Contacts of the helix formed by residues 39 - 63 (chain D) in PDB entry 1ORZ
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 TYR 39 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B ASN* 2.6 74.1 + - + -
214B TYR* 2.9 22.9 - + - -
243B LEU* 2.9 54.1 + - + +
27D PRO* 3.1 8.7 - - + -
28D PRO* 2.7 48.2 - - + +
29D GLU 3.5 6.5 - - - +
38D TRP* 1.3 85.0 - + - +
40D MET* 1.3 58.4 + - - +
42D LYS* 3.3 5.9 + - - +
43D ILE* 3.1 15.4 + - - +
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Residues in contact with MET 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D VAL* 3.1 13.9 - - + -
26D PRO* 3.7 26.7 - - + -
27D PRO* 2.9 25.3 - - + +
36D TYR 5.9 0.9 - - - +
37D HIS* 6.0 7.9 - - + -
38D TRP 2.9 6.9 + - - +
39D TYR* 1.3 67.9 - - - +
41D GLU* 1.3 67.5 + - - +
43D ILE* 2.7 38.7 - - + +
44D PHE* 2.8 47.5 + - + -
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Residues in contact with GLU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B SER* 4.0 14.7 - - - +
214B TYR* 5.1 0.2 - - - +
215B ARG* 5.2 6.5 + - - -
23D ALA* 4.8 6.5 - - - +
25D VAL* 2.9 31.8 - - + +
27D PRO 3.3 0.6 + - - +
28D PRO* 2.6 25.9 + - - +
29D GLU* 3.1 37.0 + - + +
40D MET* 1.3 71.8 - - - +
42D LYS* 1.3 61.5 + - - -
45D ALA 3.1 1.7 + - - -
80D MET* 2.8 58.3 - - + +
83D ASN* 4.6 10.9 + - - -
84D SER* 4.6 5.7 - - - -
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Residues in contact with LYS 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C HIS* 4.0 18.1 - - - -
114C LEU* 3.4 26.9 - - - +
117C ASP* 3.4 23.8 - - - -
28D PRO 2.7 13.5 + - - -
29D GLU* 2.9 13.2 - - + +
30D ASN* 2.8 32.3 - - - +
31D LYS* 2.8 31.8 + - + +
39D TYR 4.2 0.2 - - - +
41D GLU* 1.3 73.6 - - - +
43D ILE* 1.3 60.0 + - - +
45D ALA* 3.0 10.8 + - + +
46D LEU* 2.7 49.5 + - - +
49D VAL* 5.0 0.6 - - - +
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Residues in contact with ILE 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LYS* 2.9 37.2 - - + +
34D GLY 4.1 9.1 - - - +
35D SER* 3.8 20.9 - - - +
36D TYR 3.9 21.3 - - - +
38D TRP* 4.0 4.3 - - + -
39D TYR 3.1 18.2 - - - +
40D MET* 2.7 45.3 + - + +
42D LYS* 1.3 76.7 - - - +
44D PHE* 1.3 69.8 + - + +
46D LEU* 3.7 1.0 - - - +
47D SER* 2.8 32.0 + - - -
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Residues in contact with PHE 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D TYR* 6.3 2.2 - - + -
25D VAL* 3.5 7.6 - - + -
35D SER* 5.9 0.2 - - - -
40D MET* 2.8 53.8 + - + -
43D ILE* 1.3 88.6 - - + +
45D ALA* 1.3 62.9 + - - +
47D SER* 3.2 5.7 + - - -
48D VAL* 2.9 31.8 + - + +
77D TYR* 3.9 40.8 - + + +
80D MET* 3.4 19.5 - - + -
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Residues in contact with ALA 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLU* 5.4 2.5 - - - +
41D GLU 3.1 9.0 + - - +
42D LYS* 3.0 17.7 + - + +
44D PHE* 1.3 76.4 - - - +
46D LEU* 1.3 61.9 + - - +
48D VAL* 3.9 4.6 - - - +
49D VAL* 2.9 28.7 + - - +
77D TYR 6.4 0.2 - - - -
78D CYS* 5.4 6.4 - - - +
80D MET* 3.1 30.4 - - + +
81D GLU* 5.0 11.9 - - + +
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C LEU* 2.9 42.8 - - + +
31D LYS 4.1 4.3 - - - +
32D LEU* 2.9 43.5 - - - +
33D GLU* 2.9 43.3 - - + +
