Contacts of the helix formed by residues 36 - 59 (chain B) in PDB entry 1RVA
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 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLN* 3.7 29.6 - - + +
34B GLY* 4.2 1.2 - - - -
35B SER* 1.3 81.0 + - - +
37B THR* 1.3 57.9 + - - +
38B LYS* 3.0 26.7 - - - +
39B VAL* 2.8 41.0 + - - +
40B LEU* 3.2 9.2 + - - +
138B TYR* 4.1 0.4 - - - -
140B ARG* 6.1 0.2 - - - +
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Residues in contact with THR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLN* 3.2 21.1 + - - +
36B ASP* 1.3 69.3 - - - +
38B LYS* 1.3 59.5 + - - +
40B LEU* 3.7 4.9 - - - +
41B SER* 2.8 34.4 + - - -
93B THR* 4.0 27.4 - - + +
95B TYR* 4.2 0.9 - - - -
138B TYR* 2.6 25.4 + - + +
8D T 3.5 26.9 - - - +
9D C 2.6 30.6 + - - +
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Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 5.5 14.6 - - + +
41A SER* 5.0 11.4 - - - -
42A THR* 3.6 11.6 + - - +
69A GLN* 4.1 4.6 - - - +
36B ASP* 3.1 22.6 - - + +
37B THR* 1.3 79.7 - - - +
39B VAL* 1.3 59.8 + - + +
41B SER* 3.5 7.6 + - - -
42B THR* 3.3 18.2 + - - -
6C T 5.6 5.6 + - + +
7C A 3.3 51.3 + - - -
8C T 5.8 1.4 - - - -
7D A 5.7 6.4 + - + -
8D T 6.5 0.2 - - - -
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A THR* 3.9 16.4 - - + +
45A GLU* 5.9 3.4 - - + -
46A LEU* 4.1 32.3 - - + -
33B LEU* 4.4 7.6 - - + -
34B GLY* 3.8 29.8 - - - +
36B ASP* 2.8 28.2 + - - +
38B LYS* 1.3 78.5 - - + +
40B LEU* 1.3 62.9 + - + +
42B THR* 3.3 6.9 + - - -
43B ILE* 3.1 31.2 + - + +
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.8 3.1 - - + -
34B GLY 4.6 4.0 - - - +
35B SER 3.9 13.2 - - - +
36B ASP 3.2 7.8 + - - +
37B THR 4.3 1.3 - - - +
39B VAL* 1.3 79.7 - - + +
41B SER* 1.3 65.1 + - - +
43B ILE* 3.3 14.6 + - + +
44B PHE* 2.9 45.9 + - + -
93B THR* 4.6 0.2 - - - -
138B TYR* 3.3 49.4 - - + +
162B PRO* 4.1 22.7 - - + +
163B TYR* 3.9 27.6 - - + -
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Residues in contact with SER 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 3.9 19.4 + - - -
37B THR* 2.8 27.5 + - - +
38B LYS* 3.5 8.0 + - - -
40B LEU* 1.3 72.8 - - - +
42B THR* 1.3 59.2 + - - +
44B PHE* 3.9 1.0 - - - +
45B GLU* 3.0 35.8 + - - +
93B THR* 3.5 26.9 + - - +
8D T 3.9 21.7 - - - -
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Residues in contact with THR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 3.4 21.6 + - - +
39A VAL* 4.0 30.5 - - + +
42A THR* 3.1 37.1 + - + -
43A ILE* 4.8 1.8 - - + -
38B LYS 3.3 6.1 + - - -
39B VAL 3.3 9.8 + - - -
40B LEU 3.2 0.2 - - - -
41B SER* 1.3 81.0 + - - +
43B ILE* 1.3 68.3 + - + +
45B GLU* 3.3 7.6 + - - +
46B LEU* 3.1 29.2 + - + +
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.7 26.2 - - + +
42A THR* 4.7 6.1 - - + -
43A ILE* 5.2 1.3 - - + -
46A LEU* 5.0 2.5 - - + -
20B VAL* 3.9 34.3 - - + -
23B ILE* 5.1 1.1 - - + -
33B LEU* 4.0 29.6 - - + -
39B VAL* 3.1 25.8 + - + +
40B LEU* 3.3 15.0 + - + +
42B THR* 1.3 87.3 - - + +
44B PHE* 1.3 76.0 + - + +
46B LEU* 3.4 2.3 + - + -
47B PHE* 2.9 27.4 + - - +
