Contacts of the helix formed by residues 31 - 55 (chain D) in PDB entry 3KAV
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 GLN 31 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ALA* 1.3 71.0 + - + +
33D PRO* 3.4 12.8 - - - +
34D GLU* 3.3 15.1 + - - +
35D GLU* 3.3 19.8 + - - +
83D ARG* 3.1 47.1 + - - +
129D LEU* 6.2 0.2 - - - -
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Residues in contact with ALA 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D GLN* 1.3 82.9 - - + +
33D PRO* 1.4 64.0 - - + +
35D GLU* 3.0 23.3 + - - +
36D ARG* 3.2 13.1 + - - +
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Residues in contact with PRO 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D GLN* 3.5 10.1 - - - +
32D ALA* 1.4 96.7 - - + +
34D GLU* 1.3 57.3 + - - +
36D ARG* 3.2 18.1 - - + +
37D CYS* 3.0 27.7 + - - +
125D ALA 4.2 1.7 - - - +
128D PRO* 4.0 33.0 - - + +
129D LEU* 3.9 14.7 - - + +
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Residues in contact with GLU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D GLN* 3.3 15.7 - - - +
32D ALA 3.0 0.8 - - - -
33D PRO* 1.3 81.9 - - - +
35D GLU* 1.3 58.9 + - - +
37D CYS* 3.4 3.3 - - - +
38D ARG* 2.9 26.5 + - - +
80D MSE 3.4 52.2 - - + +
83D ARG* 3.3 38.0 + - - -
84D SER 5.3 0.5 - - - +
87D ALA* 4.6 6.8 - - + +
129D LEU* 3.9 23.1 - - + +
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Residues in contact with GLU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D GLN 3.3 8.7 + - - +
32D ALA* 3.0 11.7 + - - +
34D GLU* 1.3 78.2 - - - +
36D ARG* 1.3 60.8 + - - +
38D ARG* 2.7 47.1 + - - -
39D LEU* 3.0 39.5 + - + +
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Residues in contact with ARG 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ALA 3.2 5.1 + - - +
33D PRO* 3.2 31.1 - - + +
35D GLU* 1.3 77.9 - - - +
37D CYS* 1.3 55.6 + - - +
39D LEU* 3.6 9.6 - - + +
40D ALA* 2.6 36.3 + - - +
125D ALA* 4.3 18.3 - - - +
128D PRO* 5.7 2.7 - - - -
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Residues in contact with CYS 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D PRO 3.0 19.3 + - - +
34D GLU 3.4 6.7 - - - +
36D ARG* 1.3 78.0 - - - +
38D ARG* 1.3 57.9 + - - +
40D ALA* 3.2 2.9 + - - +
41D ALA* 2.8 29.1 + - - +
80D MSE 3.2 28.7 - - + -
91D CYS* 4.2 3.1 - - - -
122D PHE* 3.9 7.4 - - - -
125D ALA* 3.5 30.1 - - - +
126D CYS* 4.0 23.3 - - - -
129D LEU* 3.6 4.9 - - + -
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Residues in contact with ARG 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D GLU 2.9 15.3 + - - +
35D GLU* 2.7 47.4 + - - +
37D CYS* 1.3 77.4 - - - +
39D LEU* 1.3 70.7 + - - +
41D ALA* 3.0 9.6 + - - +
42D GLN* 3.0 46.2 + - - +
77D ALA* 4.2 14.4 - - + +
80D MSE 3.7 16.3 - - + -
81D GLU* 3.4 45.7 + - - +
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Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D GLU* 3.0 42.8 + - + +
36D ARG* 3.6 8.1 - - - +
38D ARG* 1.3 91.3 - - - +
40D ALA* 1.3 66.3 + - - +
41D ALA 3.0 1.8 - - - -
42D GLN* 2.9 29.0 + - - +
