27.1 - - + +
23C GLN* 6.0 0.2 - - - -
31C PHE* 2.6 38.9 + + + +
32C ALA 4.1 1.6 - - - +
34C GLU* 1.3 76.5 - - - +
36C PHE* 1.3 70.2 + + - +
38C ARG* 3.3 13.4 + - + +
39C LEU* 2.7 69.7 + - + +
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Residues in contact with PHE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.9 34.3 - - + -
13C LEU* 4.5 13.5 - - + -
16C TYR* 3.7 37.7 - + + -
32C ALA* 2.9 27.1 + - - +
33C VAL 4.7 0.4 - - - +
35C TYR* 1.3 79.8 - + - +
37C THR* 1.3 55.4 + - - +
39C LEU* 3.5 20.8 - - + +
40C ARG* 2.6 35.0 + - - +
29D VAL* 4.1 5.3 - - + +
32D ALA* 3.8 17.9 - - + -
33D VAL* 3.5 18.9 - - + +
36D PHE* 3.6 32.3 - + - -
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Residues in contact with THR 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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33C VAL* 2.6 31.9 + - - +
34C GLU* 3.9 3.8 - - - -
36C PHE* 1.3 77.5 - - - +
38C ARG* 1.3 59.0 - - + +
40C ARG* 3.2 25.7 + - - +
41C GLU* 2.9 29.2 + - + +
33D VAL* 3.6 25.0 - - - +
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Residues in contact with ARG 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLN* 5.6 7.5 + - - +
31C PHE* 5.6 6.7 - - - -
34C GLU* 3.0 57.8 + - - +
35C TYR* 3.7 12.2 - - + +
37C THR* 1.3 75.5 - - + +
39C LEU* 1.3 56.5 + - - +
41C GLU* 4.0 5.4 - - - +
42C ALA* 2.7 37.1 + - - +
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.7 21.8 - - + -
35C TYR* 2.7 48.9 + - + +
36C PHE* 3.5 30.7 - - + +
38C ARG* 1.3 71.7 - - - +
40C ARG* 1.3 65.2 + - - +
42C ALA* 4.5 6.1 - - + -
43C ARG* 3.0 53.6 + - + +
29D VAL* 4.4 7.5 - - + +
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Residues in contact with ARG 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PHE 2.6 20.5 + - - +
37C THR* 3.2 26.6 + - - +
39C LEU* 1.3 72.2 - - - +
41C GLU* 1.3 56.6 + - - +
43C ARG* 4.1 1.2 - - - +
44C ASN* 2.6 58.7 + - - +
29D VAL* 3.8 20.6 - - + +
30D GLU* 3.2 35.3 + - + +
33D VAL* 3.9 28.6 - - + +
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Residues in contact with GLU 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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37C THR* 2.9 18.3 + - + +
38C ARG* 4.0 5.8 - - - +
40C ARG* 1.3 85.4 + - - +
42C ALA* 1.3 52.2 + - - +
44C ASN* 3.5 9.8 + - + +
45C LYS* 2.4 60.3 + - + +
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Residues in contact with ALA 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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38C ARG 2.7 22.9 + - - +
39C LEU* 4.2 7.2 - - + +
41C GLU* 1.3 71.3 - - - +
43C ARG* 1.3 63.6 + - + +
45C LYS* 3.3 13.2 - - + +
46C GLU* 2.8 30.8 + - - +
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Residues in contact with ARG 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 4.2 10.7 - - - +
39C LEU* 3.0 39.9 + - - +
40C ARG* 4.5 1.1 - - - +
42C ALA* 1.3 76.0 - - + +
44C ASN* 1.3 54.2 + - - +
46C GLU* 3.1 30.1 + - + +
47C GLN* 2.6 34.4 + - - +
76C PRO* 5.9 1.4 + - - +
77C SER* 4.7 23.4 + - - +
79C SER* 5.7 0.9 - - - +
29D VAL* 4.0 27.2 - - + +
