Contacts of the helix formed by residues 29 - 52 (chain D) in PDB entry 2P4K
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 LYS 29 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A ASN* 3.6 42.2 - - + +
25D LEU* 2.9 27.3 + - + +
28D SER* 1.3 98.4 + - - +
30D HIS* 1.3 59.8 + - - +
32D ALA* 3.8 1.2 - - - +
33D ALA* 3.0 30.5 + - - +
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Residues in contact with HIS 30 (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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162A GLU* 3.8 6.2 + - - -
166A TYR* 2.7 38.2 + + - -
171A ASN* 3.6 27.0 - - + +
25D LEU 3.1 27.8 + - - -
26D HIS* 3.4 20.4 - - + +
29D LYS* 1.3 72.4 - - - +
31D HIS* 1.3 67.7 + - - +
33D ALA* 3.2 8.1 + - - +
34D ASN* 3.1 26.6 + - - -
74D HIS* 4.7 3.6 - - + -
163D HIS* 3.5 37.5 + + + +
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Residues in contact with HIS 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 3.4 8.3 - - + +
5D PRO* 3.4 21.7 - - + +
26D HIS 3.0 13.5 + - - +
27D HIS 3.6 11.0 - - - +
30D HIS* 1.3 72.7 - - - +
32D ALA* 1.3 68.2 + - - +
34D ASN* 3.0 10.3 + - - +
35D VAL* 3.0 27.6 + - + +
70D GLY 4.2 1.3 - - - -
71D HIS* 2.9 36.0 + - - -
74D HIS* 3.4 17.8 + - + +
75D SER* 3.4 27.1 - - - -
78D TRP* 2.9 26.4 + - + -
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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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4D LEU* 3.8 19.7 - - + +
27D HIS 3.3 6.4 + - - +
28D SER 3.1 31.2 - - - +
29D LYS* 3.8 1.8 - - - +
31D HIS* 1.3 78.0 - - - +
33D ALA* 1.3 56.7 + - - +
35D VAL* 3.2 5.4 + - - +
36D ASN* 2.9 42.4 + - - +
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Residues in contact with ALA 33 (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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29D LYS 3.0 19.8 + - - +
30D HIS* 3.6 6.3 - - - +
31D HIS 3.2 0.2 - - - -
32D ALA* 1.3 71.5 - - - +
34D ASN* 1.3 62.4 + - - +
36D ASN* 4.5 7.2 - - - +
37D ASN* 2.9 46.1 + - - +
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Residues in contact with ASN 34 (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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30D HIS 3.1 12.0 + - - +
31D HIS* 3.0 9.0 + - + +
33D ALA* 1.3 78.8 - - - +
35D VAL* 1.3 58.7 + - - +
38D LEU* 2.9 31.1 + - - +
66D PHE* 4.2 15.0 + - - -
67D ASN* 3.2 41.4 + - - +
70D GLY* 3.4 12.6 - - - -
71D HIS* 4.0 7.0 - - - +
74D HIS* 3.1 34.7 + - - -
143D GLN* 4.9 4.4 - - - +
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Residues in contact with VAL 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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2D HIS* 3.4 34.3 - - + +
3D SER* 3.9 0.7 - - - -
4D LEU* 3.9 25.4 - - + +
31D HIS* 3.0 20.7 + - + +
32D ALA* 3.6 7.9 - - - +
34D ASN* 1.3 77.2 - - - +
36D ASN* 1.3 70.2 - - - +
38D LEU* 3.2 9.2 + - - +
39D ASN* 3.0 27.4 + - - +
71D HIS* 3.6 30.7 - - + +
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Residues in contact with ASN 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* 2.9 31.1 + - - +
33D ALA* 4.0 6.6 - - - +
35D VAL* 1.3 82.8 - - - +
37D ASN* 1.3 66.5 + - - +
39D ASN* 3.3 8.9 + - - +
40D VAL* 3.3 26.2 + - - +
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Residues in contact with ASN 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 ALA* 2.9 31.4 + - - +
36D ASN* 1.3 79.3 - - - +
38D LEU* 1.3 62.4 + - - +
40D VAL* 3.3 9.7 + - - +
41D THR* 2.9 30.5 + - - +
67D ASN* 3.4 31.9 + - - +
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Residues in contact with LEU 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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54C VAL* 4.1 5.6 - - + -
2D HIS* 3.5 36.8 - - + +
34D ASN 2.9 19.1 + - - +
35D VAL* 3.5 4.0 - - - +
37D ASN* 1.3 72.9 - - - +
39D ASN* 1.3 69.0 + - - +
41D THR* 3.7 3.1 - - - -
42D GLU* 2.9 35.5 + - - +
64D LEU* 3.4 31.2 - - + -
67D ASN* 3.9 9.3 - - + +
68D GLY* 3.8 18.6 - - - +
71D HIS* 3.8 29.2 - - + -
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Residues in contact with ASN 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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1D LYS* 3.9 23.4 - - + +
2D HIS* 2.9 57.7 + - - +
35D VAL* 3.0 21.4 + - - +
36D ASN* 3.7 11.2 + - - +
37D ASN 3.3 0.2 - - - -
38D LEU* 1.3 79.0 - - - +
40D VAL* 1.3 62.4 + - + +
42D GLU* 3.5 5.2 + - - +
43D GLU* 3.1 25.4 + - - +
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Residues in contact with VAL 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 ASN 3.3 16.2 + - - +
37D ASN* 3.7 10.5 - - - +
38D LEU 3.3 0.6 - - - -
39D ASN* 1.3 76.2 - - + +
41D THR* 1.3 64.1 + - - +
43D GLU* 3.2 14.6 + - + +
44D LYS* 3.0 40.0 + - + +
