Contacts of the helix formed by residues 28 - 50 (chain A) in PDB entry 1FTA
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLY 3.1 5.8 - - - -
27A THR* 1.3 79.8 - - - +
29A GLU* 1.3 64.9 + - - +
30A LEU 3.5 1.6 - - - -
31A THR* 3.9 9.4 - - - -
32A GLN* 3.1 28.9 + - - +
338A AMP 3.1 4.8 + - - -
18C MET* 3.6 22.3 - - - +
22C ARG* 4.1 5.6 - - - -
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 3.5 7.5 + - - +
28A GLY* 1.3 75.3 - - - +
30A LEU* 1.3 67.0 + - - +
32A GLN* 3.2 3.5 + - - +
33A LEU 3.1 18.0 + - - -
88A SER 5.9 0.2 - - - +
89A PHE 4.0 10.3 - - - +
90A ALA* 3.2 28.0 - - + +
110A ARG 5.0 0.2 - - - +
111A GLY* 3.6 18.0 - - - -
112A LYS* 3.1 35.7 + - - +
113A TYR* 3.4 9.0 - - + -
338A AMP 2.8 14.2 + - - +
22C ARG* 3.7 21.5 - - - +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 1.3 79.1 - - - +
31A THR* 1.3 64.0 + - - +
33A LEU* 3.1 28.6 + - + +
34A LEU* 2.9 34.8 + - + +
113A TYR* 3.8 22.6 - - + +
138A ILE* 3.9 26.2 - - + -
160A VAL* 3.7 15.7 - - + -
161A ALA* 5.2 3.8 - - + -
177A MET* 5.5 1.6 - - - -
338A AMP 3.1 58.7 + - + +
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.0 18.4 + - + -
18A MET* 4.2 21.5 - - + -
21A GLY* 4.2 4.9 - - - -
28A GLY* 3.7 12.6 + - - -
29A GLU 3.3 0.2 - - - -
30A LEU* 1.3 77.6 - - - +
32A GLN* 1.3 57.6 + - - +
34A LEU* 3.4 2.8 + - - +
35A ASN* 2.8 48.7 + - - +
338A AMP 2.8 32.9 + - - -
18C MET* 4.2 19.1 - - + -
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Residues in contact with GLN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY 3.1 18.6 + - - +
29A GLU* 3.2 8.3 + - - +
31A THR* 1.3 74.0 - - - +
33A LEU* 1.3 53.9 + - - +
35A ASN* 2.8 17.7 + - - +
36A SER* 2.8 39.6 + - - -
88A SER* 4.1 18.0 - - - +
90A ALA* 5.0 0.2 - - + -
14C THR 4.5 0.4 + - - -
15C ARG* 3.2 40.1 - - - +
18C MET* 3.2 32.4 - - + +
19C GLU* 2.8 17.1 - - - +
22C ARG* 3.6 19.1 - - - +
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU 3.1 7.8 + - - +
30A LEU* 3.2 29.6 - - + +
32A GLN* 1.3 74.7 - - - +
34A LEU* 1.3 57.7 + - - +
36A SER* 3.4 3.1 - - - -
37A LEU* 2.9 31.0 + - + +
85A LEU* 3.5 29.2 - - + +
88A SER* 4.2 13.2 - - - +
90A ALA* 3.7 6.9 - - + +
91A THR* 3.6 21.1 - - + -
113A TYR* 3.6 34.1 - - + -
115A VAL* 3.7 8.7 - - + -
138A ILE* 3.9 16.6 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 5.5 1.0 - - - +
17A VAL* 3.8 33.9 - - + -
30A LEU* 2.9 38.6 + - + +
31A THR 3.7 4.0 - - - +
33A LEU* 1.3 74.0 - - - +
35A ASN* 1.3 58.2 + - - +
36A SER 3.2 1.8 - - - -
37A LEU* 3.8 15.6 - - + +
38A CYS* 3.0 28.9 + - - +
136A PHE* 4.9 1.3 - - + -
138A ILE* 3.7 28.0 - - + -
161A ALA* 5.0 1.8 - - + -
175A LEU* 4.7 22.2 - - + -
177A MET* 4.7 11.0 - - - -
338A AMP 4.6 4.0 - - - +
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Residues in contact with ASN 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A THR* 3.5 35.2 + - - +
17A VAL* 4.5 7.1 - - - +
18A MET* 5.8 0.8 - - - +
31A THR* 2.8 44.7 + - - +
32A GLN* 2.8 22.9 + - - +
34A LEU* 1.3 71.3 - - - +
36A SER* 1.3 59.9 + - - +
38A CYS* 3.8 9.4 + - - +
39A THR* 3.4 23.4 + - - -
14C THR* 4.0 21.7 - - + +
15C ARG* 5.6 2.5 - - + +
18C MET* 4.1 5.5 - - - +
