Contacts of the helix formed by residues 1 - 31 (chain C) in PDB entry 3CRP
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 MET 1 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LYS* 1.3 69.4 + - - +
3C VAL 3.2 2.9 - - - +
4C LYS* 3.2 40.5 + - + +
5C GLN* 2.9 44.7 + - + +
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Residues in contact with LYS 2 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL 3.2 26.5 + - - +
32A GLY* 4.6 7.7 + - - -
30B LEU* 3.6 33.7 - - + +
1C MET* 1.3 78.9 - - - +
3C VAL* 1.3 59.5 + - + +
5C GLN* 3.3 2.7 + - - +
6C LEU* 3.0 36.9 + - + +
3D VAL* 3.9 26.2 - - + -
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Residues in contact with VAL 3 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.2 0.8 - - - +
2C LYS* 1.3 75.1 - - + +
4C LYS* 1.3 61.9 + - + +
6C LEU* 3.3 3.1 + - - +
7C GLU* 2.8 56.1 + - - +
2D LYS* 3.8 27.4 - - + -
3D VAL* 4.0 21.3 - - + -
6D LEU* 3.8 17.0 - - + -
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Residues in contact with LYS 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.2 40.7 + - + +
3C VAL* 1.3 80.5 - - + +
5C GLN* 1.3 56.9 + - + +
7C GLU* 3.3 16.2 + - - +
8C ASP* 2.9 36.0 + - - +
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Residues in contact with GLN 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ARG* 3.1 40.0 + - - +
27B LEU* 5.0 1.1 - - - +
29B LYS* 4.0 4.5 - - - +
30B LEU* 3.4 51.2 + - + +
1C MET* 2.9 42.0 + - + +
2C LYS 3.8 3.8 - - - +
4C LYS* 1.3 73.8 - - + +
6C LEU* 1.3 60.8 + - - +
8C ASP* 3.3 7.7 + - - +
9C ALA* 3.0 26.5 + - - +
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Residues in contact with LEU 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA* 6.1 1.3 - - + -
31A VAL* 4.3 16.6 - - + -
27B LEU* 3.9 23.1 - - + -
30B LEU* 3.8 10.5 - - + -
2C LYS* 3.0 28.3 + - + +
3C VAL 3.8 3.1 - - - +
5C GLN* 1.3 73.4 - - - +
7C GLU* 1.3 61.8 + - - +
9C ALA* 3.2 4.4 + - - +
10C VAL* 2.9 33.9 + - - +
3D VAL* 3.8 42.4 - - + +
6D LEU* 3.8 20.9 - - + -
7D ALA* 4.9 3.8 - - - +
10D VAL* 4.6 15.5 - - + -
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Residues in contact with GLU 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C VAL* 2.8 37.5 + - - +
4C LYS* 3.6 18.4 - - - +
6C LEU* 1.3 76.0 - - - +
8C ASP* 1.3 60.8 + - - +
10C VAL* 3.3 9.3 + - - +
11C GLU* 3.0 33.6 + - + +
2D LYS* 3.8 14.9 + - - -
6D LEU* 3.8 19.7 - - + -
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Residues in contact with ASP 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ARG* 3.8 26.8 + - + -
4C LYS* 2.9 22.2 + - - +
5C GLN* 3.6 5.5 - - - +
7C GLU* 1.3 77.1 - - - +
9C ALA* 1.3 65.0 + - - +
11C GLU* 3.2 10.9 + - - +
12C GLU* 3.0 29.0 + - + +
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Residues in contact with ALA 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA* 4.2 13.1 - - + +
26B ARG* 4.7 4.8 - - + +
27B LEU* 3.9 34.8 - - + -
5C GLN 3.0 14.2 + - - +
6C LEU* 3.5 8.3 - - - +
8C ASP* 1.3 76.2 - - - +
10C VAL* 1.3 63.6 + - - +
12C GLU* 3.1 8.8 + - - +
13C LEU* 3.0 29.8 + - + +
10D VAL* 4.8 7.4 - - + -
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Residues in contact with VAL 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU 2.9 17.6 + - - +
7C GLU* 3.5 10.1 - - - +
8C ASP 3.2 0.2 - - - -
9C ALA* 1.3 76.9 - - - +
11C GLU* 1.3 63.3 + - - +
13C LEU* 3.2 9.5 + - - +
14C LEU* 2.9 39.9 + - + +
6D LEU* 4.2 19.1 - - + +
9D LYS* 3.9 31.6 - - + -
10D VAL* 3.8 22.4 - - + +
13D LEU* 3.8 8.2 - - + +
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Residues in contact with GLU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLU 3.0 19.3 + - - +
8C ASP* 3.2 13.2 + - - +
10C VAL* 1.3 79.7 - - - +
12C GLU* 1.3 65.5 + - + +
14C LEU* 3.4 26.7 + - - +
15C SER* 3.1 26.4 + - - -
