Contacts of the helix formed by residues 28 - 49 (chain H) in PDB entry 2FIE
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 28 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ARG* 3.7 6.9 + - - -
801D A74 4.1 11.1 - - - +
27H THR* 1.3 78.9 - - - +
29H GLU* 1.3 58.0 - - - +
31H THR* 3.2 6.5 + - - -
32H GLN* 3.0 28.8 + - - +
901H A74 3.0 38.1 + - - -
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Residues in contact with GLU 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ARG* 2.9 37.4 - - - +
27H THR* 3.3 7.3 + - - +
28H GLY* 1.3 74.2 - - - +
30H LEU* 1.3 55.9 + - - +
32H GLN* 2.9 3.3 + - - +
33H LEU* 2.5 35.9 + - - +
89H PHE 3.5 4.4 - - - +
90H ALA* 3.3 20.8 - - + +
110H ARG 4.7 0.3 - - - +
111H GLY* 3.1 30.5 - - - -
112H LYS* 2.6 44.2 + - - +
113H TYR* 3.9 8.7 - - + -
901H A74 4.4 0.4 + - - -
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Residues in contact with LEU 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H GLY 3.4 0.6 - - - -
29H GLU* 1.3 78.1 - - - +
31H THR* 1.3 57.4 + - - +
33H LEU* 3.9 9.4 - - + -
34H LEU* 2.8 50.9 + - + +
113H TYR* 3.6 28.0 - - + +
138H ILE* 4.1 28.0 - - + -
160H VAL* 3.8 19.1 - - + -
161H ALA* 5.0 1.1 - - + -
177H MET* 3.6 26.5 - - + -
901H A74 3.6 32.3 + - + +
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Residues in contact with THR 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D MET* 3.3 26.7 - - + -
801D A74 3.7 14.1 - - - -
17H VAL* 3.9 26.9 + - + +
18H MET* 4.6 9.2 - - - -
21H GLY* 4.2 3.3 - - - -
28H GLY 3.3 10.1 - - - -
29H GLU 3.1 0.6 - - - -
30H LEU* 1.3 75.2 - - - +
32H GLN* 1.3 58.0 + - - +
34H LEU* 3.8 1.4 + - - +
35H ASN* 3.1 26.7 + - - +
901H A74 3.1 40.4 + - + -
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Residues in contact with GLN 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ARG* 4.0 16.5 + - + +
18D MET* 3.9 31.2 - - + -
19D GLU* 3.0 43.4 + - - +
22D ARG* 2.6 42.4 + - - +
801D A74 5.2 0.9 - - - +
28H GLY 3.0 11.3 + - - +
29H GLU 2.9 8.1 + - - +
31H THR* 1.3 76.1 - - - +
33H LEU* 1.3 64.0 + - - +
35H ASN* 3.6 2.4 + - - +
36H SER* 3.1 26.0 + - - -
88H SER* 3.8 20.2 + - - +
89H PHE* 5.5 0.7 - - - +
90H ALA* 5.2 0.2 - - + -
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Residues in contact with LEU 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H GLU 2.5 19.8 + - - +
30H LEU* 3.5 13.9 - - + +
32H GLN* 1.3 70.1 - - - +
34H LEU* 1.3 68.3 + - - +
36H SER* 3.1 15.2 + - - -
37H LEU* 3.2 13.9 + - + +
85H LEU* 3.6 20.7 - - + +
88H SER* 3.7 14.3 - - - +
90H ALA* 4.1 9.6 - - + +
91H THR* 3.2 35.4 - - + -
113H TYR* 4.7 11.2 - - + -
115H VAL* 4.3 11.0 - - + -
138H ILE* 4.0 27.6 - - + -
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Residues in contact with LEU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H LEU* 5.7 1.7 - - - +
17H VAL* 4.3 15.7 - - + -
30H LEU* 2.8 31.9 + - + +
31H THR 4.1 2.7 - - - +
33H LEU* 1.3 74.0 - - - +
35H ASN* 1.3 63.2 + - - +
37H LEU* 3.4 18.2 + - + +
38H CYS* 3.1 19.9 + - - +
136H PHE* 4.5 1.3 - - + -
138H ILE* 3.8 23.3 - - + -
161H ALA* 4.9 0.4 - - + -
175H LEU* 4.1 31.9 - - + -
177H MET* 3.8 29.4 - - + -
901H A74 4.1 13.0 - - + -
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Residues in contact with ASN 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D THR* 4.9 2.9 + - - -