163B TYR* 5.6 1.1 - - + -
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Residues in contact with PHE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASN* 5.2 2.5 - - - -
20B VAL* 5.9 2.2 - - + -
40B LEU* 2.9 38.3 + - + +
41B SER 4.1 2.5 - - - +
43B ILE* 1.3 83.9 - - + +
45B GLU* 1.3 61.1 + - - +
47B PHE* 3.7 12.1 - + + +
48B SER* 2.7 33.3 + - - -
91B ILE* 4.3 3.3 - - + +
93B THR* 3.8 21.1 - - + +
136B TYR* 3.8 41.3 - + + -
138B TYR* 4.0 27.8 - + + -
163B TYR* 4.8 8.7 - + - -
166B VAL* 3.9 35.7 - - + -
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Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 3.7 20.8 + - + +
39A VAL* 5.7 5.2 - - + -
41B SER* 3.0 28.8 + - - +
42B THR* 3.5 7.6 - - - +
44B PHE* 1.3 76.3 - - - +
46B LEU* 1.3 64.2 + - + +
48B SER* 3.2 12.0 + - - -
49B ARG* 3.2 21.4 + - + +
74B ASP* 2.9 38.6 - - - +
75B PHE* 4.5 2.9 - - - -
91B ILE* 3.2 38.2 - - + +
7D A 5.4 2.4 - - - +
8D T 5.5 0.2 + - - -
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 4.1 24.7 - - + -
31A TYR* 4.1 8.0 - - + +
32A PRO* 3.7 15.8 - - - +
33A LEU* 3.9 26.0 - - + -
34A GLY* 3.5 27.8 - - - +
39A VAL* 4.2 20.2 - - + -
43A ILE* 4.9 1.8 - - + -
42B THR* 3.1 25.8 + - + +
43B ILE 3.8 3.6 - - - +
45B GLU* 1.3 82.1 - - + +
47B PHE* 1.3 61.2 + - - +
49B ARG* 3.5 19.9 + - - +
50B PRO* 3.2 20.3 - - - +
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Residues in contact with PHE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 4.3 1.1 - - - +
31A TYR* 3.2 47.9 - + - -
11B LEU 5.7 0.2 - - - -
14B GLU* 3.6 38.4 - - + -
15B ASN* 4.1 22.7 - - + -
18B TYR* 3.9 21.3 - - + -
20B VAL* 3.7 25.6 - - + -
43B ILE 2.9 17.6 + - - +
44B PHE* 3.7 13.5 - + + +
46B LEU* 1.3 76.2 - - - +
48B SER* 1.3 59.9 + - - +
50B PRO* 3.5 9.2 - - - +
51B ILE* 3.6 17.2 - - + +
136B TYR* 3.9 20.9 - + - -
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.9 4.9 - - - +
44B PHE 2.7 16.2 + - - -
45B GLU 3.6 0.4 - - - -
46B LEU 3.2 0.2 - - - -
47B PHE* 1.3 78.4 - - - +
49B ARG* 1.3 64.6 + - - +
50B PRO 3.4 0.2 - - - -
51B ILE* 3.2 13.1 + - - +
52B ILE* 3.0 33.3 + - - +
91B ILE* 3.4 26.4 - - - +
134B ILE* 5.3 1.3 - - - -
136B TYR* 2.7 32.3 + - - -
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PRO* 4.1 16.2 + - - +
33A LEU 4.1 6.7 + - - -
34A GLY* 4.4 16.9 - - - -
143A THR* 3.8 17.6 + - - +
147A SER* 3.2 24.9 + - - -
148A LEU* 3.5 25.1 - - + +
45B GLU* 3.2 15.1 + - + +
46B LEU* 4.0 22.1 + - - +
48B SER* 1.3 74.7 - - - +
50B PRO* 1.3 71.2 - - + +
52B ILE* 3.8 2.0 - - - +
53B ASN* 3.0 24.9 + - - +
65B GLU* 2.9 36.8 + - - -
75B PHE* 3.3 31.3 - - + -
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Residues in contact with PRO 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TYR* 3.7 20.2 - - + -
32A PRO* 4.6 8.5 - - + -
147A SER 5.3 0.4 - - - +
148A LEU* 3.5 25.1 - - - +
149A LYS* 4.4 7.6 - - - +
150A THR* 3.9 25.4 - - + +
14B GLU* 6.0 0.2 - - - +
46B LEU 3.2 15.3 - - - +
47B PHE 3.5 9.6 - - - +
49B ARG* 1.3 93.5 - - + +
51B ILE* 1.3 61.8 + - + +
53B ASN* 3.9 1.6 - - - +
54B LYS* 3.0 26.5 + - - +
