Contacts of the helix formed by residues 33 - 54 (chain D) in PDB entry 2AXT
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 SER 33 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481C UNK 4.0 12.5 - - - +
29D PHE* 5.2 0.2 - - - -
30D VAL 3.8 6.1 + - - -
32D TRP* 1.3 78.4 - - - +
34D GLY* 1.3 57.3 + - - +
36D LEU* 2.9 11.6 + - - +
37D LEU* 2.8 26.4 + - - +
124D GLY* 4.1 4.1 - - - -
127D LEU* 3.8 15.7 - - - -
128D ARG* 3.5 37.2 - - - +
131D GLU* 2.7 25.9 + - - -
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Residues in contact with GLY 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 VAL* 3.5 16.5 + - - -
31D GLY 3.2 5.8 + - - -
32D TRP 3.1 1.6 - - - -
33D SER* 1.3 79.2 + - - +
35D ILE* 1.3 57.8 + - - +
36D LEU 2.8 10.8 + - - -
37D LEU* 3.7 5.8 - - - -
38D PHE* 3.1 46.4 + - - +
39D PRO* 3.2 4.2 - - - +
128D ARG* 6.3 0.2 - - - -
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Residues in contact with ILE 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C UNK 4.6 18.3 - - + +
483C UNK 6.4 0.2 - - + -
18D LEU* 5.6 2.7 - - + -
22D LEU* 3.8 27.4 - - + -
30D VAL* 5.5 1.8 - - + -
31D GLY 3.9 6.7 - - - +
32D TRP* 2.8 43.7 + - + +
34D GLY* 1.3 75.4 - - - +
36D LEU* 1.3 55.5 + - - +
39D PRO* 3.1 18.9 - - + +
355D CLA 3.8 12.6 - - + +
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Residues in contact with LEU 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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518B CLA 4.5 24.5 - - + -
481C UNK 4.3 23.1 - - + -
33D SER* 2.9 9.3 + - - +
34D GLY 2.8 0.2 - - - -
35D ILE* 1.3 81.2 - - - +
37D LEU* 1.3 63.2 + - - +
39D PRO* 2.8 17.2 - - - +
40D CYS* 3.3 21.6 + - - +
120D PHE* 3.9 26.5 - - + +
123D ILE* 4.6 4.9 - - + -
124D GLY* 3.9 13.9 - - - +
127D LEU* 4.5 14.1 - - + -
355D CLA 3.7 34.3 - - + -
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Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A PHO 3.7 15.7 - - - -
564A PQ9 5.7 2.2 - - + -
485C UNK 4.9 7.2 - - + -
33D SER* 2.8 17.0 + - - +
34D GLY* 4.0 6.1 - - - -
36D LEU* 1.3 77.6 - - - +
38D PHE* 1.3 88.7 + - + +
41D ALA* 2.8 37.3 + - + +
121D GLY* 3.2 27.1 - - - +
124D GLY* 3.9 13.4 - - - +
125D PHE* 3.3 25.4 - - + +
128D ARG* 4.4 15.5 - - + +
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Residues in contact with PHE 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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564A PQ9 6.3 0.4 - - + -
485C UNK 4.4 15.7 - - + -
28D VAL* 4.1 14.1 - - + -
29D PHE 3.8 13.7 - - - -
30D VAL* 4.2 14.1 - - + -
34D GLY* 3.1 37.0 + - - +
37D LEU* 1.3 84.4 - - + +
39D PRO* 1.3 76.7 - - + +
40D CYS 3.1 2.5 + - - -
41D ALA* 4.5 3.6 - - + -
42D TYR* 3.3 27.1 + - + +
128D ARG* 2.9 33.2 - - - -
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Residues in contact with PRO 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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34D GLY 3.2 8.7 - - - +
35D ILE* 3.1 24.2 - - + +
36D LEU 2.8 22.0 - - - +
38D PHE* 1.3 86.0 - - + +
40D CYS* 1.3 56.0 + - - +
42D TYR* 4.8 1.3 - - + +
43D LEU* 2.9 31.0 + - - +
355D CLA 3.5 42.9 - - + +
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Residues in contact with CYS 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 LEU* 3.3 17.6 + - - +
38D PHE 3.1 0.8 - - - -
39D PRO* 1.3 76.6 - - - +
41D ALA* 1.3 58.5 + - - +
42D TYR 3.1 2.0 - - - -
43D LEU* 2.5 33.8 + - - +