43D ALA* 2.9 15.1 + - - +
46D ARG* 5.2 0.5 + - - -
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Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ARG* 2.6 23.9 + - - +
37D CYS 3.3 6.3 - - - +
39D LEU* 1.3 72.4 - - - +
41D ALA* 1.3 60.5 + - - +
43D ALA* 3.7 6.7 + - - +
44D CYS* 3.2 21.0 + - - +
118D ALA 4.2 3.3 - - - +
121D ARG* 4.3 6.1 - - + +
122D PHE* 3.8 19.1 - - - +
125D ALA* 3.8 21.5 - - + -
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Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D CYS 2.8 13.2 + - - +
38D ARG* 3.2 13.5 - - - +
39D LEU 3.0 0.4 - - - -
40D ALA* 1.3 75.5 - - - +
42D GLN* 1.3 61.1 + - - +
44D CYS* 3.2 5.4 + - - +
45D ILE* 2.8 34.3 + - - +
73D CYS* 3.8 21.4 - - + +
76D ALA* 5.3 0.2 - - + -
77D ALA* 4.3 8.5 - - + +
80D MSE 5.6 0.7 - - - -
122D PHE* 3.5 25.4 - - + -
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Residues in contact with GLN 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ARG* 3.0 42.3 + - + +
39D LEU* 2.9 26.8 + - - +
41D ALA* 1.3 76.0 - - - +
43D ALA* 1.3 57.2 + - - +
45D ILE* 3.3 13.2 - - + +
46D ARG* 3.0 47.0 + - - +
77D ALA* 4.8 9.0 - - + -
81D GLU* 3.7 9.5 - - - +
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Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU 2.9 13.8 + - - +
40D ALA* 3.8 8.1 - - - +
42D GLN* 1.3 74.7 - - - +
44D CYS* 1.3 55.8 + - - +
46D ARG* 3.3 27.3 + - - +
47D ALA* 2.8 35.3 + - - +
50D ARG* 5.0 1.6 + - - +
118D ALA* 3.8 6.0 - - + +
121D ARG* 4.5 18.6 - - - +
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Residues in contact with CYS 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ALA 3.2 12.6 + - - +
41D ALA 3.2 9.8 + - - +
43D ALA* 1.3 80.0 - - - +
45D ILE* 1.3 57.5 + - - +
47D ALA* 3.1 2.9 + - - +
48D CYS* 2.8 34.3 + - - +
69D CYS* 3.8 9.4 - - - -
73D CYS* 3.5 26.5 - - - -
118D ALA* 3.6 18.3 - - - +
119D CYS* 3.7 36.8 - - - -
122D PHE* 4.2 5.8 - - + -
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Residues in contact with ILE 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ALA 2.8 18.8 + - - +
42D GLN* 3.3 14.4 - - + +
44D CYS* 1.3 74.4 - - - +
46D ARG* 1.3 60.7 + - + +
48D CYS* 3.2 1.7 + - - +
49D GLU* 2.8 75.9 + - + +
70D ALA* 3.9 24.9 - - + +
73D CYS* 3.3 24.0 - - + -
74D ARG* 4.1 21.8 - - + +
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Residues in contact with ARG 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU 5.2 0.4 + - - -
42D GLN* 3.0 40.5 + - - +
43D ALA* 3.4 31.3 - - - +
45D ILE* 1.3 89.4 - - + +
47D ALA* 1.3 62.8 + - - +
49D GLU* 3.2 8.7 + - - +
50D ARG* 2.9 60.4 + - - +
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ALA 2.8 20.1 + - - +
44D CYS 3.5 1.6 - - - +
46D ARG* 1.3 73.1 - - - +
48D CYS* 1.3 62.9 + - - +
50D ARG* 3.6 17.5 + - - +
51D TYR* 3.0 23.8 + - - +
111D LEU 5.1 1.2 - - - +
114D GLU* 3.7 17.5 - - + +
115D CYS* 3.8 12.2 - - - +
118D ALA* 3.4 24.5 - - + -
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Residues in contact with CYS 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D CYS* 2.8 29.0 + - - +