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Residues in contact with SER 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLN* 2.8 14.5 + - - -
33A LEU 3.4 10.5 - - - -
35A ASN* 1.3 75.1 - - - +
37A LEU* 1.3 65.4 + - - +
39A THR* 3.0 14.4 + - - -
40A ALA* 3.1 12.3 + - - +
84A MET* 3.5 36.6 - - - +
85A LEU* 4.8 1.8 - - - -
88A SER* 3.3 18.9 - - - -
15C ARG* 3.3 18.0 + - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 2.9 18.7 + - + +
34A LEU* 3.8 18.4 - - + +
36A SER* 1.3 75.2 - - - +
38A CYS* 1.3 61.3 + - - +
40A ALA* 3.2 6.9 + - + +
41A VAL* 3.0 38.5 + - + +
81A VAL* 4.2 26.2 - - + -
85A LEU* 4.5 15.0 - - + +
115A VAL* 5.6 3.1 - - + -
117A PHE* 6.2 0.4 - - + -
134A THR* 5.4 3.6 - - + -
136A PHE* 3.7 56.1 - - + -
138A ILE* 4.8 4.9 - - + -
173A LEU* 6.0 1.8 - - + -
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Residues in contact with CYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.9 32.1 - - + -
14A THR* 4.4 16.4 - - - -
34A LEU 3.0 18.7 + - - +
35A ASN* 3.8 10.3 - - - +
37A LEU* 1.3 76.9 - - - +
39A THR* 1.4 61.1 + - - +
41A VAL* 3.5 7.0 + - - +
42A LYS* 3.2 37.2 + - - +
173A LEU* 5.2 3.8 - - + +
193A PHE* 4.0 16.2 - - - -
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Residues in contact with THR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASN 3.4 11.9 + - - -
36A SER* 3.0 9.0 + - - -
38A CYS* 1.4 73.0 - - - +
40A ALA* 1.3 65.9 + - - +
42A LYS* 3.1 22.0 + - - +
43A ALA* 3.1 12.8 + - - +
84A MET* 3.8 23.3 - - + +
12C THR* 4.5 5.9 + - + +
14C THR* 6.0 0.9 - - - -
190C ILE* 4.4 4.7 - - + +
192C GLU* 2.9 39.2 + - + +
59D ILE* 4.0 18.6 - - + -
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A SER 3.1 11.2 + - - +
37A LEU* 3.5 14.1 - - + +
39A THR* 1.3 74.7 - - - +
41A VAL* 1.3 57.7 + - - +
43A ALA* 3.3 5.8 + - - +
44A ILE* 2.9 34.7 + - - +
80A LEU* 4.0 11.5 - - - +
81A VAL* 3.9 35.0 - - + +
84A MET* 4.1 12.2 - - + +
85A LEU* 6.4 0.2 - - + -
59D ILE* 5.7 0.4 - - - -
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.0 35.6 + - + +
38A CYS* 3.7 6.7 - - - +
39A THR 3.1 0.2 - - - -
40A ALA* 1.3 78.3 - - + +
42A LYS* 1.3 56.2 + - - +
44A ILE* 3.2 5.2 + - + +
45A SER* 2.9 26.9 + - - -
81A VAL* 6.1 0.2 - - + -
134A THR* 5.0 10.1 - - + -
136A PHE* 5.5 2.9 - - + -
165A ALA* 3.7 29.2 - - + -
167A TYR* 3.9 17.1 + - + +
171A THR* 4.9 2.0 - - + -
173A LEU* 4.4 10.8 - - + -
193A PHE* 3.8 23.1 - - + -
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Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A CYS* 3.2 27.5 + - - +
39A THR* 3.1 10.5 + - - +
41A VAL* 1.3 74.1 - - - +
43A ALA* 1.3 57.3 + - - +
45A SER* 3.3 8.2 + - - -
46A SER* 2.9 29.1 + - - -
186A LEU* 4.1 16.1 - - + +
191A GLY* 3.0 32.3 + - - +
193A PHE* 3.9 19.3 - - + -
42C LYS* 4.5 1.6 - - - +
189C ALA 4.9 0.5 - - - +
190C ILE* 3.4 25.8 + - + +
191C GLY 3.2 13.5 + - - -
192C GLU* 3.0 27.4 + - - -
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR 3.1 10.3 + - - +
40A ALA* 3.6 9.4 - - - +
42A LYS* 1.3 74.8 - - - +
44A ILE* 1.3 66.6 + - - +
46A SER* 3.3 4.0 + - - -
47A ALA* 3.1 21.8 + - - +
80A LEU* 3.8 31.5 - - + +