44D ALA* 2.8 10.1 + - - -
117D HIS* 3.4 33.9 - - - +
120D PHE* 3.8 24.2 - - - -
121D GLY* 4.0 7.4 - - - +
355D CLA 3.9 31.4 - - - -
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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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562A PHO 3.4 46.1 - - + +
564A PQ9 5.4 2.5 - - + -
37D LEU* 2.8 32.8 + - + +
38D PHE* 4.3 3.6 - - + +
40D CYS* 1.3 76.3 - - - +
42D TYR* 1.3 62.3 + - - +
44D ALA* 3.1 4.1 + - - +
45D LEU* 2.9 24.9 + - - +
117D HIS 4.6 0.2 + - - -
121D GLY* 4.3 4.6 - - - -
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Residues in contact with TYR 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 PHE* 3.3 16.8 + - + +
39D PRO 5.3 1.1 - - - -
40D CYS 2.7 3.6 + - - -
41D ALA* 1.3 76.5 - - - +
43D LEU* 1.3 62.3 + - + +
44D ALA 2.9 0.3 + - - -
45D LEU* 3.2 6.5 + - + +
46D GLY* 2.6 35.7 + - - -
357D BCR 3.5 34.4 - - + +
25F THR* 2.7 43.7 + - + -
26F LEU* 3.4 34.5 - - + -
29F PRO* 3.8 10.6 - - - +
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Residues in contact with LEU 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 PRO 2.9 19.0 + - - +
40D CYS* 2.5 11.8 + - - +
42D TYR* 1.3 83.4 - - + +
44D ALA* 1.3 57.0 + - - -
46D GLY 4.0 0.7 - - - -
47D GLY 3.4 7.8 + - - -
113D PHE* 3.0 32.6 - - + -
117D HIS* 3.5 23.8 - - + +
355D CLA 3.2 56.3 - - + +
357D BCR 3.4 40.7 - - + +
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Residues in contact with ALA 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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562A PHO 4.6 11.2 - - + -
40D CYS 2.8 9.4 + - - +
41D ALA 3.5 7.2 - - - +
42D TYR 2.9 0.6 + - - -
43D LEU* 1.3 75.2 - - - +
45D LEU* 1.3 64.5 + - - +
46D GLY 2.9 4.9 + - - -
47D GLY* 2.9 12.0 + - - -
48D TRP* 3.0 12.3 + - - +
113D PHE* 4.8 2.2 - - - -
114D ILE* 4.3 18.1 - - + +
117D HIS* 4.0 7.8 - - + +
118D GLY* 3.8 32.3 - - - +
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Residues in contact with LEU 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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562A PHO 3.7 34.6 - - + +
41D ALA 2.9 16.1 + - - +
42D TYR* 3.9 5.8 - - + +
44D ALA* 1.3 75.7 - - - +
46D GLY* 1.3 58.2 + - - +
48D TRP* 3.5 3.0 + - + +
49D LEU* 3.1 59.2 + - + +
354D CLA 3.8 36.3 - - + -
357D BCR 4.5 6.7 - - + -
358D MGE 4.2 14.1 - - + -
26F LEU* 5.0 8.3 - - + -
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Residues in contact with GLY 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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42D TYR* 2.6 18.2 + - - -
45D LEU* 1.3 78.8 - - - +
47D GLY* 1.3 55.6 + - - +
49D LEU* 3.3 4.2 + - - +
50D THR* 2.7 37.1 + - - -
357D BCR 3.7 35.0 - - - +
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Residues in contact with GLY 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 LEU 3.4 11.8 + - - -
44D ALA 2.9 7.3 + - - -
46D GLY* 1.3 71.9 - - - +
48D TRP* 1.3 65.2 + - - +
50D THR* 3.4 0.5 - - - -
51D GLY* 2.9 22.9 + - - -
110D LEU* 4.1 10.5 - - - +
113D PHE* 4.4 3.8 - - - -
114D ILE* 3.8 11.6 - - - +
357D BCR 3.4 23.8 - - - +
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Residues in contact with TRP 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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562A PHO 3.5 60.2 - - + +
44D ALA 3.0 9.0 + - - +
45D LEU* 3.7 14.8 - - + +
46D GLY 3.2 0.2 - - - -
