Contacts of the helix formed by residues 32 - 57 (chain L) in PDB entry 1K6L
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 GLY 32 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L THR* 5.0 1.3 - - - -
22L PHE* 3.1 25.4 + - - +
30L TYR* 3.4 25.4 - - - -
31L VAL* 1.3 84.3 - - - +
33L PHE* 1.3 59.0 + - - +
34L PHE 3.2 1.8 - - - -
35L GLY* 2.7 20.6 + - - -
36L VAL* 3.3 4.0 + - - +
106L GLU* 3.8 5.6 - - - -
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Residues in contact with PHE 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L THR* 5.5 1.4 - - - +
17L VAL* 3.5 50.3 + - + +
22L PHE* 3.5 37.8 - + + +
32L GLY* 1.3 69.8 - - - -
34L PHE* 1.3 90.4 + + + +
36L VAL* 3.0 15.0 + - + +
37L ALA* 3.0 29.3 + - + +
106L GLU* 3.9 5.4 + - - +
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Residues in contact with PHE 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L LEU* 4.1 16.4 - - + -
17L VAL* 3.9 27.4 - - + -
32L GLY 3.2 0.4 - - - -
33L PHE* 1.3 98.8 - + - +
35L GLY* 1.3 58.7 + - - +
36L VAL 3.1 1.3 - - - -
37L ALA* 3.6 7.0 - - + -
38L THR* 2.6 38.2 + - - +
99L SER* 3.7 30.7 - - - +
102L LEU* 3.2 48.5 - - + -
103L ARG* 4.0 12.6 - - + -
106L GLU* 4.1 17.9 - - - +
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Residues in contact with GLY 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L VAL* 3.0 28.8 + - - -
32L GLY 2.7 6.7 + - - -
34L PHE* 1.3 79.8 - - - +
36L VAL* 1.3 62.5 + - - +
38L THR* 3.4 5.9 + - - -
39L PHE* 3.2 20.1 + - - +
103L ARG* 3.9 14.7 - - - +
503M U10 3.9 16.6 - - - +
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Residues in contact with VAL 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L PHE* 3.6 36.3 - - + -
24L PHE* 6.1 0.2 - - + -
31L VAL* 4.1 11.4 - - + -
32L GLY 3.8 5.4 - - - +
33L PHE* 3.1 13.2 - - + +
35L GLY* 1.3 74.5 - - - +
37L ALA* 1.3 68.1 + - - +
39L PHE* 3.1 10.3 + - + +
40L PHE* 3.0 23.3 + - + +
503M U10 5.0 2.5 - - + -
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Residues in contact with ALA 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L PHE* 3.0 18.7 + - + +
34L PHE* 3.4 22.0 + - + +
36L VAL* 1.3 79.7 - - - +
38L THR* 1.3 63.3 + - - +
40L PHE* 3.1 6.6 + - - +
41L PHE* 3.0 36.0 + - + -
99L SER* 3.4 19.3 - - - +
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Residues in contact with THR 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L PHE 2.6 27.1 + - - +
35L GLY* 3.4 7.8 + - - +
37L ALA* 1.3 74.8 - - - +
39L PHE* 1.3 60.9 + - - +
41L PHE* 3.8 5.5 - - - +
42L ALA* 2.8 33.8 + - - +
96L ALA* 4.2 11.9 - - - +
99L SER* 3.3 24.7 - - - +
100L TRP* 3.6 30.0 - - + +
103L ARG* 4.9 3.1 - - - -
402L BPH 5.2 5.6 - - - +
503M U10 3.8 17.3 - - - +
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Residues in contact with PHE 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L GLY 3.2 10.3 + - - +
36L VAL* 3.1 15.1 + - + +
38L THR* 1.3 81.9 + - - +
40L PHE* 1.3 57.7 + - + +
42L ALA* 3.2 6.4 + - + +
43L ALA* 2.8 48.5 + - + +
503M U10 4.0 42.4 - - + -
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Residues in contact with PHE 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L VAL* 3.0 12.7 + - + +
