Contacts of the helix formed by residues 3 - 28 (chain C) in PDB entry 1RM1
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 3 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER* 5.0 4.9 + - - -
87B VAL* 4.7 7.8 - - - +
2C SER* 1.3 79.3 - - - +
4C ALA* 1.3 65.5 + - - +
5C GLU* 3.5 13.8 + - - +
6C ALA* 2.8 35.3 - - + +
7C SER* 3.0 24.8 + - - -
52C THR* 3.0 7.1 + - - +
273C ASP 3.6 19.5 - - - +
274C TYR* 4.1 29.0 - - + +
275C THR 4.3 4.9 + - - +
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Residues in contact with ALA 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C SER 4.0 2.2 + - - -
3C ASN* 1.3 71.6 + - - +
5C GLU* 1.3 68.8 + - - +
7C SER* 3.0 9.1 + - - -
8C ARG* 2.8 25.1 + - - +
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Residues in contact with GLU 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASN 4.2 12.1 - - - +
56B THR* 3.2 12.1 + - - -
57B GLN* 2.7 32.2 + - - +
58B SER* 3.0 25.5 + - - +
3C ASN* 3.4 10.4 - - - +
4C ALA* 1.3 78.8 - - - +
6C ALA* 1.3 56.1 + - - +
8C ARG* 3.1 9.6 + - - +
9C VAL* 2.8 33.3 + - + +
275C THR* 2.9 35.8 + - - +
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Residues in contact with ALA 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ASN* 2.8 28.9 - - + +
4C ALA 3.3 0.2 - - - -
5C GLU* 1.3 71.3 - - - +
7C SER* 1.3 63.1 + - - +
9C VAL* 3.2 0.5 + - - +
10C TYR* 2.9 33.3 + - + -
52C THR* 4.6 9.2 - - + -
273C ASP* 3.7 25.6 - - + +
274C TYR* 4.2 0.2 - - - -
275C THR* 3.8 26.0 - - + -
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Residues in contact with SER 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C SER 5.2 0.2 + - - -
3C ASN 3.0 8.4 + - - -
4C ALA* 3.0 13.0 + - - -
6C ALA* 1.3 76.3 - - - +
8C ARG* 1.3 64.7 + - - +
10C TYR* 3.2 1.6 + - - +
11C GLU* 3.0 34.7 + - - +
52C THR* 2.5 32.8 + - - -
53C THR* 2.6 25.8 + - - -
54C PHE* 4.4 3.1 - - - -
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Residues in contact with ARG 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASN* 3.6 34.6 + - - +
4C ALA 2.8 12.6 + - - +
5C GLU* 3.4 11.7 - - - +
7C SER* 1.3 76.1 - - - +
9C VAL* 1.3 63.9 + - + +
11C GLU* 3.3 6.7 + - - +
12C ILE* 2.9 43.0 + - + +
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Residues in contact with VAL 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR* 3.8 17.2 - - + +
52B LEU* 4.2 20.9 - - + -
55B ASN* 3.6 31.4 - - + +
56B THR* 5.1 1.6 - - - -
5C GLU* 2.8 24.1 + - + +
6C ALA 3.7 4.3 - - - +
8C ARG* 1.3 71.8 - - + +
10C TYR* 1.3 64.0 + - + +
12C ILE* 3.8 3.6 - - - +
13C ILE* 3.0 52.5 + - + +
275C THR* 4.0 21.3 - - + +
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Residues in contact with TYR 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR* 3.9 6.0 + - - -
15B ILE* 3.5 42.8 + - + +
6C ALA* 2.9 22.6 + - + +
7C SER 3.6 4.3 - - - +
9C VAL* 1.3 86.4 - - + +
11C GLU* 1.3 59.8 + - - +
13C ILE* 3.2 4.8 + - + +
14C VAL* 2.9 31.4 + - - +
46C LEU* 4.1 12.6 - - + -
51C VAL* 4.0 14.4 - - + -
52C THR* 4.4 2.9 - - + -
54C PHE* 3.7 30.3 - + + -
56C TRP* 4.9 0.4 - - - -
266C VAL* 3.4 25.8 - - + +
273C ASP* 2.5 34.8 + - + -
275C THR* 4.4 10.1 - - + -
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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 SER* 3.0 21.9 + - - +
8C ARG* 3.8 5.4 - - - +
10C TYR* 1.3 73.2 - - - +
12C ILE* 1.3 67.2 + - + +