14D THR* 3.3 37.3 + - - +
15D ARG* 4.8 7.4 + - - +
18D MET* 4.5 7.4 - - + +
192D GLU* 6.0 0.2 - - - -
14H THR* 4.0 22.0 + - - +
17H VAL* 5.7 1.1 - - + +
31H THR 3.1 19.3 + - - +
32H GLN* 3.9 7.9 - - - +
33H LEU 3.1 0.8 - - - -
34H LEU* 1.3 78.1 - - - +
36H SER* 1.3 61.1 + - - +
38H CYS* 2.9 30.0 + - - +
39H THR* 3.1 15.6 + - - -
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Residues in contact with SER 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ARG* 3.5 17.9 + - - -
32H GLN 3.1 12.6 + - - -
33H LEU 3.1 8.8 + - - -
35H ASN* 1.3 75.8 + - - +
37H LEU* 1.3 66.8 + - - +
38H CYS 3.0 1.3 - - - -
39H THR* 3.2 5.9 + - - +
40H ALA* 2.9 24.3 + - - +
84H MET* 3.3 42.8 + - - +
85H LEU* 4.5 2.9 - - - -
88H SER* 3.5 8.1 - - - -
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Residues in contact with LEU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H LEU* 3.2 11.6 + - + +
34H LEU* 3.4 23.1 - - + +
36H SER* 1.3 77.9 - - - +
38H CYS* 1.3 53.3 + - - +
40H ALA* 3.4 6.7 + - + +
41H VAL* 2.8 44.8 + - + +
81H VAL* 4.4 23.3 - - + -
85H LEU* 4.5 17.8 - - + +
115H VAL* 5.1 3.4 - - + -
117H PHE* 5.9 0.4 - - + -
134H THR* 6.0 2.9 - - + -
136H PHE* 3.3 62.8 - - + -
138H ILE* 4.3 7.4 - - + -
173H LEU* 6.0 1.1 - - + -
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Residues in contact with CYS 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H LEU* 3.8 21.3 - - + -
14H THR* 5.2 7.4 - - - -
34H LEU 3.1 9.9 + - - +
35H ASN* 2.9 22.0 + - - +
37H LEU* 1.3 76.7 - - - +
39H THR* 1.3 64.4 + - - +
41H VAL* 3.3 7.8 + - - +
42H LYS* 3.1 36.4 + - - +
173H LEU* 5.0 4.5 - - - -
193H PHE* 3.4 32.7 - - - -
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Residues in contact with THR 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 4.3 15.5 - - + -
12D THR* 4.9 3.8 + - + -
190D ILE* 4.4 6.2 - - + +
192D GLU* 3.2 38.1 + - + +
35H ASN* 3.1 18.4 + - - -
36H SER 3.2 2.0 + - - -
38H CYS* 1.3 77.6 - - - +
40H ALA* 1.3 64.2 + - - +
42H LYS* 3.3 12.5 + - - +
43H ALA* 2.9 21.7 + - - +
84H MET* 3.6 30.2 - - + +
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Residues in contact with ALA 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H SER 2.9 13.1 + - - +
37H LEU* 3.4 12.8 - - + +
39H THR* 1.3 77.0 - - - +
41H VAL* 1.3 54.8 + - + +
43H ALA* 3.0 7.7 + - - +
44H ILE* 2.7 38.6 + - - +
80H LEU* 4.4 3.4 - - - -
81H VAL* 4.0 37.7 - - + +
84H MET* 4.1 12.7 - - + +
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Residues in contact with VAL 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H LEU* 2.8 35.7 + - + +
38H CYS* 3.3 7.2 + - - +
40H ALA* 1.3 73.8 - - + +
42H LYS* 1.3 57.5 + - - +
44H ILE* 3.4 5.4 - - + +
45H SER* 2.8 26.0 + - - -
81H VAL* 6.4 0.2 - - + -
134H THR* 4.9 11.9 - - + -
136H PHE* 5.4 4.9 - - + -
165H ALA* 3.5 33.7 - - + -
167H TYR* 3.5 16.6 + - + +
171H THR* 4.8 2.5 - - + -
173H LEU* 4.7 9.2 - - + -
193H PHE* 3.9 21.1 - - + -
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Residues in contact with LYS 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LYS* 4.4 1.4 - - - +
189D ALA 5.0 0.7 - - - +
190D ILE* 3.2 24.9 + - + +
191D GLY 3.2 17.4 + - - -
192D GLU* 3.5 15.4 + - - -
38H CYS* 3.1 25.1 + - - +
39H THR* 3.7 8.3 - - - +
41H VAL* 1.3 72.8 - - - +
43H ALA* 1.3 56.0 + - - +
45H SER* 3.0 9.6 + - - -
