Contacts of the helix formed by residues 6 - 36 (chain A) in PDB entry 1HGU
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 LEU 6 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE 2.7 6.9 + - - +
5A PRO* 1.3 69.9 - - - +
7A SER* 1.2 67.5 + - - +
8A ARG 3.2 0.4 - - - -
9A LEU* 2.9 41.7 + - + +
10A PHE* 3.3 41.8 - - + -
124A LEU* 5.1 4.7 - - + -
127A ARG* 3.9 35.4 - - - +
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Residues in contact with SER 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 4.6 3.3 - - - +
6A LEU* 1.2 82.8 + - - +
8A ARG* 1.3 70.5 + - - +
10A PHE* 2.9 24.1 + - - +
11A GLN* 2.8 32.8 + - - +
185A VAL* 3.7 23.7 - - - +
186A GLU* 5.5 2.1 + - - -
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Residues in contact with ARG 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 5.6 13.5 - - + +
5A PRO* 3.2 45.6 + - + +
7A SER* 1.3 92.7 - - - +
9A LEU* 1.3 60.3 + - + +
11A GLN* 3.3 38.4 + - + +
12A ASN* 2.8 30.0 + - - +
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE 5.8 0.7 - - - +
5A PRO 5.6 1.3 - - - +
6A LEU* 2.9 29.0 + - + +
8A ARG* 1.3 79.3 - - + +
10A PHE* 1.3 69.1 + - - +
11A GLN 2.9 1.4 + - - -
12A ASN* 3.1 6.9 + - + +
13A ALA* 3.1 22.3 + - - +
120A GLY* 4.9 4.0 - - - +
123A THR* 3.5 35.9 - - + +
124A LEU* 3.5 23.6 - - + -
127A ARG* 5.3 8.7 - - - +
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Residues in contact with PHE 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.3 43.5 - - + -
7A SER* 2.9 15.1 + - - +
9A LEU* 1.3 78.0 - - + +
11A GLN* 1.3 64.4 + - - +
13A ALA* 3.7 4.4 + - - +
14A MET* 3.0 22.3 + - - +
76A LEU* 6.1 1.3 - - + -
124A LEU* 4.3 22.4 - - + +
128A LEU* 6.3 4.3 - - + -
180A VAL* 3.7 31.4 - - + -
181A GLN* 3.1 31.5 - - + +
184A SER* 4.1 22.4 - - - -
185A VAL* 4.4 15.9 - - + -
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Residues in contact with GLN 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER* 2.8 11.1 + - - -
8A ARG* 3.3 47.7 + - + +
9A LEU 2.9 1.0 + - - -
10A PHE* 1.3 73.6 - - - +
12A ASN* 1.3 56.5 - - - +
14A MET* 2.5 28.8 + - + +
15A LEU* 2.9 31.2 + - + +
181A GLN* 3.6 17.5 + - - +
188A SER* 5.8 4.9 + - - -
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Residues in contact with ASN 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG 2.8 20.2 + - - +
9A LEU* 3.7 9.2 - - + +
11A GLN* 1.3 71.3 - - - +
13A ALA* 1.3 69.4 + - - +
15A LEU* 3.5 7.8 + - - +
16A ARG* 2.7 75.2 + - - +
116A ASP 4.7 6.1 - - - +
117A LEU* 5.3 0.5 - - - -
120A GLY* 5.0 9.2 - - - -
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU 3.1 12.6 + - - +
10A PHE* 3.9 4.5 - - - +
12A ASN* 1.3 87.4 + - - +
14A MET* 1.3 52.6 + - - +
16A ARG* 3.4 1.6 - - - +
17A ALA* 2.6 38.8 + - - +
117A LEU* 3.6 26.7 - - + +
120A GLY 5.7 1.6 - - - -
121A ILE* 4.6 17.9 - - + +
124A LEU* 5.7 3.6 - - + -
177A LEU* 4.7 8.3 - - + -
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Residues in contact with MET 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE 3.0 12.7 + - - +
11A GLN* 2.5 16.7 + - - +
13A ALA* 1.3 71.3 - - - +
15A LEU* 1.3 62.6 + - - +
17A ALA* 3.2 4.8 + - - +
18A HIS* 3.1 39.2 + - + +
174A GLU* 3.3 28.5 - - + +
177A LEU* 5.1 5.8 - - + +
178A ARG* 3.4 32.5 - - + +
181A GLN* 3.1 41.3 - - + +
189A CYS* 5.5 0.4 - - - -
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLN* 2.9 36.9 + - + +
12A ASN* 4.0 8.1 - - - +
14A MET* 1.3 71.8 - - - +
16A ARG* 1.3 60.6 + - + +
18A HIS* 3.2 2.1 + - - +
19A ARG* 2.8 30.1 + - + +
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Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASN* 2.7 59.8 + - - +
13A ALA* 3.9 3.6 - - - +
15A LEU* 1.3 81.1 - - + +
17A ALA* 1.3 57.5 + - - +
