Contacts of the helix formed by residues 22 - 45 (chain C) in PDB entry 3CUQ
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 ASN 22 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 3.7 32.5 + - + +
218A LYS* 4.1 11.1 + - - +
220A GLY 5.3 1.2 - - - +
372B VAL 3.5 13.5 + - - +
373B GLU 3.4 9.5 - - - +
374B GLY* 3.9 9.9 - - - -
20C GLN* 3.4 2.4 - - + +
21C PRO* 1.3 83.0 - - - +
23C VAL* 1.3 62.6 + - - +
24C ASP* 3.1 16.0 + - - +
25C THR* 2.8 46.8 + - - +
26C ARG* 3.0 26.0 + - - +
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Residues in contact with VAL 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B THR* 3.8 25.4 - - + -
341B GLU* 3.8 18.6 - - - +
373B GLU* 2.9 29.7 + - + +
376B ARG* 4.3 24.2 - - - +
21C PRO 3.2 4.3 + - - +
22C ASN* 1.3 74.6 - - - +
24C ASP* 1.3 65.0 + - - +
26C ARG* 3.8 18.2 - - + +
27C GLN* 3.2 27.5 + - + +
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Residues in contact with ASP 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LYS 5.4 3.3 - - - +
338B THR* 2.6 39.1 + - - +
339B SER 5.1 0.2 + - - -
340B GLU* 3.3 42.2 + - + +
341B GLU* 3.8 10.7 - - - +
22C ASN* 3.1 12.8 + - - +
23C VAL* 1.3 76.7 - - - +
25C THR* 1.3 64.4 - - - +
27C GLN* 3.6 9.6 + - - +
28C LYS* 3.5 26.8 + - - +
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Residues in contact with THR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU 4.5 0.9 + - - -
220A GLY* 4.2 17.8 - - - -
222A ALA 5.1 2.9 + - - +
223A TRP* 3.6 44.2 - - + +
20C GLN* 4.1 15.9 - - + +
22C ASN* 2.8 27.9 + - - +
24C ASP* 1.3 76.2 - - - +
26C ARG* 1.3 59.4 + - - +
28C LYS* 3.0 12.9 + - + +
29C GLN* 2.8 26.2 + - - +
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Residues in contact with ARG 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B GLU* 6.0 5.3 - - - +
19C LEU* 3.6 37.8 - - - +
20C GLN* 3.1 28.8 + - - +
21C PRO* 4.1 13.8 + - - +
22C ASN 3.0 17.2 + - - +
23C VAL* 3.9 16.9 - - + +
24C ASP 3.3 0.6 - - - -
25C THR* 1.3 70.5 - - - +
27C GLN* 1.3 69.4 + - + +
28C LYS 2.8 3.0 + - - -
29C GLN* 3.0 13.5 + - - +
30C LEU* 2.9 46.2 + - + +
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Residues in contact with GLN 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B GLU* 2.9 39.7 - - - +
344B LYS* 6.0 3.6 - - - +
23C VAL* 3.2 21.4 + - + +
24C ASP* 3.9 9.8 - - - +
25C THR 3.3 0.4 - - - -
26C ARG* 1.3 75.8 - - + +
28C LYS* 1.3 56.9 + - + +
30C LEU* 3.6 8.0 + - - +
31C ALA* 3.1 27.4 + - - +
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Residues in contact with LYS 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A HIS* 3.3 35.4 + - + +
223A TRP* 5.1 13.3 - - + -
340B GLU* 4.5 17.2 + - - -
10C GLN* 5.3 0.5 - - - +
24C ASP* 3.5 16.6 + - - +
25C THR* 3.0 14.6 + - - +
26C ARG 2.9 0.4 - - - -
27C GLN* 1.3 78.8 - - + +
29C GLN* 1.3 67.4 + - - +
30C LEU 3.2 0.4 - - - -
31C ALA* 3.5 5.7 + - + +
32C ALA* 3.1 22.3 + - - +
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Residues in contact with GLN 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TRP* 4.0 15.6 - - + -
15C PRO 3.7 2.6 + - - -
16C PHE* 2.7 49.2 + - + +
18C THR 2.5 27.0 + - - +
19C LEU* 3.7 6.6 - - - +
