Contacts of the helix formed by residues 32 - 55 (chain B) 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 ALA 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B GLN* 1.3 74.1 - - - +
33B PRO* 1.3 67.8 - - + +
34B GLU* 4.2 7.2 - - + +
35B GLU* 2.7 47.1 + - + +
36B ARG* 3.0 10.6 + - - +
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Residues in contact with PRO 33 (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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31B GLN 3.7 1.7 - - - +
32B ALA* 1.3 86.0 - - + +
34B GLU* 1.3 58.8 + - + +
36B ARG* 2.9 19.5 - - + +
37B CYS* 2.9 29.5 + - - +
125B ALA 4.2 1.4 - - - +
128B PRO* 4.0 32.1 - - + +
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Residues in contact with GLU 34 (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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32B ALA* 3.0 6.2 - - + +
33B PRO* 1.3 82.2 - - + +
35B GLU* 1.3 73.2 + - - +
37B CYS 3.8 0.2 - - - -
38B ARG* 3.0 21.1 + - - +
80B MSE 3.0 66.7 - - + +
81B GLU* 5.2 0.2 - - - -
83B ARG* 3.9 19.2 + - - +
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Residues in contact with GLU 35 (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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31B GLN* 3.9 13.6 - - + +
32B ALA* 2.7 35.3 + - + +
34B GLU* 1.3 93.1 - - - +
36B ARG* 1.3 59.6 + - - +
38B ARG* 3.4 5.6 + - - +
39B LEU* 3.0 42.6 + - + +
83B ARG* 4.6 10.1 + - - +
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Residues in contact with ARG 36 (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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31B GLN* 5.0 12.5 - - + +
32B ALA 3.0 5.9 + - - +
33B PRO* 2.9 37.2 - - + +
35B GLU* 1.3 75.3 - - - +
37B CYS* 1.3 60.2 + - - +
39B LEU* 3.8 9.1 - - - +
40B ALA* 2.8 30.3 + - - +
121B ARG* 5.9 0.3 + - - -
124B GLU* 3.3 10.3 + - - +
125B ALA* 3.1 36.4 - - - +
128B PRO* 3.4 15.7 - - - +
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Residues in contact with CYS 37 (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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33B PRO 2.9 16.5 + - - +
35B GLU 3.3 0.2 - - - -
36B ARG* 1.3 74.2 - - - +
38B ARG* 1.3 61.2 + - - +
40B ALA* 3.4 1.6 + - - +
41B ALA* 2.9 29.1 + - - +
80B MSE 3.3 26.7 - - + -
91B CYS* 4.3 6.7 - - - -
122B PHE* 4.1 7.5 - - - -
125B ALA* 3.2 40.8 - - - +
126B CYS* 4.0 20.4 - - - -
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Residues in contact with ARG 38 (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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34B GLU* 3.0 30.5 + - - +
35B GLU* 3.6 6.5 - - - +
37B CYS* 1.3 78.0 - - - +
39B LEU* 1.3 82.0 + - - +
41B ALA* 3.0 6.6 + - - +
42B GLN* 2.9 60.3 + - + +
77B ALA* 4.3 12.3 - - + +
80B MSE 3.7 11.8 - - + -
81B GLU* 3.7 36.5 + - + +
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Residues in contact with LEU 39 (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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35B GLU* 3.0 34.9 + - + +
36B ARG* 3.8 8.7 - - - +
38B ARG* 1.3 110.7 - - - +
40B ALA* 1.3 57.0 + - - +
42B GLN* 3.3 9.5 + - - +
43B ALA* 2.9 30.5 + - - +
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Residues in contact with ALA 40 (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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36B ARG 2.8 19.3 + - - +
37B CYS 3.7 4.0 - - - +