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 4.4 4.3 - - + -
10B ALA* 3.6 35.7 - - + +
11B LEU* 4.0 26.9 - - + +
14B GLU* 3.5 42.0 - - + +
47B PHE* 3.6 28.7 - - + +
48B SER* 3.2 8.9 + - - +
50B PRO* 1.3 76.2 - - + +
52B ILE* 1.3 63.9 + - - +
54B LYS* 3.2 8.2 + - + +
55B ILE* 3.1 24.7 + - - +
136B TYR* 4.8 0.4 - - - +
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Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 4.1 24.4 - - + +
11B LEU* 5.4 1.1 - - + -
48B SER* 3.0 23.0 + - - +
49B ARG* 3.8 4.0 - - - +
51B ILE* 1.3 78.7 - - + +
53B ASN* 1.3 60.0 + - - +
55B ILE* 3.4 1.6 + - - +
56B ALA* 2.9 30.8 + - - +
63B VAL* 4.5 4.0 - - + -
75B PHE* 3.6 45.5 - - + -
77B LEU* 4.2 28.3 - - + +
89B ILE* 4.3 9.2 - - + -
91B ILE* 4.4 0.4 - - + -
134B ILE* 4.0 25.1 - - + -
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Residues in contact with ASN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LYS* 5.6 3.8 + - - +
148A LEU* 3.7 46.9 + - + +
49B ARG 3.0 18.1 + - - +
50B PRO 3.9 3.1 - - - +
52B ILE* 1.3 77.7 - - - +
54B LYS* 1.3 65.0 + - - +
56B ALA* 3.8 0.3 - - - +
57B GLU* 3.0 45.3 + - - +
63B VAL* 3.8 28.6 - - + +
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Residues in contact with LYS 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PRO 3.0 18.1 + - - +
51B ILE* 3.6 7.6 - - + +
53B ASN* 1.3 79.1 - - - +
55B ILE* 1.3 74.7 + - + +
57B GLU* 3.4 6.4 + - - +
58B LYS* 3.2 21.5 + - - +
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Residues in contact with ILE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 3.9 17.3 - - + +
6B ASP* 3.8 33.2 - - + +
7B LEU* 3.8 20.6 - - + +
10B ALA* 3.9 29.8 - - + -
51B ILE* 3.1 16.4 + - + +
52B ILE 4.0 2.2 - - - +
54B LYS* 1.3 88.5 - - + +
56B ALA* 1.3 62.6 + - - +
58B LYS* 3.3 18.2 + - + +
59B HIS* 3.1 27.8 - - + +
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.1 10.5 - - - +
52B ILE 2.9 18.6 + - - +
53B ASN 3.8 0.7 - - - +
55B ILE* 1.3 74.2 - - - +
57B GLU* 1.3 65.8 + - - +
59B HIS* 3.0 8.0 + - - -
61B TYR* 2.9 31.7 + - + +
63B VAL* 3.4 29.6 - - + -
77B LEU* 3.9 17.5 - - + -
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LYS* 3.7 27.7 + - - +
53B ASN* 3.0 39.3 + - - +
54B LYS* 3.7 6.5 - - - +
56B ALA* 1.3 76.5 - - + +
58B LYS* 1.3 64.7 + - - +
59B HIS 2.9 1.7 + - - -
60B GLY* 3.0 13.7 + - - +
61B TYR 4.1 8.3 + - - +
63B VAL* 6.2 0.4 - - + -
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ASP* 2.9 34.5 + - - +
54B LYS* 3.2 10.5 + - + +
55B ILE* 3.4 21.0 - - + +
56B ALA 3.2 0.4 - - - -
57B GLU* 1.3 77.6 - - - +
59B HIS* 1.3 68.1 + - + +
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Residues in contact with HIS 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER* 3.6 22.4 - - - -
3B LEU* 3.7 21.6 + - + +
6B ASP* 2.7 32.1 + - - +
55B ILE* 3.1 26.9 + - + +
56B ALA 3.0 3.8 + - - +
57B GLU 3.0 1.0 - - - -
58B LYS* 1.3 92.2 + - + +
60B GLY* 1.3 61.3 + - - +
61B TYR* 3.3 27.3 - - + -
79B LYS* 3.6 14.2 + - - -
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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