20C GLN* 3.0 31.7 + - + +
25C THR 2.8 12.4 + - - +
26C ARG* 3.4 14.1 - - - +
28C LYS* 1.3 76.9 - - - +
30C LEU* 1.3 60.8 + - + +
32C ALA* 3.0 17.5 + - - +
33C TRP* 3.0 20.3 + - + +
69C LEU* 6.0 0.8 - - - +
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 4.6 13.2 - - + -
26C ARG* 2.9 36.5 + - + +
27C GLN* 4.0 5.8 - - - +
29C GLN* 1.3 79.8 - - + +
31C ALA* 1.3 65.9 + - - +
32C ALA 3.0 1.1 - - - -
33C TRP* 4.0 12.9 - - + +
34C CYS* 3.1 30.1 + - - -
73C SER 5.7 0.4 - - - +
76C ILE* 4.4 28.3 - - + -
77C VAL* 5.0 13.6 - - + +
80C GLU* 4.6 21.8 - - + +
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLN 3.1 18.8 + - - +
28C LYS* 4.0 6.1 - - - +
29C GLN 3.4 0.2 - - - -
30C LEU* 1.3 76.5 - - - +
32C ALA* 1.3 63.0 + - - +
34C CYS* 3.8 5.6 - - - +
35C SER* 3.1 24.1 + - - -
84C LYS* 6.0 1.6 - - - +
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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
----------------------------------------------------------
223A TRP* 6.3 0.2 - - + -
8C PRO* 5.4 3.8 - - + +
10C GLN* 3.5 29.8 - - + +
16C PHE* 3.8 16.7 - - + -
28C LYS 3.1 12.1 + - - +
29C GLN* 3.0 10.3 + - - +
31C ALA* 1.3 80.0 - - - +
33C TRP* 1.3 59.6 + - - +
35C SER* 3.5 5.8 + - - -
36C LEU* 3.2 23.2 + - - +
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Residues in contact with TRP 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TYR* 5.1 0.4 - + - -
16C PHE* 3.1 60.2 + + - -
17C PHE* 3.9 23.6 - + - -
29C GLN* 3.0 23.8 + - + +
30C LEU* 4.0 14.1 - - + +
31C ALA 3.4 0.4 - - - -
32C ALA* 1.3 73.4 - - - +
34C CYS* 1.3 61.0 + - - +
36C LEU* 3.0 19.6 + - + +
37C VAL* 2.8 31.2 + - - +
59C LEU* 3.2 28.7 - - + -
60C PHE* 3.2 32.1 - + - -
69C LEU* 3.5 33.8 - - + +
77C VAL* 4.3 17.3 - - + -
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Residues in contact with CYS 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 3.1 22.8 + - - +
31C ALA* 3.8 5.6 - - - +
33C TRP* 1.3 79.5 - - - +
35C SER* 1.3 61.7 + - - +
37C VAL* 3.2 14.5 - - - +
38C LEU* 3.2 26.1 - - + +
77C VAL* 4.4 7.8 - - - +
80C GLU* 3.9 20.0 - - - -
81C LEU* 3.7 24.7 - - + -
84C LYS* 3.7 26.9 - - - +
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Residues in contact with SER 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ALA 3.1 18.4 + - - -
32C ALA* 3.8 7.0 - - - -
33C TRP 3.2 0.4 - - - -
34C CYS* 1.3 77.5 - - - +
36C LEU* 1.3 57.2 - - - +
38C LEU* 3.9 6.8 - - - +
39C SER* 3.2 28.9 + - - -
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Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 4.0 15.9 - - + -
6C GLU 5.2 0.2 - - - +
7C TRP* 3.8 14.4 - - + -
8C PRO* 3.4 35.9 - - + -
11C TYR* 4.1 20.9 - - + -
16C PHE* 4.5 7.0 - - + -
32C ALA 3.2 14.1 + - - +
33C TRP* 3.0 31.6 + - + +
35C SER* 1.3 78.3 - - - +
37C VAL* 1.3 69.5 + - - +
39C SER* 3.2 5.7 + - - +
40C PHE* 2.9 23.5 + - + +
59C LEU* 4.0 11.7 - - + -
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Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C TRP 2.8 21.9 + - - +
34C CYS* 3.2 11.9 - - - +
36C LEU* 1.3 70.1 - - - +
38C LEU* 1.3 68.3 + - - +
40C PHE* 2.8 14.9 + - - +
41C CYS* 3.0 24.9 + - - -
49C MET* 5.9 2.2 - - - -
59C LEU* 4.1 30.7 - - + +