39B LEU* 1.3 77.1 - - - +
41B ALA* 1.3 58.6 + - - +
43B ALA* 3.3 8.4 + - - +
44B CYS* 3.0 26.7 + - - +
118B ALA 4.5 2.3 - - - +
121B ARG* 3.9 25.6 - - + +
122B PHE* 3.7 26.6 - - - +
125B ALA* 3.9 7.6 - - + -
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Residues in contact with ALA 41 (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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37B CYS 2.9 14.8 + - - +
38B ARG* 3.0 12.1 + - - +
40B ALA* 1.3 74.1 - - - +
42B GLN* 1.3 64.4 + - - +
44B CYS* 3.1 13.3 + - - +
45B ILE* 3.1 20.5 + - - +
73B CYS* 3.9 19.3 - - - +
76B ALA* 5.7 0.9 - - + -
77B ALA* 4.5 9.4 - - + +
80B MSE 5.5 2.2 - - - -
122B PHE* 3.5 27.1 - - + -
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Residues in contact with GLN 42 (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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38B ARG* 2.9 63.4 + - + +
39B LEU* 3.8 13.3 - - - +
41B ALA* 1.3 71.0 - - - +
43B ALA* 1.3 62.5 + - - +
44B CYS 3.0 4.9 - - - -
45B ILE* 3.1 33.9 - - + +
46B ARG* 3.1 19.6 + - - +
77B ALA* 4.8 12.1 - - + +
81B GLU* 5.0 7.2 - - - +
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Residues in contact with ALA 43 (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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39B LEU 2.9 18.4 + - - +
40B ALA* 3.6 9.0 - - - +
41B ALA 3.3 0.2 - - - -
42B GLN* 1.3 76.3 - - - +
44B CYS* 1.3 60.0 + - - +
46B ARG* 4.0 7.9 - - - +
47B ALA* 3.3 21.8 + - - +
50B ARG* 5.2 1.7 + - - -
118B ALA* 3.6 8.7 - - + +
121B ARG* 5.4 9.6 - - - -
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Residues in contact with CYS 44 (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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40B ALA 3.0 13.0 + - - +
41B ALA* 3.2 12.1 - - - +
42B GLN 3.0 0.2 - - - -
43B ALA* 1.3 76.2 - - - +
45B ILE* 1.3 60.6 + - - +
46B ARG 3.2 0.9 - - - -
47B ALA* 3.0 4.0 + - - +
48B CYS* 2.8 31.0 + - - +
69B CYS* 3.6 30.7 - - - -
73B CYS* 3.9 13.0 - - - -
118B ALA* 3.9 11.0 - - - +
119B CYS* 3.9 29.4 - - - -
122B PHE* 4.2 6.1 - - + -
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Residues in contact with ILE 45 (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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41B ALA 3.1 6.0 + - - +
42B GLN* 3.1 22.7 - - + +
44B CYS* 1.3 74.2 - - - +
46B ARG* 1.3 97.7 - - - +
48B CYS* 4.3 5.8 - - - -
49B GLU* 2.8 40.3 + - - +
70B ALA* 3.4 24.0 - - + +
73B CYS* 3.3 31.6 - - + +
74B ARG* 4.0 29.8 - - + +
77B ALA* 6.2 0.2 - - + -
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Residues in contact with ARG 46 (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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42B GLN* 3.1 23.3 + - - +
43B ALA* 4.0 8.1 - - - +
45B ILE* 1.3 104.9 - - - +
47B ALA* 1.3 57.5 + - - +
49B GLU* 3.0 28.5 + - - +
50B ARG* 3.1 47.5 + - - +
74B ARG* 3.0 20.6 - - - +
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Residues in contact with ALA 47 (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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43B ALA 3.3 17.5 + - - +
44B CYS 3.0 5.5 + - - +
46B ARG* 1.3 79.3 - - - +
48B CYS* 1.3 59.4 + - - +
50B ARG* 3.5 16.7 + - - +
51B TYR* 3.0 27.4 + - - +
111B LEU* 5.1 0.7 - - - +
114B GLU* 4.0 6.1 - - + +
115B CYS* 4.0 21.1 + - - +
118B ALA* 3.4 20.6 - - + -