47D GLY* 1.3 76.8 - - - +
49D LEU* 1.3 88.0 + - + +
50D THR 2.9 0.5 + - - -
51D GLY 3.7 0.2 - - - -
52D THR* 2.6 66.5 + - + -
67D TYR* 5.6 0.2 - - - -
73D PHE* 4.7 18.2 - + - -
76D VAL* 5.4 5.2 - - + -
77D ALA* 5.0 0.8 - - - +
78D VAL* 3.6 16.2 - - + +
114D ILE* 3.6 11.8 - - + +
173D PHE* 3.4 32.5 + - + -
174D GLY* 4.9 2.2 - - - -
175D VAL* 6.2 0.2 - - + -
354D CLA 4.0 23.1 - - + -
358D MGE 4.7 7.9 - - + -
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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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45D LEU* 3.1 43.9 + - + +
46D GLY 3.7 4.3 - - - +
48D TRP* 1.3 104.1 - - + +
50D THR* 1.3 63.6 + - - +
52D THR* 3.7 6.5 - - + -
53D THR* 2.9 27.2 + - + +
67D TYR* 6.6 0.4 - - + -
357D BCR 3.4 47.3 - - + -
358D MGE 3.8 35.9 - - + -
33F PHE* 3.4 4.3 - - - -
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Residues in contact with THR 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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46D GLY 2.7 19.4 + - - -
47D GLY 3.4 7.4 - - - -
48D TRP 2.9 1.0 + - - -
49D LEU* 1.3 72.9 - - - +
51D GLY* 1.3 58.7 + - - +
52D THR 2.9 0.4 - - - -
53D THR* 2.7 29.6 + - - -
54D PHE* 3.0 18.1 + - + -
55D VAL* 4.9 2.5 - - + -
110D LEU* 5.0 2.7 - - + -
357D BCR 3.5 33.8 - - + +
47E PHE* 4.0 33.2 - - + -
33F PHE* 4.0 12.7 - - + -
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Residues in contact with GLY 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 GLY 2.9 13.4 + - - -
48D TRP 3.8 0.4 - - - -
50D THR* 1.3 78.3 - - - +
52D THR* 1.3 60.4 + - - +
53D THR 3.3 0.5 + - - -
55D VAL* 3.1 33.1 + - - +
66D SER* 3.6 2.1 - - - -
77D ALA 4.2 5.7 - - - +
78D VAL* 4.0 13.4 - - - -
110D LEU* 3.8 21.0 - - - +
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Residues in contact with THR 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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48D TRP* 2.6 61.1 + - + -
49D LEU* 3.7 11.4 - - + -
50D THR 2.7 4.2 + - - -
51D GLY* 1.3 72.5 - - - -
53D THR* 1.3 57.4 + - - +
65D SER 4.6 4.7 - - - -
66D SER* 3.1 19.3 - - - -
67D TYR* 3.1 24.5 + - + +
76D VAL* 3.4 32.5 - - + +
77D ALA* 4.8 3.2 - - - +
78D VAL* 4.0 3.3 - - - +
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Residues in contact with THR 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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49D LEU* 2.9 21.6 + - + +
50D THR 2.7 11.0 + - - -
52D THR* 1.3 75.9 - - - +
54D PHE* 1.3 84.8 + - - -
66D SER* 3.6 4.9 - - - -
67D TYR* 3.3 37.2 - - + +
68D LEU* 2.9 31.7 + - - +
357D BCR 5.3 2.0 - - + -
33F PHE* 4.0 10.0 - - + -
37F ILE* 3.9 16.6 - - + +
40F MET* 3.6 4.6 - - - +
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Residues in contact with PHE 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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50D THR* 3.0 19.7 + - + +
51D GLY 3.8 0.2 + - - -
53D THR* 1.3 98.7 - - - +
55D VAL* 1.3 57.7 + - + +
66D SER* 3.7 5.3 + - - -
68D LEU* 4.1 8.2 - - + +
37E PHE* 3.8 31.4 - + - -
38E VAL* 4.2 4.3 - - + -
43E ALA* 4.0 18.2 - - + -
47E PHE* 3.2 37.0 - + + +
49E THR* 2.7 30.1 + - - +
32F PHE* 4.8 3.4 - + - -
33F PHE* 3.9 26.0 - + - -
36F ALA* 3.9 15.7 - - + -
37F ILE* 6.1 0.2 - - + -
40F MET* 3.7 24.0 - - + -
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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