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Residues in contact with ASN 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ARG* 2.6 50.2 + - - +
41C GLU* 3.2 13.5 + - + +
43C ARG* 1.3 73.3 - - - +
45C LYS* 1.3 63.0 + - - +
47C GLN* 2.9 32.5 + - - +
48C GLN* 3.0 16.7 + - - +
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Residues in contact with LYS 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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41C GLU* 2.4 57.4 + - + +
42C ALA* 3.3 13.0 - - + +
44C ASN* 1.3 68.6 - - - +
46C GLU* 1.3 62.4 + - - +
48C GLN* 3.4 7.2 + - - +
49C ASN* 2.9 32.0 + - - +
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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 ALA* 2.8 15.5 + - - +
43C ARG* 3.1 36.5 + - + +
45C LYS* 1.3 75.0 - - - +
47C GLN* 1.3 64.3 + - - +
49C ASN* 3.3 9.3 + - - +
50C ALA* 3.2 21.1 + - - +
79C SER* 3.7 24.1 + - - +
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Residues in contact with GLN 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 ARG 2.6 16.0 + - - +
44C ASN* 2.9 24.8 + - - +
46C GLU* 1.3 72.7 - - - +
48C GLN* 1.3 59.9 + - - +
50C ALA* 2.9 6.7 + - - +
51C PHE* 2.8 59.7 + - + +
72C LEU* 4.2 23.7 - - + +
73C LYS* 4.6 5.2 - - - +
76C PRO* 4.9 24.2 - - + +
79C SER* 5.3 5.6 - - - -
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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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44C ASN 3.0 13.5 + - - +
45C LYS* 4.0 6.0 - - - +
47C GLN* 1.3 79.3 - - - +
49C ASN* 1.3 66.4 + - - +
50C ALA 3.3 0.4 + - - -
51C PHE* 3.7 9.2 - - + -
52C TYR* 3.5 26.4 + - + +
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Residues in contact with ASN 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LYS* 2.9 23.1 + - - +
46C GLU* 3.3 11.0 - - - +
47C GLN 3.0 0.2 - - - -
48C GLN* 1.3 83.8 + - - +
50C ALA* 1.3 58.8 + - + +
52C TYR* 4.5 4.3 + - - +
53C GLU* 3.8 18.7 + - - +
83C LEU* 5.1 0.7 - - - +
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Residues in contact with ALA 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLU 3.2 11.7 + - - +
47C GLN* 2.9 4.4 + - - +
49C ASN* 1.3 75.7 - - - +
51C PHE* 1.3 59.8 + - - +
52C TYR 3.3 2.5 - - - -
53C GLU* 4.3 2.9 - - - -
54C ILE* 3.7 27.0 + - - +
72C LEU* 3.9 8.2 - - + +
79C SER* 4.1 21.3 - - - +
83C LEU* 3.6 32.7 - - + +
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Residues in contact with PHE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLN* 2.8 44.0 + - + +
48C GLN* 3.5 7.8 + - + -
49C ASN 3.5 0.2 - - - -
50C ALA* 1.3 78.5 - - - +
52C TYR* 1.3 59.6 - - - +
53C GLU 3.6 0.2 - - - -
54C ILE* 4.7 3.3 - - + +
55C LEU* 4.2 12.8 + - - +
69C ILE* 3.4 54.0 - - + +
72C LEU* 3.1 24.7 - - + -
73C LYS* 4.2 21.3 - - + -
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Residues in contact with TYR 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C GLN* 3.5 20.2 + - + +
49C ASN 5.0 2.5 - - - +
50C ALA* 3.3 0.6 - - - +
51C PHE* 1.3 80.4 - - - +
53C GLU* 1.3 74.6 + - + +
54C ILE 3.6 0.2 - - - -
55C LEU* 3.4 27.7 - - + +
56C HIS* 3.4 39.8 + + - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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