60C PHE* 4.8 9.0 - - + -
77C VAL* 4.7 5.2 - - + -
78C LEU* 5.5 4.9 - - + -
81C LEU* 3.1 36.6 - - + -
97C PHE* 6.2 0.7 - - + -
99C ILE* 4.2 11.9 - - + -
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C CYS* 3.2 18.4 + - + +
35C SER* 3.9 6.1 - - - +
37C VAL* 1.3 77.1 - - - +
39C SER* 1.3 56.9 + - - +
41C CYS* 4.0 3.0 - - - +
42C ARG* 3.1 23.1 + - - +
81C LEU* 3.8 23.8 - - + -
84C LYS* 5.7 2.9 - - + -
86C ASN* 3.4 34.3 - - + +
99C ILE* 3.6 27.1 - - + -
101C TRP* 3.3 33.3 - - - +
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Residues in contact with SER 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 3.2 33.9 - - - +
6C GLU 5.5 0.2 + - - -
35C SER 3.2 15.0 + - - -
36C LEU* 3.2 9.2 + - - +
37C VAL 3.0 1.0 + - - -
38C LEU* 1.3 78.1 - - - +
40C PHE* 1.3 63.1 + - - +
42C ARG* 4.1 10.3 - - - +
43C LEU* 3.4 14.6 + - - +
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Residues in contact with PHE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 3.9 15.0 - + + -
7C TRP* 3.8 34.8 - + - -
36C LEU* 2.9 15.9 + - + +
37C VAL 2.8 4.2 + - - +
39C SER* 1.3 76.2 - - - +
41C CYS* 1.3 68.8 + - - +
43C LEU* 3.4 2.2 + - - +
44C HIS* 3.0 70.8 + + - -
46C GLN* 4.4 13.9 - - - -
49C MET* 5.2 4.3 - - + -
57C SER* 4.6 6.7 - - - -
58C PRO* 4.2 23.8 - - + -
59C LEU* 3.7 38.4 - - + -
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Residues in contact with CYS 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C VAL* 3.0 24.1 + - - +
38C LEU* 4.0 4.7 - - - +
40C PHE* 1.3 82.5 - - - +
42C ARG* 1.3 67.7 + - - +
43C LEU 2.7 3.3 + - - -
44C HIS* 2.8 14.2 + - - +
45C LYS* 2.8 13.9 + - - -
46C GLN* 3.6 27.4 - - - +
49C MET* 4.8 13.2 - - - -
59C LEU* 5.6 0.2 - - - -
99C ILE* 3.6 37.2 - - + +
101C TRP* 5.1 4.3 - - + -
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Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU 3.1 17.2 + - - +
39C SER* 4.1 10.6 - - - +
41C CYS* 1.3 76.7 - - - +
43C LEU* 1.3 61.2 + - - +
45C LYS* 3.9 14.1 + - - +
101C TRP* 3.3 77.0 + - + +
102C ARG* 5.4 1.8 - - - +
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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
----------------------------------------------------------
4C SER* 5.0 6.3 - - - +
5C PHE* 3.7 44.6 - - + +
39C SER 3.4 16.7 + - - +
40C PHE 3.4 3.8 + - - +
41C CYS 2.7 4.9 + - - -
42C ARG* 1.3 78.1 - - - +
44C HIS* 1.3 89.7 + - + +
45C LYS* 3.2 13.3 + - - +
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Residues in contact with HIS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 6.1 0.6 - - - -
40C PHE* 3.0 62.6 + + - +
41C CYS 2.8 5.8 + - - +
43C LEU* 1.3 93.5 - - + +
45C LYS* 1.3 64.0 + - - +
46C GLN* 3.0 41.1 + - + +
58C PRO* 6.0 1.1 - - + +
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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
----------------------------------------------------------
41C CYS 2.8 8.9 + - - -
42C ARG* 4.4 10.1 - - - +
43C LEU 3.2 10.2 - - - +
44C HIS* 1.3 79.5 - - - +
46C GLN* 1.3 60.4 + - - +
47C SER* 3.9 2.4 + - - -
145C ASP* 5.5 1.9 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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