45D ILE 3.6 3.6 - - - +
47D ALA* 1.3 73.8 - - - +
49D GLU* 1.3 57.2 + - - +
51D TYR* 3.2 5.6 + - - +
52D LEU* 2.9 32.5 + - - +
66D ALA* 3.4 26.0 - - - +
69D CYS* 3.9 27.1 - - - -
70D ALA* 4.1 9.2 - - + -
101D CYS* 4.1 4.7 - - - -
115D CYS* 3.8 26.5 - - - -
119D CYS* 4.2 0.9 - - - -
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Residues in contact with GLU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ILE* 2.8 39.5 + - + +
46D ARG* 3.7 8.8 - - - +
48D CYS* 1.3 69.0 - - - +
50D ARG* 1.3 67.6 + - - +
52D LEU* 2.9 24.4 + - + +
53D ALA* 3.0 15.3 + - - +
70D ALA* 4.8 5.2 - - + -
74D ARG* 2.5 44.4 + - - +
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Residues in contact with ARG 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ALA 5.0 1.2 + - - -
46D ARG* 2.9 52.6 + - - +
47D ALA* 3.7 22.3 - - - +
49D GLU* 1.3 74.8 - - - +
51D TYR* 1.3 56.9 + - - +
53D ALA* 3.1 1.6 + - - -
54D LEU* 2.7 62.0 + - + +
111D LEU* 4.5 10.5 - - + -
114D GLU* 5.9 5.9 + - - +
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Residues in contact with TYR 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ALA 3.0 15.5 + - - +
48D CYS* 3.2 10.8 - - - +
50D ARG* 1.3 75.7 - - - +
52D LEU* 1.3 66.6 + - + +
55D CYS* 3.1 48.8 + - + +
58D SER* 3.1 34.3 + - - -
62D GLN* 3.3 32.6 + - - +
63D ARG* 4.7 2.0 - - - -
66D ALA* 3.6 23.8 - - + -
105D CYS* 3.8 35.3 + - + +
111D LEU* 3.8 25.3 - - - +
112D GLU* 3.9 6.5 + - + +
115D CYS* 4.2 13.5 - - + -
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 4.1 16.5 - - - +
82C ARG* 6.0 1.1 - - - +
48D CYS 2.9 16.7 + - - +
49D GLU* 2.9 17.9 + - + +
51D TYR* 1.3 81.4 - - + +
53D ALA* 1.3 60.6 + - + +
55D CYS 4.6 0.3 - - - +
58D SER* 5.4 1.7 + - - -
63D ARG* 3.3 54.4 - - + +
66D ALA* 4.2 10.1 - - + +
67D GLY* 3.8 24.7 - - - +
70D ALA* 5.7 1.8 - - + -
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Residues in contact with ALA 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ALA* 3.4 25.6 - - + +
35A GLU* 3.6 12.3 - - - +
49D GLU 3.0 13.9 + - - +
50D ARG* 4.0 2.0 - - - +
52D LEU* 1.3 78.4 - - + +
54D LEU* 1.3 72.6 + - + +
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA* 3.9 16.2 - - + +
31A GLN* 3.4 54.0 + - + +
32A ALA* 3.9 17.0 - - + +
50D ARG* 2.7 60.0 + - + +
53D ALA* 1.3 86.2 - - + +
55D CYS* 1.3 65.8 + - - +
56D THR* 3.3 3.6 + - - +
111D LEU* 3.8 18.6 - - + +
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Residues in contact with CYS 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 3.0 25.3 - - - +
50D ARG 4.0 0.6 + - - -
51D TYR* 3.1 51.4 + - + +
52D LEU 4.6 0.5 - - - +
54D LEU* 1.3 76.6 - - - +
56D THR* 1.3 62.5 + - - +
57D GLU* 3.7 23.7 + - - -
58D SER* 3.9 16.5 + - - -
109D GLU* 4.3 7.6 - - - -
111D LEU* 3.7 15.9 - - + +
112D GLU* 4.2 10.1 - - - -
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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) + - + + + + + -
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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