34D GLY 5.8 0.2 - - - +
42D LYS* 2.7 30.9 + - + +
43D ILE 4.0 1.6 - - - +
45D ALA* 1.3 74.2 - - - +
47D SER* 1.3 63.2 + - - +
49D VAL* 2.9 2.5 - - + +
50D PRO* 2.8 28.0 - - + +
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Residues in contact with SER 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D GLU* 5.8 1.1 - - - -
34D GLY* 5.3 9.1 + - - +
35D SER* 5.0 9.8 + - - -
43D ILE 2.8 19.0 + - - -
44D PHE* 3.8 6.7 - - - -
46D LEU* 1.3 79.0 - - - +
48D VAL* 1.3 65.1 + - - +
50D PRO* 3.5 5.2 - - - +
51D LEU* 3.3 18.5 + - - +
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Residues in contact with VAL 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 PHE* 2.9 20.2 + - + +
45D ALA* 3.9 2.2 - - - +
47D SER* 1.3 77.5 - - - +
49D VAL* 1.3 65.3 + - - +
51D LEU* 3.0 5.3 + - - +
52D ALA* 2.8 26.3 + - + +
74D LEU* 3.1 46.0 - - + +
75D LEU 4.4 0.2 - - - +
77D TYR* 3.6 32.1 - - + -
78D CYS* 3.2 22.2 - - - +
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Residues in contact with VAL 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C HIS* 5.6 5.6 - - + +
107C TYR* 6.2 1.8 - - + -
110C ALA* 4.4 18.6 - - + -
111C ILE* 5.0 2.7 - - + -
114C LEU* 3.9 15.9 - - + -
42D LYS* 5.0 0.4 - - - +
45D ALA 2.9 21.3 + - - +
46D LEU* 2.9 30.3 - - + +
48D VAL* 1.3 78.2 - - - +
50D PRO* 1.3 74.3 - - + +
52D ALA* 3.2 7.0 + - + +
53D THR* 2.8 32.6 + - - +
78D CYS* 5.3 1.1 - - - -
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Residues in contact with PRO 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ILE* 5.9 0.2 - - + -
114C LEU* 3.8 4.9 - - + -
33D GLU* 3.6 28.7 - - + +
46D LEU* 2.8 28.2 - - + +
47D SER* 4.2 3.4 - - - +
49D VAL* 1.3 94.7 - - + +
51D LEU* 1.3 62.3 + - - +
53D THR* 3.1 17.6 + - - +
54D THR* 3.1 14.2 + - - -
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D SER 3.3 11.7 + - - +
48D VAL* 3.0 5.7 + - - +
50D PRO* 1.3 75.4 - - - +
52D ALA* 1.3 58.4 + - - +
54D THR* 2.7 34.6 - - + +
55D ALA* 3.2 4.0 + - + -
67D ASP* 5.2 3.6 - - - +
70D PHE* 3.0 40.4 - - + -
71D SER* 4.6 7.9 - - - +
74D LEU* 2.9 29.2 - - + -
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Residues in contact with ALA 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PHE* 5.6 6.6 - - + -
48D VAL* 2.8 23.3 + - + +
49D VAL* 3.6 7.9 - - + +
51D LEU* 1.3 80.2 - - - +
53D THR* 1.3 63.4 + - - +
55D ALA* 3.1 9.9 + - - +
56D MET* 2.9 23.7 + - - +
71D SER* 4.8 5.8 - - - +
74D LEU* 4.1 4.4 - - + +
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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
----------------------------------------------------------
107C TYR* 5.6 6.5 - - + +
111C ILE* 4.1 22.1 - - + +
49D VAL* 2.8 30.9 + - - +
50D PRO* 3.1 13.9 + - - +
52D ALA* 1.3 76.5 - - - +
54D THR* 1.3 60.4 + - - +
56D MET* 2.8 22.7 - - + +
57D LEU* 2.7 39.9 - - + +
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Residues in contact with THR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D PRO 3.1 6.6 + - - +
51D LEU* 2.7 43.7 - - + +
53D THR* 1.3 78.7 - - - +
55D ALA* 1.3 65.0 + - - +
57D LEU* 3.1 9.7 + - - +
58D THR* 2.8 30.4 + - - +
67D ASP* 5.6 2.5 - - - +
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D LEU* 3.8 7.6 - - + +