14C VAL* 3.5 2.0 + - - +
15C GLU* 3.2 30.9 + - + +
53C THR 4.4 1.7 - - - +
54C PHE* 3.4 10.7 - - + -
55C SER* 2.6 49.6 + - - -
56C TRP* 3.6 30.9 - - + -
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Residues in contact with ILE 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR* 3.8 17.7 - - + +
55B ASN* 3.6 34.8 - - + +
8C ARG* 2.9 50.2 + - + +
9C VAL* 3.8 4.5 - - - +
11C GLU* 1.3 77.0 - - + +
13C ILE* 1.3 58.0 + - - +
15C GLU* 4.0 3.4 - - - +
16C SER* 2.9 46.2 + - - +
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Residues in contact with ILE 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 3.5 30.5 - - + -
44B PHE* 4.0 15.0 - - + -
47B VAL* 4.1 10.8 - - + -
48B VAL* 4.1 28.9 - - + +
51B THR* 3.6 20.6 - - - +
52B LEU* 5.8 0.2 - - + -
9C VAL* 3.0 42.8 + - + +
10C TYR* 3.2 7.2 + - + +
12C ILE* 1.3 77.6 - - - +
14C VAL* 1.3 56.0 + - - +
16C SER* 3.3 0.9 + - - -
17C VAL* 2.8 49.9 + - + +
42C TRP* 4.2 2.2 - - + -
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Residues in contact with VAL 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 4.1 12.3 - - + -
10C TYR 2.9 21.3 + - - +
11C GLU 3.7 7.2 - - - +
13C ILE* 1.3 75.1 - - - +
15C GLU* 1.3 80.4 + - - +
17C VAL 3.5 0.2 + - - -
18C VAL* 3.1 29.8 + - - +
39C LYS* 4.4 13.9 - - + -
42C TRP* 3.6 29.8 - - + -
43C GLN* 4.5 4.7 - - + +
46C LEU* 4.1 17.0 - - + -
56C TRP* 4.2 16.6 - - + -
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Residues in contact with GLU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLU* 3.2 19.5 + - + +
12C ILE* 4.0 4.3 - - - +
14C VAL* 1.3 88.3 - - + +
16C SER* 1.3 62.8 + - - +
18C VAL* 3.6 4.4 + - - +
19C ASN* 3.2 32.7 + - - +
39C LYS* 3.2 39.8 + - - +
43C GLN* 4.0 6.1 - - - +
56C TRP* 5.4 2.9 - - + -
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Residues in contact with SER 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.7 21.8 - - - -
51B THR* 5.2 0.4 + - - -
12C ILE* 2.9 33.7 + - - +
15C GLU* 1.3 76.9 - - - +
17C VAL* 1.3 58.0 + - - +
19C ASN* 3.3 9.0 + - - +
20C GLU* 2.7 40.4 + - - +
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Residues in contact with VAL 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 4.1 29.6 - - + +
43B THR* 4.7 1.6 - - + -
44B PHE* 4.0 14.6 - - + -
47B VAL* 3.8 25.1 - - + -
13C ILE* 2.8 29.2 + - + +
16C SER* 1.3 74.1 - - - +
18C VAL* 1.3 62.2 + - - +
20C GLU* 3.1 8.0 + - - +
21C VAL* 3.0 31.0 + - + +
38C LEU* 6.1 0.9 - - + -
42C TRP* 3.6 32.5 - - + -
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Residues in contact with VAL 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL 3.1 19.3 + - - +
15C GLU* 3.8 5.6 - - - +
16C SER 3.3 0.2 - - - -
17C VAL* 1.3 76.4 - - + +
19C ASN* 1.3 59.9 + - - +
21C VAL* 3.6 7.1 - - - +
22C ARG* 3.2 36.6 + - - +
35C LEU* 3.4 35.2 - - + +
36C GLN* 4.5 2.5 - - - +
38C LEU* 5.7 2.9 - - + -
39C LYS* 3.9 47.6 - - + +
42C TRP* 4.8 7.4 - - + -
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Residues in contact with ASN 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLU* 3.2 21.4 + - - +
16C SER* 3.7 9.8 - - - +
17C VAL 3.2 0.6 - - - -
18C VAL* 1.3 77.7 - - - +
20C GLU* 1.3 69.7 + - - +
21C VAL 3.5 0.2 + - - -
22C ARG* 2.9 40.8 + - - +
23C GLU* 4.6 2.8 + - - +
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Residues in contact with GLU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B THR* 3.2 24.0 + - + +