46H SER* 2.7 36.2 + - - -
186H LEU* 3.7 29.3 - - + +
191H GLY* 3.0 28.6 + - - +
192H GLU* 5.0 0.6 - - - +
193H PHE* 3.5 25.6 - - + -
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Residues in contact with ALA 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A HIS* 5.2 8.6 + - - +
59A ILE* 3.7 24.7 - - + -
190D ILE* 3.9 19.4 - - + +
39H THR 2.9 14.2 + - - +
40H ALA* 3.4 9.2 - - - +
42H LYS* 1.3 72.7 - - - +
44H ILE* 1.3 64.5 + - - +
46H SER* 3.0 13.5 + - - -
47H ALA* 3.1 13.2 + - - +
80H LEU* 3.6 19.9 - - + +
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Residues in contact with ILE 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H ALA 2.7 23.3 + - - +
41H VAL* 3.4 5.4 - - + +
43H ALA* 1.3 71.3 - - - +
45H SER* 1.3 58.4 + - - +
47H ALA* 2.9 8.5 + - - +
48H VAL* 2.8 39.0 + - + +
77H SER* 4.0 22.7 - - - +
80H LEU* 3.6 19.5 - - + +
81H VAL* 3.7 28.3 - - + -
119H PRO 3.8 6.7 - - - +
120H LEU* 4.2 2.9 - - + -
134H THR* 3.7 12.3 - - + +
167H TYR* 3.0 40.6 - - + +
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Residues in contact with SER 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H VAL 2.8 15.0 + - - -
42H LYS* 3.2 13.0 - - - -
44H ILE* 1.3 75.2 - - - +
46H SER* 1.3 64.9 + - - +
48H VAL* 3.1 3.1 + - - -
49H ARG* 3.0 36.5 + - - -
167H TYR* 3.6 19.6 - - - -
171H THR* 2.8 31.0 + - - -
186H LEU* 4.4 8.0 - - - +
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Residues in contact with SER 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A HIS* 6.4 0.4 - - - -
189D ALA* 3.6 33.3 + - - +
190D ILE* 4.2 8.8 - - - +
42H LYS 2.7 15.4 + - - -
43H ALA 3.0 10.7 + - - -
45H SER* 1.3 74.6 - - - +
47H ALA* 1.3 62.2 + - - +
49H ARG* 3.6 7.5 + - - +
51H ALA* 3.1 35.4 + - - +
188L PRO* 5.4 0.2 - - - +
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Residues in contact with ALA 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A HIS* 6.1 2.7 - - - +
43H ALA 3.1 9.3 + - - +
44H ILE* 2.9 10.8 + - - +
46H SER* 1.3 75.4 - - - +
48H VAL* 1.3 60.5 + - - +
50H LYS* 2.9 28.1 + - - -
51H ALA* 4.4 7.6 - - - +
73H LEU* 3.7 24.0 - - + +
76H LEU* 4.2 18.4 - - + -
80H LEU* 5.7 0.9 - - + -
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Residues in contact with VAL 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H ILE* 2.8 40.3 + - + +
45H SER* 3.1 7.2 + - - +
47H ALA* 1.3 72.7 - - - +
49H ARG* 1.3 59.8 + - - +
50H LYS* 3.0 19.9 + - - +
73H LEU* 4.0 18.6 - - + -
120H LEU* 4.0 16.8 - - + -
126H ILE* 4.8 6.2 - - + +
132H VAL* 3.9 12.8 - - + -
167H TYR* 4.2 12.8 - - + -
169L SER* 3.5 35.5 - - - +
170L ALA* 3.7 3.6 - - - +
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Residues in contact with ARG 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H SER* 3.0 30.7 + - - +
46H SER* 4.2 4.7 - - - +
47H ALA 3.2 0.4 - - - -
48H VAL* 1.3 77.4 - - - +
50H LYS* 1.3 70.1 + - - +
51H ALA 3.5 1.1 - - - -
167H TYR* 3.6 10.4 + - - +
168H GLY 2.9 31.3 + - - +
169H SER 3.9 0.2 + - - -
170H ALA* 3.2 23.4 + - - +
171H THR* 3.0 28.4 + - - +
49L ARG* 3.7 27.4 - - + +
168L GLY 3.2 4.8 + - - -
169L SER* 2.6 40.5 + - - +
170L ALA* 4.2 6.5 - - - +
171L THR 5.0 1.2 + - - -
186L LEU 3.7 2.3 - - - +
188L PRO* 3.1 24.1 - - + +
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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