52D ALA 3.1 9.7 + - - +
54D THR* 1.3 84.2 - - + +
56D MET* 1.3 57.8 + - - +
58D THR* 3.0 9.0 + - - -
59D THR* 2.8 31.0 + - - +
62D LEU* 4.8 0.3 - - - +
66D ALA 5.0 5.7 - - - +
67D ASP* 4.3 14.8 - - - +
71D SER* 2.9 29.2 - - - +
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Residues in contact with MET 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PHE* 3.5 40.8 - - + -
107C TYR* 4.1 36.3 - - + -
52D ALA 2.9 10.1 + - - +
53D THR* 2.8 31.9 - - - +
55D ALA* 1.3 73.1 - - - +
57D LEU* 1.3 79.8 + - + +
59D THR* 2.7 13.0 - - + +
60D GLY* 2.7 30.9 + - - -
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Residues in contact with LEU 57 (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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53D THR* 2.7 43.7 + - + +
54D THR* 3.6 8.7 - - - +
56D MET* 1.3 101.1 - - + +
58D THR* 1.3 66.0 + - - +
61D PRO* 2.8 32.0 - - + +
143D SER* 5.5 0.7 + - - -
144D GLN* 4.8 23.6 - - + +
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Residues in contact with THR 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D THR* 2.8 23.2 + - - +
55D ALA* 3.4 10.2 - - - -
57D LEU* 1.3 78.2 - - - +
59D THR* 1.3 48.8 - - - +
61D PRO* 4.6 0.7 - - - +
62D LEU* 2.5 71.6 + - + +
66D ALA* 4.3 8.3 - - + -
67D ASP* 4.5 7.7 + - - +
143D SER* 4.6 5.2 + - - +
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Residues in contact with THR 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ALA 2.8 9.9 + - - +
56D MET* 2.7 39.7 - - + +
58D THR* 1.3 75.6 - - - +
60D GLY* 1.3 60.4 + - - +
62D LEU* 2.7 18.4 - - - -
63D SER* 2.3 61.0 + - - -
65D ALA* 3.1 24.8 + - + +
66D ALA 4.6 0.4 - - - -
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Residues in contact with GLY 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D MET* 2.7 19.6 + - - -
59D THR* 1.3 76.3 - - - +
61D PRO* 1.3 67.8 - - - +
63D SER* 4.1 1.7 - - - -
139D GLU* 4.0 5.3 - - - +
140D LYS* 2.9 25.1 + - - -
141D ASP 3.7 1.4 + - - -
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Residues in contact with PRO 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D MET 4.4 0.2 - - - +
57D LEU* 2.8 33.2 - - + +
60D GLY* 1.3 80.2 - - - +
62D LEU* 1.5 51.8 - - - +
140D LYS* 2.3 34.5 - - - +
141D ASP* 2.1 29.9 - - + +
142D ASN 3.4 7.0 - - - +
143D SER* 3.0 33.9 - - - +
144D GLN* 4.3 18.4 - - + +
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ALA 4.8 0.2 - - - +
58D THR* 2.5 44.0 + - + +
59D THR* 2.7 24.4 + - - +
61D PRO* 1.5 70.4 - - - +
63D SER 1.4 48.2 - - - +
66D ALA* 3.4 15.3 - - + +
132D LYS* 2.7 29.6 - - - +
136D ASP* 2.4 55.0 - - - +
137D SER* 4.4 0.3 + - - -
140D LYS* 2.8 22.4 - - - +
143D SER* 4.2 1.7 + - - +
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Residues in contact with SER 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D THR* 2.3 33.0 + - - +
60D GLY* 4.8 1.2 - - - -
62D LEU* 1.4 57.6 - - - +
64D THR* 1.3 54.8 + - - +
135D TRP* 2.4 25.8 + - - -
136D ASP* 2.4 25.6 + - - -
138D SER 2.8 0.9 + - - -
139D GLU* 2.5 47.9 + - - +
140D LYS* 2.9 9.4 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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