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Residues in contact with THR 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 ASN* 2.9 18.8 + - - +
38D LEU* 3.3 6.7 + - - -
40D VAL* 1.3 78.5 - - - +
42D GLU* 1.3 57.9 + - - +
44D LYS* 3.2 7.7 + - - +
45D TYR* 2.8 29.4 + - + +
60D LEU* 4.0 24.0 - - + +
63D ALA* 3.8 17.3 + - + +
64D LEU* 3.9 38.8 - - + +
67D ASN* 5.0 0.7 + - - -
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Residues in contact with GLU 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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49C LEU* 3.6 29.9 - - + +
52C GLY* 4.6 2.4 - - - -
54C VAL* 3.7 7.3 - - - +
57C GLN* 3.0 29.6 + - - +
1D LYS* 6.0 0.3 - - - -
2D HIS* 2.8 41.3 + - - -
38D LEU* 2.9 30.4 + - + +
39D ASN* 3.9 5.1 - - - +
41D THR* 1.3 72.3 - - - +
43D GLU* 1.3 64.3 + - - +
45D TYR* 3.8 3.8 - - - +
46D GLN* 2.9 24.1 + - - +
64D LEU* 4.1 3.4 - - + -
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Residues in contact with GLU 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 ASN 3.1 14.7 + - - +
40D VAL* 3.2 15.1 + - - +
42D GLU* 1.3 76.0 - - - +
44D LYS* 1.3 80.0 + - + +
46D GLN* 3.3 8.0 + - - +
47D GLU* 3.1 39.8 + - + +
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Residues in contact with LYS 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 VAL* 3.0 32.6 + - + +
41D THR* 3.2 8.5 + - - +
43D GLU* 1.3 94.9 + - - +
45D TYR* 1.3 57.7 + - - +
47D GLU* 3.2 25.0 + - - +
48D ALA* 2.9 27.4 + - - +
60D LEU* 3.8 24.5 - - + +
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Residues in contact with TYR 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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45C TYR* 3.3 55.7 - + + +
49C LEU* 4.5 4.3 - - + -
57C GLN* 5.7 0.2 - - - +
61C GLN* 6.2 0.9 - - + -
64C LEU* 3.6 16.1 - - - +
41D THR* 2.8 17.6 + - + +
42D GLU* 3.8 7.9 - - - +
44D LYS* 1.3 74.8 - - - +
46D GLN* 1.3 66.3 + - - +
48D ALA* 3.1 1.6 + - - +
49D LEU* 2.9 31.7 + - + +
57D GLN* 2.8 66.9 + - + +
60D LEU* 3.7 22.1 - - + +
61D GLN* 5.0 8.3 + - + -
64D LEU* 5.5 6.3 - - + -
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Residues in contact with GLN 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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46C GLN* 2.9 43.1 + - - -
49C LEU* 3.3 18.0 - - + +
42D GLU 2.9 13.9 + - - +
43D GLU* 3.3 10.7 + - - +
45D TYR* 1.3 74.9 - - - +
47D GLU* 1.3 64.8 + - + +
49D LEU* 3.4 3.8 + - - +
50D ALA* 3.0 32.3 + - + +
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Residues in contact with GLU 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 GLU* 3.1 29.9 + - + +
44D LYS* 3.2 32.6 + - - +
45D TYR 3.2 0.2 - - - -
46D GLN* 1.3 77.2 - - + +
48D ALA* 1.3 64.0 + - - +
50D ALA* 3.3 6.6 + - - +
51D LYS* 3.1 50.3 + - - +
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Residues in contact with ALA 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 LYS 2.9 15.9 + - - +
45D TYR* 3.1 6.7 + - - +
47D GLU* 1.3 77.2 - - - +
49D LEU* 1.3 61.7 + - - +
51D LYS* 3.2 4.1 + - - -
52D GLY 3.0 3.5 + - - -
53D ASP* 2.9 40.6 + - - +
56D ALA* 4.0 19.3 - - + -
57D GLN* 3.9 22.3 - - + +
60D LEU* 4.6 1.3 - - + -
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Residues in contact with LEU 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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42C GLU* 4.2 31.8 - - + +
45C TYR* 4.1 5.2 - - + -
46C GLN* 3.5 38.6 - - + +
49C LEU* 3.8 26.7 - - + -
45D TYR* 2.9 29.8 + - + +
46D GLN* 3.6 4.5 - - - +
48D ALA* 1.3 75.3 - - - +
50D ALA* 1.3 59.9 - - - +
52D GLY* 3.0 17.8 + - - -
57D GLN* 3.7 27.5 - - - +
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Residues in contact with ALA 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D GLN* 3.0 27.1 + - + +
47D GLU* 3.6 7.9 - - - +
49D LEU* 1.3 76.9 - - - +
51D LYS* 1.3 61.9 + - + +
52D GLY 3.8 0.2 + - - -
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Residues in contact with LYS 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 GLU* 3.1 42.3 + - - +
48D ALA* 3.7 5.6 - - - +
49D LEU 3.1 0.6 - - - -
50D ALA* 1.3 81.7 - - + +
52D GLY* 1.3 60.4 + - - +
53D ASP* 3.3 13.5 + - + +
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Residues in contact with GLY 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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2C HIS* 3.8 22.2 - - - -
42C GLU* 4.6 5.6 - - - -
48D ALA 3.0 4.7 + - - -
49D LEU 3.0 13.0 + - - -
50D ALA 3.5 0.4 + - - -
51D LYS* 1.3 78.2 - - - +
53D ASP* 1.3 59.5 + - - +
54D VAL* 3.1 15.6 + - - +
57D GLN* 4.5 1.6 - - - -
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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
------------------------------------------------------------
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