Contacts of the helix formed by residues 32 - 55 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ALA 3.8 8.2 + - - +
30C ALA 3.3 6.9 + - - +
31C GLN* 1.3 76.2 - - - +
33C PRO* 1.3 71.5 - - + +
34C GLU* 3.1 8.1 - - + +
35C GLU* 2.8 24.0 + - + +
36C ARG* 3.0 14.4 + - - +
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Residues in contact with PRO 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C GLN 4.7 0.2 - - - +
32C ALA* 1.3 88.7 - - + +
34C GLU* 1.3 57.8 + - + +
36C ARG* 3.3 12.0 + - + +
37C CYS* 2.9 27.9 + - - +
125C ALA 4.4 2.9 - - - +
128C PRO* 4.0 28.9 - - + +
129C LEU* 4.0 7.8 - - + +
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Residues in contact with GLU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ALA* 3.1 5.1 - - + -
33C PRO* 1.3 80.3 - - + +
35C GLU* 1.3 60.2 + - - +
37C CYS* 3.5 1.7 + - - +
38C ARG* 3.0 29.0 + - - +
80C MSE 3.2 54.5 - - + +
83C ARG* 4.2 19.1 - - - +
84C SER 5.7 0.2 - - - +
87C ALA* 4.9 7.4 - - - +
88C PRO* 5.9 1.0 - - - +
129C LEU* 3.2 25.2 - - + +
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Residues in contact with GLU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ALA 3.7 12.3 - - - +
31C GLN* 3.0 37.6 - - - +
32C ALA* 2.8 21.0 + - + +
34C GLU* 1.3 78.6 - - - +
36C ARG* 1.3 71.7 + - - +
38C ARG* 3.4 32.7 + - - +
39C LEU* 3.0 47.6 + - - +
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Residues in contact with ARG 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLN* 3.5 34.5 + - - +
32C ALA 3.0 15.7 + - - +
33C PRO* 3.6 12.8 - - + +
35C GLU* 1.3 95.5 + - - +
37C CYS* 1.3 54.2 + - - +
39C LEU* 3.1 29.3 + - - +
40C ALA* 2.7 36.2 + - - +
125C ALA* 4.6 6.1 - - + -
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Residues in contact with CYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C PRO 2.9 16.3 + - - +
34C GLU 3.6 0.2 - - - +
36C ARG* 1.3 75.8 - - - +
38C ARG* 1.3 51.9 + - - +
40C ALA* 3.0 4.7 + - - +
41C ALA* 2.7 34.7 + - - +
80C MSE 3.4 35.4 - - + -
91C CYS* 4.0 2.7 - - - -
122C PHE* 3.9 7.7 - - - -
125C ALA* 3.7 27.1 - - - +
126C CYS* 3.7 33.9 - - - -
129C LEU* 3.8 1.3 - - + -
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Residues in contact with ARG 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLU* 3.0 20.7 + - - +
35C GLU* 3.4 40.9 + - - +
37C CYS* 1.3 75.8 - - - +
39C LEU* 1.3 70.0 + - - +
41C ALA* 3.0 16.7 + - - +
42C GLN* 3.0 24.4 + - - +
77C ALA* 4.1 15.5 - - + +
80C MSE 3.7 17.6 + - + +
81C GLU* 3.3 53.6 + - - +
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLU* 3.0 34.9 + - - +
36C ARG* 3.1 31.9 + - - +
38C ARG* 1.3 92.7 - - - +
40C ALA* 1.3 63.4 + - - +
42C GLN* 3.3 22.0 + - - +
43C ALA* 3.1 23.1 + - - +
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ARG 2.7 15.6 + - - +
37C CYS 3.3 8.3 - - - +
39C LEU* 1.3 70.1 - - - +
41C ALA* 1.3 65.9 + - - +
43C ALA* 3.4 8.1 + - - +
44C CYS* 3.0 22.7 + - - +
118C ALA 4.5 2.3 - - - +
121C ARG* 4.1 17.0 - - - +
122C PHE* 3.8 26.5 - - - +
125C ALA* 3.8 14.6 - - + -
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Residues in contact with ALA 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C CYS 2.7 16.8 + - - +
38C ARG* 3.0 11.4 + - - +
40C ALA* 1.3 72.5 - - - +
42C GLN* 1.3 55.6 + - - +
44C CYS* 2.7 27.4 + - - +
45C ILE* 2.9 17.3 + - - +
73C CYS* 4.1 23.3 - - + +
76C ALA* 5.4 0.4 - - + -
77C ALA* 4.2 12.3 - - + +
80C MSE 5.8 0.7 - - - -
122C PHE* 3.7 24.2 - - + -
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Residues in contact with GLN 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ARG* 3.0 22.4 + - - +
39C LEU* 3.6 28.2 + - - +
41C ALA* 1.3 74.8 - - - +
43C ALA* 1.3 63.6 + - - +
45C ILE* 3.3 11.5 + - - +
46C ARG* 3.0 35.3 + - + +
77C ALA* 4.9 10.5 - - + -
81C GLU* 3.8 17.3 - - - +
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Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU 3.1 13.0 + - - +
40C ALA* 3.7 11.0 - - - +
42C GLN* 1.3 76.2 - - - +
44C CYS* 1.3 57.3 + - - +
46C ARG* 3.4 23.8 + - - +
47C ALA* 2.9 29.6 + - - +
50C ARG* 5.0 0.9 + - - -
118C ALA* 3.9 9.4 - - + +
121C ARG* 6.1 5.2 - - - +
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Residues in contact with CYS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ALA 3.0 12.9 + - - +
