Contacts of the helix formed by residues 28 - 51 (chain B) in PDB entry 2O38
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 PRO 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A GLU* 4.9 1.0 - - - +
86A THR* 5.7 1.9 - - - +
27B MSE 1.3 91.8 - - + +
29B ASP* 1.3 71.1 + - + +
30B ALA 3.2 1.1 - - - +
31B GLU* 3.3 13.6 + - + +
32B GLU* 3.4 10.9 + - - +
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Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B PRO* 1.3 83.5 - - + +
30B ALA* 1.3 62.0 + - - +
32B GLU* 3.2 20.4 + - - +
33B ARG* 2.8 57.9 + - - +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B MSE 3.5 18.3 + - - +
28B PRO* 3.2 1.6 - - - +
29B ASP* 1.3 78.2 - - - +
31B GLU* 1.3 63.1 + - - +
33B ARG* 3.4 30.0 + - - +
34B GLN* 3.1 24.3 + - - +
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU* 3.8 9.9 - - - +
86A THR* 3.5 15.6 - - + +
89A ASN* 3.4 11.0 + - - +
27B MSE 3.6 24.6 + - - +
28B PRO* 3.3 7.8 + - + +
29B ASP 3.3 0.6 - - - -
30B ALA* 1.3 77.6 - - - +
32B GLU* 1.3 62.9 + - - +
34B GLN* 3.3 9.7 + - + +
35B THR* 3.0 28.0 + - - +
110B ARG* 4.1 4.9 - - - +
111B ILE* 3.3 42.8 + - + +
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Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A SER* 5.2 2.9 + - - -
82A GLU* 3.3 42.5 + - + +
28B PRO 3.4 8.8 + - - +
29B ASP* 3.2 23.7 + - - +
31B GLU* 1.3 80.3 - - - +
33B ARG* 1.3 63.3 + - + +
35B THR* 3.2 2.9 + - - -
36B LYS* 3.0 47.5 + - + +
80B SER* 5.5 1.6 - - - -
81B VAL* 4.5 5.5 + - + +
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ASP* 2.8 63.0 + - - +
30B ALA* 3.5 30.7 - - - +
32B GLU* 1.3 76.2 - - + +
34B GLN* 1.3 57.6 + - - +
36B LYS* 3.4 11.7 + - + +
37B LEU* 3.0 40.2 + - + +
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Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ALA 3.1 13.0 + - - +
31B GLU* 3.5 12.5 - - + +
33B ARG* 1.3 74.0 - - - +
35B THR* 1.3 65.3 - - - +
37B LEU* 3.3 10.3 + - + +
38B ARG* 3.1 64.4 + - + +
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Residues in contact with THR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU* 3.5 24.5 + - - +
85A MSE 4.5 0.4 - - + -
97A ILE* 3.9 27.8 - - + -
31B GLU* 3.0 15.6 + - - +
32B GLU 3.6 7.0 - - - -
34B GLN* 1.3 76.0 - - - +
36B LYS* 1.3 58.7 + - - +
38B ARG* 3.2 12.4 + - - +
39B LEU* 2.9 39.8 + - + +
81B VAL* 4.2 7.9 - - + -
111B ILE* 3.7 21.4 + - + +
113B VAL* 4.6 2.7 - - + -
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Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLU* 3.0 36.9 + - + +
33B ARG* 3.6 14.1 - - + +
35B THR* 1.3 77.2 - - - +
37B LEU* 1.3 53.5 + - - +
39B LEU* 3.3 1.1 + - - -
40B ALA* 2.7 36.2 + - - +
76B LEU* 2.9 34.1 + - + +
77B GLU* 3.7 13.9 + - - +
79B PHE 2.7 28.9 + - - +
80B SER* 4.3 5.8 - - - +
81B VAL* 3.9 16.8 - - + +
84B LEU* 3.7 19.5 - - + +
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ARG* 3.0 28.1 + - + +
34B GLN* 3.3 8.9 + - - +
36B LYS* 1.3 75.4 - - - +
38B ARG* 1.3 59.3 + - + +
40B ALA* 3.7 1.6 - - - +
41B TYR* 2.8 29.3 + - - +
74B TYR* 3.8 39.0 - - + +
76B LEU* 3.8 13.7 - - + -
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Residues in contact with ARG 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLN* 3.1 54.3 + - + +
35B THR* 3.6 5.3 + - - +
37B LEU* 1.3 75.7 - - + +
39B LEU* 1.3 59.0 + - - +
41B TYR* 3.3 9.7 + - - +
42B ALA* 3.0 27.7 + - - +
111B ILE 3.1 26.1 + - - -
112B SER* 4.2 7.4 - - - +
113B VAL* 3.6 40.5 - - + +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 4.0 20.6 - - + -
99A ILE* 3.7 26.2 - - + -
35B THR* 2.9 28.5 + - + +
36B LYS 3.8 3.1 - - - +
38B ARG* 1.3 76.4 - - - +
40B ALA* 1.3 58.4 + - - +
42B ALA* 3.2 5.1 + - - +
43B LEU* 2.9 27.9 + - - +
81B VAL* 3.6 42.4 - - + +
84B LEU* 4.0 19.7 - - + +
85B MSE 4.2 9.6 - - + -
88B LEU* 3.9 15.0 - - + +
95B VAL* 5.6 0.2 - - + -
113B VAL* 4.2 6.5 - - + -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LYS 2.7 21.0 + - - +
37B LEU 3.7 2.7 - - - +