37L ALA* 3.4 12.1 - - - +
39L PHE* 1.3 86.7 - - + +
41L PHE* 1.3 89.0 + + - +
43L ALA* 3.2 5.6 + - + +
44L LEU* 3.0 53.6 + - + +
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Residues in contact with PHE 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L ALA* 3.0 37.7 + - + +
38L THR 3.8 3.6 - - - +
40L PHE* 1.3 99.6 - + - +
42L ALA* 1.3 57.6 + - - +
44L LEU* 4.5 3.1 - - + -
45L GLY* 3.1 24.8 + - - -
91L ILE* 4.8 9.6 - - + -
92L CYS* 3.6 37.9 - - - +
95L GLY* 3.7 27.4 - - - -
96L ALA* 3.8 7.2 - - - +
99L SER* 3.9 13.7 - - - -
402L BPH 3.8 7.5 - - - +
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Residues in contact with ALA 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L THR 2.8 19.8 + - - +
39L PHE* 3.5 7.6 - - + +
41L PHE* 1.3 75.2 - - - +
43L ALA* 1.3 66.2 + - - +
45L GLY 4.2 0.2 - - - -
46L ILE* 3.1 37.3 + - + +
96L ALA* 5.2 0.9 - - + -
402L BPH 4.1 40.1 - - + +
503M U10 5.3 5.4 - - + -
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Residues in contact with ALA 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L PHE* 2.8 34.2 + - + +
40L PHE* 3.5 8.7 - - + +
42L ALA* 1.3 79.4 - - - +
44L LEU* 1.3 63.3 + - - +
46L ILE* 3.9 4.8 - - - +
47L ILE* 3.1 32.7 + - + +
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Residues in contact with LEU 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L PHE* 3.0 42.3 + - + +
41L PHE* 3.9 4.7 - - + +
43L ALA* 1.3 81.0 - - - +
45L GLY* 1.3 62.8 + - - +
47L ILE* 3.1 18.1 + - + +
48L LEU* 3.0 42.8 + - + +
88L ILE* 5.7 3.1 - - + -
92L CYS* 3.7 20.6 - - - -
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Residues in contact with GLY 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L PHE 3.1 15.5 + - - -
42L ALA 4.2 0.4 - - - -
44L LEU* 1.3 81.5 - - - +
46L ILE* 1.3 56.7 + - - +
48L LEU* 3.4 7.3 + - - +
49L ILE* 2.9 35.8 + - - +
89L ILE* 4.1 5.5 - - - +
92L CYS* 4.0 16.1 - - - -
402L BPH 4.2 12.8 - - - -
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Residues in contact with ILE 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L ALA* 3.1 29.4 + - + +
43L ALA* 3.9 4.7 - - - +
45L GLY* 1.3 73.9 - - - +
47L ILE* 1.3 68.6 + - + +
49L ILE* 3.2 10.1 + - + +
50L ALA* 3.0 22.7 + - + +
304L BCL 4.3 33.9 - - + -
402L BPH 4.7 8.7 - - + +
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Residues in contact with ILE 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L ALA* 3.1 26.0 + - + +
44L LEU* 3.2 19.1 - - + +
46L ILE* 1.3 79.2 - - + +
48L LEU* 1.3 75.9 + - + +
50L ALA* 2.8 20.2 + - - +
51L TRP* 2.9 16.0 + - + +
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Residues in contact with LEU 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L LEU* 3.0 35.4 + - + +
45L GLY 3.7 6.5 - - - +
47L ILE* 1.3 83.0 - - + +
49L ILE* 1.3 56.4 + - - +
51L TRP* 3.2 36.6 + - + +
52L SER* 2.9 28.2 + - - -
85L LEU* 3.9 15.2 - - + +
88L ILE* 3.4 43.7 - - + -
89L ILE* 3.7 19.4 - - + +
92L CYS* 4.7 2.7 - - - -
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Residues in contact with ILE 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L GLY 2.9 18.4 + - - +