19A ARG* 3.4 9.0 - - - +
20A LEU* 2.8 29.5 + - - +
107A ASP* 5.0 10.5 + - - -
112A ASP 4.8 3.0 + - - -
113A LEU* 4.3 30.1 - - + +
116A ASP* 2.7 47.9 + - - +
117A LEU* 4.7 10.5 - - + +
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA 2.6 22.3 + - - +
14A MET* 3.2 4.2 + - - +
16A ARG* 1.3 73.5 - - - +
18A HIS* 1.4 56.9 + - - +
20A LEU* 3.2 7.7 + - - +
21A HIS 2.8 9.7 + - - -
117A LEU* 3.8 20.0 - - + -
173A VAL 4.5 2.2 - - - +
174A GLU* 2.7 58.9 - - + +
177A LEU* 5.7 1.1 - - + -
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Residues in contact with HIS 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MET* 3.1 30.3 + - + +
15A LEU* 4.3 2.0 - - - +
17A ALA* 1.4 68.6 - - - +
19A ARG* 1.3 54.4 + - - +
20A LEU 2.7 13.7 + - - -
21A HIS* 2.8 35.6 + - + +
22A GLN* 3.1 26.4 + - - +
174A GLU* 3.2 32.5 - - + +
175A THR* 3.8 10.2 + - - -
178A ARG* 3.3 26.4 + - - -
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Residues in contact with ARG 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 2.8 19.1 + - + +
16A ARG* 3.4 12.6 - - - +
18A HIS* 1.3 76.4 - - - +
20A LEU* 1.3 56.7 + - - +
22A GLN* 4.1 22.5 - - - +
23A LEU* 3.0 28.3 + - + +
106A SER* 3.5 35.1 + - - +
107A ASP* 6.0 1.1 - - + -
113A LEU* 4.4 21.3 - - + -
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG 2.8 13.6 + - - +
17A ALA* 3.3 10.1 - - - +
18A HIS 2.7 0.8 + - - -
19A ARG* 1.3 76.4 - - - +
21A HIS* 1.3 64.9 + - - +
22A GLN 3.0 1.7 + - - -
23A LEU* 3.6 6.5 + - + +
24A ALA* 3.5 13.9 + - - +
110A VAL* 6.5 0.2 - - + -
113A LEU* 3.4 37.7 - - + +
114A LEU* 3.5 25.6 - - + +
117A LEU* 3.7 18.6 - - + -
166A PHE* 3.7 22.4 - - + -
170A MET* 3.6 22.2 - - + +
174A GLU* 4.0 2.9 - - - +
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Residues in contact with HIS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA 2.8 7.1 + - - -
18A HIS* 2.8 33.0 + - - +
20A LEU* 1.3 68.5 - - - +
22A GLN* 1.3 52.8 + - + +
24A ALA* 3.0 6.6 + - - +
25A PHE* 2.8 56.5 + + + +
167A ARG* 4.0 23.2 + - - +
170A MET* 4.2 6.7 - - + -
171A ASP* 3.7 37.4 - - + -
174A GLU* 3.1 15.4 + - - +
175A THR* 5.2 0.4 + - - -
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A HIS* 3.1 25.5 + - - +
19A ARG* 4.1 28.4 - - - +
20A LEU 3.0 0.6 - - - -
21A HIS* 1.3 76.9 - - + +
23A LEU* 1.3 62.3 + - + +
25A PHE* 3.7 6.4 - - + +
26A ASP* 2.8 28.2 + - - +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 3.0 28.7 - - + +
20A LEU* 4.2 9.4 - - + +
21A HIS 3.4 0.4 - - - -
22A GLN* 1.3 77.3 - - + +
24A ALA* 1.3 65.4 + - - +
26A ASP* 4.0 14.4 - - - +
27A THR* 2.7 32.9 + - - +
100A SER* 4.5 13.7 - - - +
102A VAL 5.3 1.3 - - - +
103A TYR* 6.0 2.0 - - - -
104A GLY 5.9 2.9 - - - +
106A SER* 5.4 9.2 - - - +
109A ASP 5.1 4.9 - - - +
110A VAL* 4.8 20.9 - - + -
113A LEU* 3.7 24.0 - - + -
166A PHE* 5.3 4.2 - - + -
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU 3.5 9.9 + - - +
21A HIS 3.0 8.1 + - - +
23A LEU* 1.3 79.8 - - - +
25A PHE* 1.3 50.1 + - - +
27A THR* 3.4 3.4 - - - -
28A TYR* 2.7 33.6 + - - +
163A LEU* 4.3 4.3 - - - +
166A PHE* 3.0 66.8 - - + +
167A ARG 5.3 0.2 - - - -
170A MET* 5.0 0.2 - - + -
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Residues in contact with PHE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A HIS* 2.8 34.5 + + + +
22A GLN* 4.4 5.2 - - + +
24A ALA* 1.3 73.1 - - - +
26A ASP* 1.4 67.3 + - - +
28A TYR* 3.6 10.3 - + - -
29A GLU* 3.1 51.6 + - + +
166A PHE 4.9 0.4 + - - -
167A ARG* 4.0 26.4 - - + +
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Residues in contact with ASP 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN 2.8 24.8 + - - +
23A LEU* 3.4 12.7 + - - +
25A PHE* 1.4 71.4 - - - +