39B LEU* 1.3 70.1 - - - +
41B TYR* 1.3 59.4 + - - +
43B LEU* 3.3 7.1 + - - +
44B ASN* 2.9 38.5 + - - +
71B LEU* 5.2 2.2 - - + -
74B TYR* 3.9 11.9 - - + -
76B LEU* 3.3 34.1 - - + -
84B LEU* 4.5 10.0 - - + +
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Residues in contact with TYR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU 2.8 21.1 + - - +
38B ARG* 3.6 9.9 - - - +
39B LEU 3.3 0.2 - - - -
40B ALA* 1.3 72.2 - - - +
42B ALA* 1.3 66.1 + - + +
44B ASN* 3.1 2.1 + - - +
45B ALA* 2.8 43.9 + - + +
49B ARG* 5.7 0.7 + - - -
74B TYR* 3.3 17.7 - - + +
115B ALA* 5.2 13.0 - - + -
201B ACY 3.7 23.6 - - + -
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ILE* 3.6 30.1 - - + -
38B ARG 3.0 12.2 + - - +
39B LEU 3.2 8.0 + - - +
41B TYR* 1.3 85.3 - - + +
43B LEU* 1.3 60.9 + - - +
45B ALA* 3.4 1.2 + - - -
46B VAL* 3.1 27.7 + - - +
88B LEU* 4.0 6.5 - - + -
113B VAL* 5.0 2.0 - - + -
115B ALA* 5.0 6.1 - - + -
202B ACY 3.3 17.1 - - - +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU 2.9 16.0 + - - +
40B ALA* 3.7 5.6 - - - +
42B ALA* 1.3 76.0 - - - +
44B ASN* 1.3 64.2 + - - +
46B VAL* 3.3 4.1 + - - +
47B ILE* 3.0 35.6 + - + +
61B LEU* 4.6 3.1 - - + -
71B LEU* 4.1 24.9 - - + -
84B LEU* 4.3 11.7 - - + +
87B LEU* 3.7 51.8 - - + +
88B LEU* 3.7 19.4 - - + +
91B LEU* 3.6 27.6 - - + -
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Residues in contact with ASN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ALA* 2.9 23.5 + - - +
43B LEU* 1.3 78.6 - - - +
45B ALA* 1.3 57.3 + - - +
47B ILE* 3.3 7.8 + - - +
48B ASP* 2.8 35.6 + - - +
71B LEU* 2.8 28.6 + - - +
72B ARG* 3.0 39.6 + - - +
74B TYR* 3.3 22.0 - - - +
201B ACY 3.3 24.9 - - + -
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B TYR* 2.8 38.3 + - + +
42B ALA* 3.7 4.9 - - - +
44B ASN* 1.3 78.0 - - - +
46B VAL* 1.3 55.7 + - - +
48B ASP* 3.3 12.6 + - - +
49B ARG* 2.9 52.3 + - - +
201B ACY 3.9 3.8 - - + +
202B ACY 4.2 4.9 - - - +
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA 3.1 18.2 + - - +
43B LEU* 3.6 7.6 - - - +
44B ASN 3.2 0.2 - - - -
45B ALA* 1.3 73.7 - - - +
47B ILE* 1.3 65.3 + - - +
49B ARG* 3.4 13.1 + - - +
50B ALA* 2.9 30.6 + - + +
88B LEU* 4.3 3.6 - - + -
91B LEU* 3.8 27.8 - - + +
93B GLN* 3.5 34.1 - - + +
202B ACY 3.4 25.6 - - - +
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 3.0 25.0 + - + +
44B ASN* 3.6 20.0 - - - +
46B VAL* 1.3 76.1 - - - +
48B ASP* 1.3 62.5 + - - +
50B ALA* 3.4 4.5 + - - -
51B ARG 3.0 17.5 + - - -
52B LEU* 3.3 35.9 + - + +
53B SER 5.2 0.2 - - - +
54B GLN* 6.4 0.2 - - - -
57B ALA* 4.2 22.2 - - + -
61B LEU* 4.6 8.7 - - + -
68B VAL* 5.2 4.3 - - + -
71B LEU* 5.3 4.9 - - + -
72B ARG* 3.9 25.6 - - - +
91B LEU* 3.5 22.2 - - + -
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Residues in contact with ASP 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ASN 2.8 20.8 + - - +
45B ALA* 3.4 9.8 - - - +
46B VAL 3.2 0.2 - - - -
47B ILE* 1.3 72.5 - - - +
49B ARG* 1.3 60.0 + - + +
51B ARG* 2.9 26.8 + - - +
72B ARG* 2.8 34.8 + - - -
201B ACY 2.4 32.0 - - - +
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B TYR* 5.7 0.8 + - - -
45B ALA* 2.9 34.7 + - - +
46B VAL* 3.5 19.0 - - - +
48B ASP* 1.3 79.1 - - + +
50B ALA* 1.3 60.6 + - - +
51B ARG* 3.2 11.1 + - - +
93B GLN* 4.8 1.4 + - - -
202B ACY 2.9 45.1 + - - +
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 2.9 22.4 + - + +
47B ILE 3.9 0.7 - - - +
49B ARG* 1.3 73.3 - - - +
51B ARG* 1.3 69.4 + - - +
52B LEU* 3.2 33.9 + - + +
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Residues in contact with ARG 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE 3.0 2.1 + - - -
48B ASP* 2.9 19.7 + - - +
49B ARG* 3.6 13.0 - - - +
50B ALA* 1.3 78.5 - - - +
52B LEU* 1.3 64.5 + - - +
53B SER 3.6 1.9 + - - -
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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
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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