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Residues in contact with GLU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B HIS* 2.9 54.8 + - - +
22B ASN* 3.0 35.1 + - + +
23B ALA* 3.9 11.9 - - + +
26B ARG* 5.3 4.3 - - + -
8C ASP* 3.0 21.0 + - + +
9C ALA 3.5 7.0 - - - +
11C GLU* 1.3 78.8 - - - +
13C LEU* 1.3 58.5 + - - +
15C SER* 3.2 3.4 + - - -
16C ALA* 2.8 25.1 + - - +
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 4.1 7.6 - - + -
20B LEU* 3.4 30.7 - - + -
23B ALA* 3.9 14.8 - - + -
9C ALA* 3.0 21.0 + - + +
10C VAL* 3.6 7.6 - - - +
12C GLU* 1.3 74.7 - - - +
14C LEU* 1.3 58.3 - - - +
16C ALA* 3.6 3.2 - - - +
17C ASN* 2.9 34.6 + - - +
10D VAL* 3.7 50.5 - - + +
13D LEU* 3.9 17.9 - - + -
14D LEU* 4.1 13.5 - - + -
17D ASN* 5.7 1.1 - - + +
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Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 2.9 25.9 + - + +
11C GLU* 3.6 35.9 - - - +
13C LEU* 1.3 74.8 - - - +
15C SER* 1.3 57.9 + - - +
17C ASN* 3.4 6.3 + - + +
18C TYR* 2.9 28.3 + - - +
9D LYS* 6.1 0.7 - - + -
13D LEU* 3.8 28.2 - - + +
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Residues in contact with SER 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B HIS* 3.4 36.6 + - - -
35B NA 4.4 2.5 - - - -
11C GLU 3.1 14.5 + - - -
12C GLU* 3.6 4.6 - - - -
13C LEU 3.2 0.2 - - - -
14C LEU* 1.3 74.5 - - - +
16C ALA* 1.3 65.9 + - - +
18C TYR* 3.2 9.1 + - - +
19C HIS* 3.1 30.6 + - - -
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Residues in contact with ALA 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA* 3.7 28.1 - - + +
19B HIS* 3.7 8.9 - - + +
20B LEU* 3.8 24.5 - - + -
12C GLU 2.8 16.4 + - - +
13C LEU 3.3 5.8 + - - +
15C SER* 1.3 76.2 - - - +
17C ASN* 1.3 63.3 + - - +
19C HIS* 3.3 2.9 + - - -
20C LEU* 3.0 25.3 + - - +
17D ASN* 4.0 9.0 - - - +
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Residues in contact with ASN 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU 2.9 19.5 + - - +
14C LEU* 3.8 6.2 - - + +
16C ALA* 1.3 72.6 - - - +
18C TYR* 1.3 61.1 + - - +
20C LEU* 3.3 1.5 + - - +
21C GLU* 2.9 35.8 + - - +
13D LEU* 3.2 35.1 + - - +
16D LYS* 3.7 27.3 - - - +
17D ASN* 3.0 38.8 + - - +
20D LEU* 3.7 15.4 - - + +
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Residues in contact with TYR 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU 2.9 13.9 + - - +
15C SER* 3.3 12.1 - - - +
17C ASN* 1.3 77.0 - - - +
19C HIS* 1.3 85.5 + + - +
21C GLU* 3.3 18.7 + - - +
22C ASN* 3.0 56.5 + - - +
26E ARG* 2.8 25.3 + - + -
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Residues in contact with HIS 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLU* 2.7 50.2 + - - +
15B SER* 3.4 23.1 - - - -
16B ALA 3.8 7.2 - - - +
19B HIS* 3.6 12.5 + + - -
35B NA 2.3 30.9 - - - -
15C SER* 3.1 22.8 + - - -
16C ALA 3.9 3.6 - - - +
18C TYR* 1.3 98.6 - + - +
20C LEU* 1.3 65.5 + - - +
22C ASN* 3.1 6.4 + - - +
23C ALA 3.0 18.4 + - - -
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Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 5.0 0.2 - - + -
17A ASN* 4.2 10.8 - - - +
13B LEU* 3.5 32.3 - - + -
16B ALA* 3.7 15.7 - - + -
16C ALA 3.0 15.8 + - - +
17C ASN* 3.3 4.9 + - - +
19C HIS* 1.3 75.7 - - - +
21C GLU* 1.3 58.8 + - - +
23C ALA* 3.1 4.5 + - + +
24C VAL* 2.9 33.3 + - - +
17D ASN* 3.6 47.1 - - - +
20D LEU* 3.7 21.8 - - + -
21D ALA* 3.9 9.2 - - - +
24D VAL* 4.2 9.1 - - + +
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Residues in contact with GLU 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASN 2.9 17.5 + - - +
18C TYR* 3.3 23.4 - - - +
20C LEU* 1.3 76.3 - - - +
22C ASN* 1.3 59.9 + - - +
24C VAL* 3.3 8.1 + - - +
25C ALA* 2.9 28.6 + - - +
16D LYS* 2.7 31.2 + - - -
20D LEU* 3.9 20.6 - - + +
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Residues in contact with ASN 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLU* 3.2 30.0 + - + +
18C TYR* 3.0 49.3 + - - +
19C HIS* 3.1 6.4 + - - +