46L ILE* 3.5 13.7 - - + +
47L ILE 3.1 0.2 - - - -
48L LEU* 1.3 77.8 - - - +
50L ALA* 1.3 62.2 + - - +
52L SER* 3.3 7.4 + - - -
53L ALA* 3.1 18.9 + - - +
64L ILE* 4.6 14.6 - - + +
66L VAL* 4.7 11.4 - - + -
89L ILE* 3.3 22.4 - - + -
148L TYR* 5.5 3.8 - - + -
304L BCL 5.0 10.8 - - + -
402L BPH 3.8 39.3 - - + -
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Residues in contact with ALA 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L ILE* 3.0 12.2 + - + +
47L ILE* 2.8 12.6 + - - +
49L ILE* 1.3 77.1 - - - +
51L TRP* 1.3 56.2 + - - +
53L ALA* 2.8 32.3 + - - +
54L VAL* 3.0 13.1 + - - +
59L TRP* 4.1 21.6 - - + -
64L ILE* 6.1 0.2 - - - -
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Residues in contact with TRP 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L ILE* 2.9 15.5 + - + +
48L LEU* 3.3 37.0 - - + +
50L ALA* 1.3 75.6 - - - +
52L SER* 1.3 63.5 + - - +
54L VAL* 3.2 28.5 - - + +
55L LEU* 3.4 24.1 + - + +
80L LEU* 3.2 33.4 - - + -
85L LEU* 3.9 11.0 - - + -
88L ILE* 6.1 0.7 - - + -
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Residues in contact with SER 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L LEU 2.9 12.6 + - - -
49L ILE 3.4 9.6 - - - -
50L ALA 3.1 0.2 - - - -
51L TRP* 1.3 77.4 - - - +
53L ALA* 1.3 57.1 + - - +
55L LEU* 3.2 8.0 + - - +
56L GLN* 3.0 28.8 + - - +
64L ILE* 5.5 1.0 - - - +
65L SER 4.1 10.4 + - - -
66L VAL* 3.4 32.3 - - - +
85L LEU* 3.8 17.9 - - - +
89L ILE* 5.4 0.2 - - - -
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Residues in contact with ALA 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L ILE 3.1 11.3 + - - +
50L ALA* 2.8 17.2 + - - +
52L SER* 1.3 78.4 - - - +
54L VAL* 1.3 55.4 + - - +
56L GLN* 3.3 6.9 + - - +
57L GLY 2.8 21.5 + - - -
58L THR 3.2 28.8 + - - +
59L TRP* 4.2 10.3 - - + -
64L ILE* 3.5 28.3 - - + -
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Residues in contact with VAL 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L ALA 3.0 10.0 + - - +
51L TRP* 3.2 28.5 - - + +
53L ALA* 1.3 71.1 - - - +
55L LEU* 1.3 67.4 + - + +
56L GLN 3.0 4.7 - - - -
57L GLY* 2.9 20.5 + - - +
59L TRP* 3.6 32.3 - - + +
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Residues in contact with LEU 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L TRP* 3.5 32.5 - - + +
52L SER* 3.5 8.1 - - - +
54L VAL* 1.3 85.5 - - + +
56L GLN* 1.3 58.5 + - - +
80L LEU* 5.1 2.9 - - + -
81L ALA* 4.0 35.4 - - + +
85L LEU* 4.3 14.8 - - + -
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Residues in contact with GLN 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L SER* 3.0 16.3 + - - +
53L ALA 3.6 5.6 - - - +
55L LEU* 1.3 79.9 - - - +
57L GLY* 1.3 60.8 + - - +
58L THR* 3.5 22.5 - - + +
63L LEU* 3.1 26.3 + - - +
64L ILE* 3.6 7.3 - - - +
65L SER* 3.1 36.6 + - - +
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Residues in contact with GLY 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L ALA 2.8 8.6 + - - -
54L VAL* 2.9 14.8 + - - -
56L GLN* 1.3 78.7 - - - +
58L THR* 1.3 60.6 + - - -
59L TRP* 6.1 0.9 - - - -
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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