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Residues in contact with CYS 48 (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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44B CYS* 2.8 19.3 + - - +
45B ILE 3.7 3.1 - - - +
47B ALA* 1.3 74.0 - - - +
49B GLU* 1.3 60.5 + - - +
50B ARG 3.1 1.8 - - - -
51B TYR* 3.3 6.5 + - - +
52B LEU* 2.9 35.0 + - - +
66B ALA* 3.5 31.7 - - - +
69B CYS* 4.1 24.2 - - - -
70B ALA* 3.8 11.2 - - + -
101B CYS* 4.1 2.2 - - - -
115B CYS* 4.0 20.2 - - - -
119B CYS* 4.4 4.5 - - - -
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Residues in contact with GLU 49 (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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82A ARG* 3.7 16.2 + - - +
45B ILE* 2.8 24.0 + - - +
46B ARG* 3.0 33.5 + - - +
48B CYS* 1.3 72.6 - - - +
50B ARG* 1.3 61.1 + - - +
52B LEU* 3.4 14.0 + - + +
53B ALA* 3.2 24.4 + - - +
70B ALA* 4.4 13.1 - - + +
74B ARG* 2.8 32.4 + - - -
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Residues in contact with ARG 50 (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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43B ALA 5.2 1.6 + - - -
46B ARG* 3.1 37.9 + - - +
47B ALA* 3.6 18.3 - - - +
49B GLU* 1.3 76.0 - - - +
51B TYR* 1.3 60.6 + - - +
53B ALA 3.4 0.2 + - - -
54B LEU* 2.8 55.2 + - + +
111B LEU* 3.9 16.2 - - + -
114B GLU* 4.6 16.7 + - - +
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Residues in contact with TYR 51 (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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47B ALA 3.0 16.9 + - - +
48B CYS 3.6 2.5 - - - +
50B ARG* 1.3 75.6 - - - +
52B LEU* 1.3 63.5 + - + +
55B CYS* 3.1 58.7 + - + +
58B SER* 3.3 19.8 + - - -
62B GLN* 3.1 39.6 + - - +
63B ARG* 4.5 3.6 - - + -
66B ALA* 3.5 25.8 - - + -
105B CYS* 3.6 28.8 - - + +
111B LEU* 4.1 28.0 - - - +
112B GLU* 4.3 10.5 - - + -
115B CYS* 3.9 19.3 - - + -
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Residues in contact with LEU 52 (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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48B CYS 2.9 26.0 + - - +
49B GLU* 3.5 19.1 - - + +
50B ARG 3.2 0.2 - - - -
51B TYR* 1.3 80.9 - - + +
53B ALA* 1.3 59.4 + - + +
55B CYS 4.8 4.5 - - - +
58B SER* 5.0 0.2 + - - -
63B ARG* 3.1 57.8 - - + +
66B ALA* 3.5 12.3 - - + +
67B GLY* 4.0 21.5 - - - +
70B ALA* 5.2 2.2 - - + -
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Residues in contact with ALA 53 (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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49B GLU 3.2 12.6 + - - +
52B LEU* 1.3 79.4 - - + +
54B LEU* 1.3 75.6 + - + +
55B CYS 5.1 0.7 - - - -
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Residues in contact with LEU 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 ARG* 2.8 51.7 + - + +
53B ALA* 1.3 90.8 - - + +
55B CYS* 1.3 64.4 + - - +
56B THR* 3.1 12.6 + - - -
111B LEU* 3.3 26.2 - - + +
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Residues in contact with CYS 55 (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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51B TYR* 3.1 52.5 + - + +
52B LEU 4.8 3.8 - - - +
53B ALA 5.1 0.5 - - - -
54B LEU* 1.3 77.1 - - - +
56B THR* 1.3 60.9 + - - +
57B GLU* 3.7 16.2 - - - -
58B SER* 3.5 33.3 + - - -
109B GLU* 4.5 5.4 - - - -
111B LEU* 3.4 14.4 - - + +
112B GLU* 4.1 12.3 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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