190C ILE* 3.6 19.7 - - + -
55D HIS* 5.3 6.3 + - - +
59D ILE* 4.1 11.2 - - + -
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Residues in contact with ILE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA 2.9 22.9 + - - +
41A VAL* 3.2 6.0 + - + +
43A ALA* 1.3 74.1 - - - +
45A SER* 1.3 65.3 + - - +
47A ALA* 3.1 5.7 + - + +
48A VAL* 2.9 26.7 + - + +
77A SER* 3.5 30.3 - - - +
80A LEU* 3.9 19.1 - - + -
81A VAL* 3.5 32.1 - - + -
119A PRO 4.4 0.9 - - - +
120A LEU* 3.8 20.2 - - + -
134A THR* 4.0 16.8 - - + +
167A TYR* 4.0 11.7 - - + +
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Residues in contact with SER 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL 2.9 14.4 + - - -
42A LYS 3.5 9.6 - - - -
44A ILE* 1.3 75.8 - - - +
46A SER* 1.3 62.9 + - - +
48A VAL* 3.1 3.4 + - - +
49A ARG* 3.0 35.4 + - - -
167A TYR* 3.4 19.6 - - - -
171A THR* 2.8 29.5 + - - +
186A LEU* 4.1 16.1 - - - +
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Residues in contact with SER 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS 2.9 17.5 + - - -
43A ALA 3.4 6.3 - - - -
45A SER* 1.3 76.4 - - - +
47A ALA* 1.3 62.3 + - - +
49A ARG* 3.7 5.8 + - - +
50A LYS 3.6 2.4 + - - -
51A ALA* 3.2 35.3 + - - +
189C ALA* 3.7 35.1 + - - +
190C ILE* 4.1 6.7 - - - +
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA 3.1 10.8 + - - +
44A ILE* 3.1 11.2 + - + +
46A SER* 1.3 74.0 - - - +
48A VAL* 1.3 59.0 + - + +
50A LYS* 2.8 32.3 + - - +
51A ALA 4.9 4.9 - - - +
73A LEU* 4.3 17.3 - - + +
76A LEU* 4.0 26.2 - - + -
77A SER* 6.0 0.9 - - - +
80A LEU* 5.5 0.9 - - + -
55D HIS* 6.3 0.9 - - - +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 2.9 36.1 + - + +
45A SER* 3.1 6.9 + - - +
47A ALA* 1.3 75.1 - - + +
49A ARG* 1.3 57.9 + - - +
50A LYS* 3.2 17.3 + - - +
73A LEU* 3.9 22.5 - - + +
120A LEU* 4.1 14.4 - - + -
126A ILE* 5.9 3.1 - - + +
132A VAL* 4.4 7.4 - - + -
167A TYR* 3.9 22.9 - - + -
169B SER* 3.5 35.9 - - - +
170B ALA* 3.9 4.5 - - - +
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Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A SER* 3.0 26.7 + - - +
46A SER* 3.8 7.6 - - - +
47A ALA 3.2 0.2 - - - -
48A VAL* 1.3 78.0 - - - +
50A LYS* 1.3 68.3 + - - +
51A ALA* 5.5 0.2 - - + -
167A TYR* 4.2 7.7 - - - +
168A GLY 3.0 29.4 + - - +
170A ALA* 3.4 17.2 + - - +
171A THR* 3.0 28.0 + - - +
49B ARG* 3.1 36.3 - - + +
169B SER* 2.8 29.6 + - - +
170B ALA* 4.4 9.0 - - - +
171B THR 5.3 0.9 + - - -
186B LEU 3.9 3.3 - - - +
188B PRO* 3.3 27.2 - - + +
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA 2.8 15.2 + - - +
48A VAL 3.7 8.7 - - - +
49A ARG* 1.3 80.5 - - - +
51A ALA* 1.3 59.1 + - - +
52A GLY 2.8 10.6 + - - -
53A ILE* 3.1 44.9 + - + +
73A LEU* 4.2 30.1 - - + -
126A ILE* 4.4 16.0 + - - +
129A LEU* 5.4 3.6 - - - +
170B ALA* 4.1 12.6 - - + -
185B MET* 4.0 29.4 - - + +
186B LEU 4.6 1.8 - - - +
187B ASP* 3.8 5.0 - - - +
188B PRO* 4.2 0.9 - - - -
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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
------------------------------------------------------------
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