Contacts of the helix formed by residues 12 - 39 (chain C) in PDB entry 4WOL
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 SER 12 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 5.3 1.1 - - - -
11C VAL* 1.3 77.4 - - - +
13C PRO* 1.3 70.2 - - - +
14C GLY* 3.6 4.4 + - - -
15C VAL* 3.0 31.3 + - - +
16C LEU* 2.8 27.2 + - - +
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Residues in contact with PRO 13 (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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11B VAL* 5.0 19.1 - - + +
11C VAL 4.5 1.3 - - - +
12C SER* 1.3 86.7 - - - +
14C GLY* 1.3 55.7 + - - +
16C LEU* 3.8 9.9 - - + +
17C ALA* 3.0 29.5 + - - +
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Residues in contact with GLY 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C SER* 3.2 5.6 + - - -
13C PRO* 1.3 76.7 - - - +
15C VAL* 1.3 64.1 + - - +
17C ALA* 3.2 7.6 + - - +
18C GLY 3.1 18.0 + - - -
103C OLC 3.5 17.2 + - - -
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Residues in contact with VAL 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 5.2 6.5 - - + -
11C VAL* 3.9 16.8 - - + -
12C SER* 3.0 27.8 + - - +
14C GLY* 1.3 75.3 - - - +
16C LEU* 1.3 64.5 + - - +
18C GLY* 3.1 3.1 + - - -
19C ILE* 3.0 35.6 + - + +
103C OLC 3.6 22.3 + - - +
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Residues in contact with LEU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 3.9 28.0 - - + -
15B VAL* 4.0 15.5 - - + -
16B LEU* 4.4 11.2 - - + -
19B ILE* 4.2 15.9 - - + -
11C VAL* 3.7 15.0 - - + +
12C SER 2.8 15.9 + - - +
13C PRO* 3.8 7.2 - - + +
15C VAL* 1.3 76.7 - - - +
17C ALA* 1.3 58.1 + - - +
19C ILE* 3.2 10.2 + - + +
20C VAL* 2.8 47.1 + - + +
101C OLC 4.3 24.0 - - + -
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Residues in contact with ALA 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PRO 3.0 18.6 + - - +
14C GLY* 3.5 8.1 - - - +
16C LEU* 1.3 76.4 - - - +
18C GLY* 1.3 61.7 + - - +
20C VAL* 3.3 7.0 + - - +
21C VAL* 3.1 33.2 + - + +
103C OLC 5.6 0.4 - - - +
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Residues in contact with GLY 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLY 3.1 11.1 + - - -
15C VAL 3.1 1.9 + - - -
17C ALA* 1.3 76.3 - - - +
19C ILE* 1.3 56.9 + - - +
21C VAL* 4.0 3.3 - - - +
22C GLY* 2.9 25.8 + - - -
103C OLC 3.2 49.3 + - - +
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Residues in contact with ILE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.2 29.8 - - + -
20A VAL* 4.5 11.9 - - + -
11C VAL* 4.9 3.6 - - + -
15C VAL* 3.0 30.5 + - + +
16C LEU* 3.5 14.1 - - + +
18C GLY* 1.3 75.0 - - - +
20C VAL* 1.3 64.7 + - - +
23C ASP* 2.9 29.6 + - + +
101C OLC 4.2 34.8 - - + -
103C OLC 3.8 26.6 - - + +
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Residues in contact with VAL 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 4.0 25.1 - - + -
16C LEU* 2.8 30.6 + - + +
17C ALA* 3.7 7.9 - - - +
18C GLY 3.3 0.2 - - - -
19C ILE* 1.3 77.5 - - - +
21C VAL* 1.3 67.5 + - + +
23C ASP* 3.8 0.7 - - - +
24C LEU* 3.0 47.5 + - + +
101C OLC 4.1 31.1 - - + +
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Residues in contact with VAL 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ALA* 3.1 20.0 + - + +
18C GLY* 4.0 4.7 - - - +