41C ALA 2.7 14.1 + - - +
43C ALA* 1.3 75.5 - - - +
45C ILE* 1.3 57.3 + - - +
47C ALA* 3.0 2.4 + - - +
48C CYS* 2.8 34.0 + - - -
69C CYS* 3.8 8.5 - - - -
73C CYS* 3.6 25.6 - - - -
118C ALA* 3.6 16.8 - - - +
119C CYS* 3.7 39.3 - - - -
122C PHE* 4.1 6.5 - - + -
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Residues in contact with ILE 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ALA 2.9 19.2 + - - +
42C GLN* 3.6 10.5 - - - +
44C CYS* 1.3 75.3 - - - +
46C ARG* 1.3 67.4 + - + +
48C CYS* 3.4 0.5 + - - +
49C GLU* 2.9 61.2 + - + +
70C ALA* 3.9 24.5 - - + +
73C CYS* 3.4 25.6 - - + -
74C ARG* 3.4 32.5 - - + +
77C ALA* 6.1 1.3 - - + -
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Residues in contact with ARG 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLN* 3.0 25.1 + - + +
43C ALA* 3.6 24.7 + - - +
44C CYS 3.2 0.2 - - - -
45C ILE* 1.3 85.8 - - + +
47C ALA* 1.3 59.8 + - - +
49C GLU* 4.0 5.8 - - - +
50C ARG* 3.0 67.1 + - - +
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ALA 2.9 17.9 + - - +
44C CYS 3.5 1.3 - - - +
46C ARG* 1.3 78.1 - - - +
48C CYS* 1.3 57.1 + - - +
50C ARG* 3.3 18.2 + - - +
51C TYR* 2.9 30.2 + - - +
111C LEU* 5.1 1.0 - - - +
114C GLU* 3.8 17.0 - - + +
115C CYS* 4.0 9.9 + - - +
118C ALA* 3.5 23.8 - - + -
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Residues in contact with CYS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C CYS* 2.8 24.8 + - - +
45C ILE 3.9 3.6 - - - +
47C ALA* 1.3 75.6 - - - +
49C GLU* 1.3 56.9 + - - +
51C TYR* 3.3 2.9 + - - +
52C LEU* 2.8 30.3 + - - +
66C ALA* 3.4 26.2 - - + +
69C CYS* 3.8 18.8 - - - -
70C ALA* 4.2 7.2 - - + -
101C CYS* 4.4 2.5 - - - -
115C CYS* 3.8 16.6 - - - -
119C CYS* 3.7 29.6 - - - -
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Residues in contact with GLU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE* 2.9 35.2 + - + +
46C ARG* 4.0 5.6 - - - +
48C CYS* 1.3 72.7 - - - +
50C ARG* 1.3 67.3 + - - +
51C TYR 3.0 1.3 - - - -
52C LEU* 3.3 7.5 + - + +
53C ALA* 3.0 28.1 + - - +
70C ALA* 4.5 10.5 - - + +
74C ARG* 2.6 30.0 + - - -
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Residues in contact with ARG 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ALA 5.0 0.4 + - - -
46C ARG* 3.0 63.0 + - - +
47C ALA* 3.7 23.8 - - - +
49C GLU* 1.3 76.8 - - - +
51C TYR* 1.3 57.1 + - - +
53C ALA* 4.8 1.6 - - - -
54C LEU* 3.0 56.9 + - + +
111C LEU* 3.7 16.0 - - + +
114C GLU* 5.3 13.1 + - - +
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Residues in contact with TYR 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ALA 2.9 17.4 + - - +
48C CYS 3.4 3.8 - - - +
50C ARG* 1.3 74.8 - - - +
52C LEU* 1.3 63.1 + - - +
53C ALA 3.0 4.3 - - - -
55C CYS* 3.0 60.2 + - + +
57C GLU 5.3 0.2 + - - -
58C SER* 3.3 21.2 + - - -
62C GLN* 3.3 38.9 + - - +
63C ARG* 4.7 1.8 - - - -
66C ALA* 3.6 21.8 - - + -
105C CYS* 3.8 27.4 + - + +
111C LEU* 3.7 26.9 - - - +
112C GLU* 4.0 14.2 - - + +
115C CYS* 4.1 15.9 - - + -
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C CYS 2.8 18.5 + - - +
49C GLU* 3.3 8.7 + - + +
51C TYR* 1.3 78.2 - - + +
53C ALA* 1.3 58.3 + - - +
55C CYS 4.9 1.6 - - - +
58C SER* 5.8 0.2 - - - -
63C ARG* 3.3 63.9 - - + +
66C ALA* 4.2 2.9 - - + -
67C GLY* 3.4 24.5 - - - +
82D ARG* 5.7 0.9 - - - +
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Residues in contact with ALA 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C GLU 3.0 17.3 + - - +
50C ARG* 4.3 2.5 - - - +
52C LEU* 1.3 81.3 - - - +
54C LEU* 1.3 72.7 + - + +
55C CYS 3.7 0.9 - - - -
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ARG* 3.0 38.9 + - + +
53C ALA* 1.3 88.5 - - + +
55C CYS* 1.3 60.3 + - - +
56C THR* 3.2 14.2 + - - -
111C LEU* 3.4 20.8 - - + +
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Residues in contact with CYS 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TYR* 3.0 51.8 + - + +
52C LEU 5.5 1.6 - - - +
53C ALA 3.7 1.1 - - - -
54C LEU* 1.3 73.4 - - - +
56C THR* 1.3 68.4 + - - +
57C GLU 4.3 7.4 - - - -
58C SER* 3.6 24.5 + - - -
63C ARG* 5.3 1.0 + - - -
109C GLU* 4.3 9.0 - - - -
111C LEU* 3.6 15.1 - - + +
112C GLU* 4.0 23.8 - - - -
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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