46B LYS* 3.8 21.9 + - - +
47B VAL* 3.8 17.5 - - + +
50B GLU* 6.0 0.2 - - - -
16C SER* 2.7 30.5 + - - +
17C VAL 3.1 1.1 + - - +
19C ASN* 1.3 83.0 - - - +
21C VAL* 1.3 58.6 + - - +
23C GLU* 4.4 10.1 + - - +
24C ASP* 3.8 9.5 - - - +
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Residues in contact with VAL 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 4.8 0.7 - - - +
40B VAL* 4.0 28.3 - - + -
43B THR* 3.8 27.6 - - + +
17C VAL* 3.0 26.0 + - + +
18C VAL* 3.6 4.0 - - - +
20C GLU* 1.3 76.7 - - - +
22C ARG* 1.3 69.4 + - - +
23C GLU 3.0 2.9 - - - -
24C ASP* 2.8 24.0 + - + +
25C PHE* 3.0 22.7 + - + -
35C LEU* 3.5 27.1 - - + -
38C LEU* 5.4 1.8 - - + -
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Residues in contact with ARG 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C VAL* 3.2 23.3 + - - +
19C ASN* 2.9 37.3 + - - +
20C GLU 3.5 1.4 - - - -
21C VAL* 1.3 77.3 - - - +
23C GLU* 1.3 61.6 + - - +
25C PHE* 3.4 3.0 + - + +
26C GLU* 3.2 42.9 + - + +
32C GLU* 2.9 42.3 + - - +
35C LEU* 3.5 15.0 - - + +
36C GLN* 3.7 11.1 - - - +
39C LYS* 5.9 0.4 - - - +
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ASN 4.6 2.3 + - - +
20C GLU 4.4 11.1 + - - +
21C VAL 3.0 0.4 - - - -
22C ARG* 1.3 81.5 - - - +
24C ASP* 1.3 61.8 + - - +
26C GLU* 3.8 14.7 + - - +
27C ASN* 3.2 25.0 + - + +
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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
----------------------------------------------------------
36B LEU* 4.0 17.7 - - + +
39B ARG* 2.9 43.3 + - + +
43B THR* 4.5 1.6 + - - -
20C GLU 3.8 15.5 - - - +
21C VAL* 2.8 12.3 + - + +
23C GLU* 1.3 82.0 - - - +
25C PHE* 1.3 65.7 + - - +
27C ASN* 3.3 9.4 + - - +
28C ALA* 3.0 24.4 + - - +
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Residues in contact with PHE 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 5.5 0.9 - - + -
32B ILE* 4.4 8.3 - - + -
36B LEU* 4.0 25.8 - - + -
40B VAL* 3.9 17.0 - - + -
21C VAL* 3.0 30.0 + - + -
22C ARG* 3.6 9.9 - - + +
24C ASP* 1.3 75.1 - - - +
26C GLU* 1.3 62.4 + - + +
28C ALA* 2.8 16.6 + - - +
29C GLY 3.0 10.2 + - - -
30C ILE* 3.0 44.2 + - + +
31C ASP 4.4 3.1 - - - +
34C THR* 4.0 7.4 - - + -
35C LEU* 3.5 52.5 - - + -
38C LEU* 4.0 16.8 - - + -
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Residues in contact with GLU 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ARG* 3.2 39.5 + - + +
23C GLU* 3.9 13.8 - - - +
25C PHE* 1.3 77.2 - - + +
27C ASN* 1.3 63.2 + - - +
28C ALA 3.2 0.5 + - - -
29C GLY* 3.3 11.6 + - - +
30C ILE 3.9 6.7 + - - +
32C GLU* 5.1 1.6 - - - +
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Residues in contact with ASN 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLU* 3.2 17.1 + - + +
24C ASP* 3.6 12.1 - - - +
25C PHE 3.1 0.6 - - - -
26C GLU* 1.3 78.5 - - - +
28C ALA* 1.3 58.1 + - - +
29C GLY 3.5 0.4 + - - -
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Residues in contact with ALA 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU* 6.5 0.7 - - + -
36B LEU* 4.1 15.3 - - + -
24C ASP 3.0 15.3 + - - +
25C PHE 2.8 6.3 + - - +
27C ASN* 1.3 80.8 - - - +
29C GLY* 1.3 57.0 + - - +
30C ILE* 3.2 22.6 + - + +
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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