20C VAL* 1.3 82.2 - - + +
22C GLY* 1.3 63.4 + - - +
24C LEU* 3.3 6.5 + - - +
25C VAL* 3.1 27.9 + - + +
103C OLC 4.0 27.4 - - + -
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Residues in contact with GLY 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLY 2.9 19.8 + - - -
21C VAL* 1.3 74.3 - - - +
23C ASP* 1.3 62.7 + - - +
25C VAL* 3.4 2.3 + - - +
26C LEU* 3.0 24.8 + - - +
103C OLC 3.6 45.8 - - - +
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Residues in contact with ASP 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.7 4.2 - - - +
23A ASP* 2.5 23.8 - - - +
24A LEU* 3.7 13.2 - - - +
101A K 2.7 25.3 - - - -
23B ASP* 3.6 5.9 - - - +
19C ILE 2.9 22.1 + - - +
20C VAL 3.8 0.2 - - - +
22C GLY* 1.3 76.8 - - - +
24C LEU* 1.3 51.7 + - - +
26C LEU* 3.3 3.9 + - - +
27C THR* 2.7 40.5 + - - -
101C OLC 3.3 23.1 - - + +
103C OLC 3.8 15.1 - - + +
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASP* 5.0 3.6 - - - +
26B LEU* 3.8 36.1 - - + -
27B THR* 5.5 1.3 - - - +
30B ILE* 4.1 17.3 - - + +
20C VAL* 3.0 36.2 + - + +
21C VAL* 3.3 5.1 + - - +
23C ASP* 1.3 75.1 - - - +
25C VAL* 1.3 68.0 + - + +
27C THR* 3.3 8.9 + - + +
28C VAL* 3.1 28.3 + - - +
101C OLC 4.4 17.3 - - + -
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Residues in contact with VAL 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C VAL* 3.1 21.6 + - + +
22C GLY 3.8 4.3 - - - +
24C LEU* 1.3 75.9 - - + +
26C LEU* 1.3 63.5 + - - +
28C VAL* 3.2 9.2 + - - +
29C LEU* 3.2 39.4 + - + +
102C OLC 5.2 2.7 - - + -
103C OLC 4.1 39.5 - - + -
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Residues in contact with LEU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.8 29.8 - - + -
22C GLY 3.0 16.6 + - - +
23C ASP* 3.7 5.6 - - - +
25C VAL* 1.3 74.1 - - + +
27C THR* 1.3 60.6 + - - +
29C LEU* 3.3 9.8 + - + +
30C ILE* 2.9 49.7 + - + +
102C OLC 4.6 29.2 - - + -
103C OLC 3.7 34.3 - - + +
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Residues in contact with THR 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP* 4.7 0.2 + - - -
24A LEU* 5.3 1.4 - - - +
27A THR* 3.7 25.3 + - + +
101A K 2.8 20.1 - - - -
27B THR* 3.9 24.7 - - + +
30B ILE* 3.9 22.7 - - + -
31B ALA* 5.4 0.7 - - + +
23C ASP* 2.7 29.8 + - - -
24C LEU* 3.5 12.1 - - + +
25C VAL 3.2 0.2 - - - -
26C LEU* 1.3 72.9 - - - +
28C VAL* 1.3 62.6 + - - +
30C ILE* 3.4 1.8 + - - +
31C ALA* 3.2 24.1 + - + +
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Residues in contact with VAL 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 3.6 31.2 - - + -
34B VAL* 4.3 15.1 - - + +
24C LEU 3.1 15.1 + - - +
25C VAL* 3.2 9.4 + - - +
27C THR* 1.3 76.3 - - - +
29C LEU* 1.3 67.3 + - + +
31C ALA* 3.5 3.6 + - - +
32C LEU* 3.0 29.8 + - + +
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C VAL* 3.2 37.1 + - + +
26C LEU* 3.8 9.2 - - + +
28C VAL* 1.3 82.1 - - + +
30C ILE* 1.3 59.5 + - - +
32C LEU* 3.3 20.6 + - + +
33C ALA* 2.8 30.8 + - - +
102C OLC 3.6 56.4 - - + +
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Residues in contact with ILE 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.3 31.0 - - + +
27A THR* 4.1 14.8 - - + +
28A VAL* 4.0 35.0 - - + -
31A ALA* 4.7 0.7 - - + -
26C LEU* 2.9 39.1 + - + +
27C THR 3.9 3.6 - - - +
29C LEU* 1.3 73.9 - - + +
31C ALA* 1.3 67.8 + - - +