27A THR* 1.3 71.7 + - - +
29A GLU* 2.8 31.4 + - - +
30A GLU* 2.7 37.2 + - - +
100A SER* 4.3 2.1 + - - -
102A VAL* 2.5 42.4 + - + +
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Residues in contact with THR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 2.7 23.0 + - - +
24A ALA* 3.4 4.3 - - - -
26A ASP* 1.3 85.6 + - - +
28A TYR* 1.3 68.7 + - - +
30A GLU* 3.8 8.1 - - - +
31A PHE* 3.1 24.9 + - + +
98A ALA* 4.7 18.3 + - + +
99A ASN 5.2 4.7 - - - +
100A SER* 4.2 12.0 + - - +
102A VAL 4.7 0.2 + - - -
163A LEU* 3.3 31.4 - - + +
166A PHE* 6.0 0.9 - - + -
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Residues in contact with TYR 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA 2.7 19.3 + - - +
25A PHE* 3.8 12.1 - + - -
26A ASP 3.2 0.4 - - - -
27A THR* 1.3 79.5 - - - +
29A GLU* 1.4 78.9 + - - +
31A PHE* 3.0 13.0 + + + +
32A GLU* 3.3 43.6 + - + +
41A LYS* 3.4 17.7 + - - +
160A TYR* 5.1 8.3 - + - -
163A LEU* 3.0 31.8 + - + +
164A TYR* 3.2 53.5 - + + -
167A ARG* 4.3 18.6 - - + -
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 3.1 50.7 + - + +
26A ASP* 2.8 13.2 + - - +
28A TYR* 1.4 88.4 - - - +
30A GLU* 1.3 58.5 + - - +
32A GLU* 3.0 42.4 - - - +
33A GLU* 3.7 8.6 - - - +
----------------------------------------------------------
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP* 2.7 34.9 - - - +
27A THR* 3.8 8.8 - - - +
29A GLU* 1.3 77.0 - - - +
31A PHE* 1.4 58.8 + - + +
33A GLU* 2.8 40.0 + - - +
34A ALA* 3.0 14.9 + - + +
101A LEU* 2.9 43.4 + - + +
102A VAL* 2.8 25.0 + - + +
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Residues in contact with PHE 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 3.1 21.1 - - + +
28A TYR* 3.0 9.7 + + - +
30A GLU* 1.4 80.4 - - + +
32A GLU* 1.3 68.3 + - - +
34A ALA* 3.5 5.5 + - + +
35A TYR* 3.3 59.0 + + + +
36A ILE* 5.0 1.6 - - + -
97A PHE 5.3 8.3 - - - -
101A LEU* 6.5 0.4 - - - -
156A LEU* 4.4 12.6 - - + -
159A ASN* 4.7 6.1 - - + -
160A TYR* 3.6 44.0 - + + -
163A LEU* 4.7 18.4 - - + -
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.3 35.4 + - + +
29A GLU* 3.0 33.0 - - - +
31A PHE* 1.3 77.6 - - - +
33A GLU* 1.3 74.1 + - - +
35A TYR 3.2 0.3 + - - -
36A ILE* 2.8 46.5 + - + +
41A LYS* 3.1 38.1 + - + -
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 4.0 7.2 - - - +
30A GLU* 2.8 27.9 + - - +
32A GLU* 1.3 97.2 - - - +
34A ALA* 1.3 52.9 + - - +
35A TYR* 2.8 16.3 + - - -
36A ILE 4.0 5.7 + - - -
----------------------------------------------------------
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 3.0 15.5 + - + +
31A PHE* 4.0 7.9 - - + +
32A GLU 3.3 0.6 - - - -
33A GLU* 1.3 74.9 - - - +
35A TYR* 1.4 74.7 + - + +
101A LEU* 5.6 10.5 - - + -
----------------------------------------------------------
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Residues in contact with TYR 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 3.3 56.9 - + + +
32A GLU 3.2 0.6 + - - -
33A GLU 2.8 7.2 + - - -
34A ALA* 1.4 83.3 - - + +
36A ILE* 1.3 72.2 + - + +
37A PRO 3.4 6.3 - - - -
151A HIS* 5.9 1.4 - - - +
156A LEU* 3.4 50.1 - - + +
----------------------------------------------------------
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Residues in contact with ILE 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.7 2.9 - - + +
32A GLU* 2.8 40.3 + - + +
33A GLU* 4.5 1.6 - - - -
35A TYR* 1.3 80.4 - - + +
37A PRO 1.3 43.7 - - - -
40A GLN* 3.8 42.8 + - + +
41A LYS* 4.1 10.1 - - + +
45A LEU* 4.1 17.9 - - + -
157A LEU* 4.2 21.3 - - + -
160A TYR* 3.5 35.9 - - + -
----------------------------------------------------------
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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