21C GLU* 1.3 79.5 - - - +
23C ALA* 1.3 63.3 + - - +
25C ALA* 3.2 7.2 + - - +
26C ARG* 3.0 37.9 + - - +
26E ARG* 3.4 31.9 + - - +
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Residues in contact with ALA 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA* 4.2 17.5 - - + +
12B GLU* 3.9 18.7 - - + +
13B LEU* 4.6 8.3 - - + -
19C HIS 3.0 12.8 + - - +
20C LEU* 3.1 10.1 + - - +
22C ASN* 1.3 75.7 - - - +
24C VAL* 1.3 61.9 + - - +
26C ARG* 3.2 7.3 + - - +
27C LEU* 3.0 30.5 + - - +
24D VAL* 3.9 16.2 - - + -
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Residues in contact with VAL 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU 2.9 19.2 + - - +
21C GLU* 3.6 9.4 - - - +
23C ALA* 1.3 76.3 - - - +
25C ALA* 1.3 57.1 + - - +
27C LEU* 3.3 1.2 + - - -
28C LYS* 3.0 59.8 + - + +
20D LEU* 3.7 25.4 - - + +
23D GLU* 4.0 16.2 - - + +
24D VAL* 3.7 20.2 - - + +
27D LEU* 3.6 13.8 - - + +
----------------------------------------------------------
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLU 2.9 15.1 + - - +
22C ASN* 3.5 11.7 - - - +
24C VAL* 1.3 77.6 - - - +
26C ARG* 1.3 68.4 + - - +
28C LYS* 3.4 7.9 + - - +
29C LYS* 3.3 21.8 + - - +
22E ASN* 5.6 3.1 - - - +
25E ALA* 6.3 2.9 - - + -
----------------------------------------------------------
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Residues in contact with ARG 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLN* 4.2 19.0 + - - +
8B ASP* 4.2 22.3 + - + +
9B ALA 4.7 3.6 - - - +
12B GLU* 3.7 13.3 + - + +
22C ASN* 3.0 30.1 + - - +
23C ALA* 3.2 8.7 + - - +
25C ALA* 1.3 79.1 - - - +
27C LEU* 1.3 60.3 + - + +
29C LYS* 3.4 8.9 - - - +
30C LEU* 3.1 23.9 + - - +
18E TYR* 3.4 27.0 + - - +
19E HIS* 5.3 3.0 + - - -
22E ASN* 3.2 36.1 - - - +
26E ARG* 2.5 44.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 5.5 0.9 - - + -
5B GLN 4.4 5.4 - - - +
6B LEU* 3.9 28.3 - - + -
9B ALA* 3.9 21.5 - - + -
23C ALA 3.0 17.6 + - - +
24C VAL* 4.0 2.2 - - - +
25C ALA 3.3 0.2 - - - -
26C ARG* 1.3 75.6 - - - +
28C LYS* 1.3 60.8 + - - +
30C LEU* 3.3 7.8 + - + -
31C VAL* 3.0 35.0 + - - +
24D VAL* 3.7 43.5 - - + +
27D LEU* 3.7 16.6 - - + -
28D ALA* 4.2 5.6 - - + +
31D VAL* 3.4 16.2 - - + +
----------------------------------------------------------
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Residues in contact with LYS 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 3.0 44.1 + - + +
25C ALA* 3.9 6.3 - - - +
26C ARG 3.4 0.2 - - - -
27C LEU* 1.3 71.9 - - - +
29C LYS* 1.3 61.2 + - - +
31C VAL* 2.8 37.4 + - + +
23D GLU* 4.6 4.8 + - - -
26D ARG* 4.5 11.7 - - - +
27D LEU* 3.5 20.6 - - + -
----------------------------------------------------------
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Residues in contact with LYS 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLN* 3.8 17.1 + - - +
25C ALA 3.3 11.2 + - - +
26C ARG* 3.4 12.3 - - - +
27C LEU 3.2 0.2 - - - -
28C LYS* 1.3 81.3 - - - +
30C LEU* 1.3 62.9 + - - +
31C VAL 3.6 4.3 - - - +
17E ASN* 4.9 6.4 - - - +
18E TYR* 4.2 22.4 - - + +
21E GLU* 3.1 32.5 + - - -
22E ASN* 5.3 5.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LYS* 3.6 45.8 - - + +
5B GLN* 2.8 35.3 - - + +
6B LEU* 3.8 8.5 - - + +
26C ARG 3.1 11.9 + - - +
27C LEU* 3.5 6.3 - - + +
28C LYS 3.2 0.4 - - - -
29C LYS* 1.3 78.0 - - - +
31C VAL* 1.3 61.7 + - - +
31D VAL* 3.1 54.3 - - + +
----------------------------------------------------------
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Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU 3.0 14.8 + - - +
28C LYS* 2.8 30.2 + - + +
29C LYS 3.6 4.5 - - - +
30C LEU* 1.3 81.1 - - - +
27D LEU* 3.6 24.5 - - + +
30D LEU* 3.6 34.1 - - + +
31D VAL* 3.1 22.0 - - + +
----------------------------------------------------------
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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