33C ALA* 3.1 6.7 + - - +
34C VAL* 2.9 30.0 + - + +
102C OLC 5.2 4.5 - - + -
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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
----------------------------------------------------------
27A THR* 5.4 1.5 - - + +
31A ALA* 3.9 15.3 - - + -
30B ILE* 4.9 0.2 - - + -
31B ALA* 4.1 21.5 - - + +
34B VAL* 4.1 9.6 - - + -
27C THR* 3.2 11.4 + - + +
28C VAL* 3.7 7.6 - - - +
30C ILE* 1.3 79.3 - - - +
32C LEU* 1.3 64.3 + - - +
34C VAL* 3.2 0.9 + - - +
35C TYR* 3.1 48.1 + - + +
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 3.9 21.7 - - + +
28C VAL* 3.0 17.7 + - + +
29C LEU* 3.5 21.5 - - + +
31C ALA* 1.3 75.5 - - - +
33C ALA* 1.3 57.5 + - - +
35C TYR* 3.3 4.1 + - + +
36C PHE* 2.9 30.8 + - - +
102C OLC 4.1 56.9 + - + +
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Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU 2.8 20.4 + - - +
30C ILE* 3.1 6.5 + - - +
32C LEU* 1.3 72.0 - - - +
34C VAL* 1.3 61.4 + - + +
36C PHE* 3.6 6.8 - - + +
37C LEU* 2.9 42.0 + - + +
102C OLC 3.7 30.7 - - + +
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Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 4.6 9.9 - - + +
31A ALA* 3.8 39.5 - - + +
32A LEU* 4.0 25.6 - - + -
35A TYR* 4.2 9.6 - - + -
30C ILE* 2.9 26.9 + - + +
31C ALA 3.7 3.8 - - - +
33C ALA* 1.3 77.3 - - + +
35C TYR* 1.3 63.9 + - + +
37C LEU* 3.9 7.1 - - + +
38C GLY* 2.9 25.8 + - - -
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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
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31A ALA* 3.3 26.6 - - + -
34A VAL* 3.4 13.9 - - - +
35A TYR* 4.1 18.6 - + + -
31B ALA* 2.7 31.3 + - - +
34B VAL* 4.0 9.6 - - + -
35B TYR* 3.4 55.2 - + + -
31C ALA* 3.1 31.4 + - + +
32C LEU* 4.0 3.4 - - + +
34C VAL* 1.3 80.0 - - + +
36C PHE* 1.3 65.6 + - - +
38C GLY* 3.3 0.7 + - - -
39C ARG* 3.1 31.9 + - - +
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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
----------------------------------------------------------
32C LEU 2.9 18.7 + - - +
33C ALA* 3.6 5.8 - - - +
35C TYR* 1.3 79.8 - - - +
37C LEU* 1.3 77.5 + - + +
39C ARG* 3.3 38.8 + - - +
40C LEU* 3.4 40.3 - - + +
102C OLC 3.5 53.6 - - + +
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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
----------------------------------------------------------
33C ALA* 2.9 26.0 + - + +
34C VAL* 4.0 5.8 - - - +
36C PHE* 1.3 92.0 - - + +
38C GLY* 1.3 60.7 + - - +
40C LEU* 3.2 34.5 + - + +
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Residues in contact with GLY 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TYR* 2.8 47.8 + - - -
39A ARG* 4.0 4.7 + - - -
34C VAL 2.9 15.7 + - - -
35C TYR 3.7 0.7 - - - -
36C PHE 3.2 0.4 - - - -
37C LEU* 1.3 77.6 - - - +
39C ARG* 1.3 58.5 + - - +
40C LEU 3.3 3.4 + - - +
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Residues in contact with ARG 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TYR* 5.4 1.3 - - + -
39A ARG* 5.8 0.2 - - - +
35C TYR* 3.1 17.5 + - - +
36C PHE* 3.3 29.4 - - - +
37C LEU 3.2 0.2 - - - -
38C GLY* 1.3 77.6 - - - +
40C LEU* 1.3 69.1 + - - +
102C OLC 3.2 43.5 + - - -
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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