Contacts of the helix formed by residues 95 - 122 (chain L) in PDB entry 1QGH
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 MET 95 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E HIS* 5.4 2.0 - - + -
34L MET* 3.7 35.7 - - + -
35L ARG 3.4 34.4 + - - +
36L GLY* 4.6 2.0 - - - +
38L ASN* 4.0 15.0 - - + +
39L PHE* 3.9 24.2 - - - +
42L LEU* 3.4 31.9 - - + -
93L LYS 4.1 0.6 + - - -
94L THR* 1.3 75.2 - - + +
96L ASP* 1.3 55.3 + - - +
98L LEU* 3.1 9.0 + - - +
99L MET* 2.6 45.8 + - - +
149L PHE* 3.9 12.8 - - + -
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Residues in contact with ASP 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E HIS* 2.9 40.7 + - - -
94L THR* 3.0 14.0 - - + +
95L MET* 1.3 77.1 - - - +
97L GLN* 1.3 68.5 + - + +
99L MET* 3.7 0.5 - - - +
100L GLU* 2.8 37.4 + - - +
149L PHE* 3.7 9.5 - - - -
150L LEU* 3.8 23.4 - - + +
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Residues in contact with GLN 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91L LYS* 4.8 9.4 - - - +
92L PRO 4.4 2.6 - - - +
93L LYS* 3.5 33.1 - - + +
94L THR* 2.6 48.9 + - - +
96L ASP* 1.3 76.6 - - + +
98L LEU* 1.3 62.4 + - - +
100L GLU* 3.3 13.9 + - - +
101L ASP* 3.0 21.5 + - - +
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Residues in contact with LEU 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29L GLN* 5.4 1.6 - - + +
30L ILE* 3.8 26.9 - - + +
33L TYR* 4.7 3.1 - - + +
34L MET* 3.9 37.2 - - + +
35L ARG 5.2 0.4 - - - +
89L TYR* 4.3 11.9 - - + +
93L LYS* 2.8 55.9 - - + +
94L THR 2.6 23.5 + - - +
95L MET* 3.4 9.6 - - - +
97L GLN* 1.3 73.0 - - - +
99L MET* 1.3 71.0 + - + +
101L ASP* 2.9 20.3 + - - +
102L LEU* 2.9 13.0 + - - +
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Residues in contact with MET 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L ILE* 3.7 32.5 - - + -
34L MET* 4.8 0.4 - - + -
42L LEU* 4.2 17.7 - - + -
46L MET* 4.4 10.3 - - + -
95L MET* 2.6 26.7 + - - +
96L ASP 3.8 2.9 - - - +
98L LEU* 1.3 77.1 - - + +
100L GLU* 1.3 52.7 + - - +
102L LEU* 3.0 9.2 + - + +
103L VAL* 2.7 37.3 + - - +
146L PHE* 3.7 35.2 - - + +
149L PHE* 3.5 26.0 - - + -
150L LEU* 4.0 22.0 - - + -
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Residues in contact with GLU 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96L ASP* 2.8 27.5 + - - +
97L GLN* 3.6 15.5 + - - +
99L MET* 1.3 74.8 - - - +
101L ASP* 1.3 64.5 + - - +
103L VAL* 4.0 3.4 - - - +
104L GLY* 2.9 21.7 + - - -
150L LEU* 3.8 26.4 - - + +
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Residues in contact with ASP 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L LYS* 3.2 40.4 + - - +
29L GLN* 4.6 5.7 + - - -
30L ILE* 5.1 3.6 - - + +
93L LYS* 3.8 19.9 + - - +
97L GLN 3.0 11.1 + - - +
98L LEU 2.9 11.2 + - - +
100L GLU* 1.3 77.2 - - - +
102L LEU* 1.3 63.4 + - - +
104L GLY* 3.4 1.1 + - - -
105L THR* 3.1 22.7 + - - -
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Residues in contact with LEU 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L PHE* 3.4 34.3 - - + -
26L LYS* 5.2 1.3 - - - -
27L ILE* 4.9 2.5 - - + -
30L ILE* 4.1 18.8 - - + +
46L MET* 4.0 8.5 - - + -
49L LEU* 3.8 27.8 - - + -
98L LEU 2.9 11.0 + - - +
99L MET* 3.1 13.2 - - + +
101L ASP* 1.3 77.7 - - - +
103L VAL* 1.3 63.3 + - - +
105L THR* 3.0 6.2 + - - -
106L LEU* 2.9 26.2 + - + +
146L PHE* 3.8 38.4 - - + -
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Residues in contact with VAL 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99L MET 2.7 20.3 + - - +
100L GLU* 4.0 6.1 - - - +
102L LEU* 1.3 74.1 - - - +
104L GLY* 1.3 59.5 + - - +
106L LEU* 3.2 11.5 + - + +
107L GLU* 2.8 39.3 + - + +
143L ILE* 5.0 7.6 - - + +
146L PHE* 3.4 39.9 - - + -
147L LYS* 3.7 32.3 - - + +
150L LEU* 4.4 9.4 - - + -
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Residues in contact with GLY 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100L GLU 2.9 17.5 + - - -
101L ASP* 3.8 1.6 - - - -
103L VAL* 1.3 77.6 - - - +
105L THR* 1.3 56.7 + - - +
107L GLU* 3.1 15.3 + - - +
108L LEU* 2.9 27.0 + - - +
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Residues in contact with THR 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L PHE* 3.4 36.3 - - + -
26L LYS* 3.4 19.2 + - - -
84L VAL* 3.8 31.2 - - + +
85L GLU 5.1 0.3 + - - -
101L ASP* 3.1 14.2 + - - -
102L LEU 3.0 9.0 + - - -
104L GLY* 1.3 72.8 - - - +
106L LEU* 1.3 65.4 + - - +
108L LEU* 3.2 7.9 + - + +
109L LEU* 2.9 25.3 + - + +
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Residues in contact with LEU 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L PHE* 3.8 19.7 - - + -
49L LEU* 5.6 2.0 - - + -
53L PHE* 3.9 24.9 - - + -
102L LEU* 2.9 31.4 + - + +
103L VAL* 3.2 15.9 + - + +
105L THR* 1.3 75.6 - - - +
107L GLU* 1.3 58.8 + - - +
109L LEU* 3.1 7.2 + - + +
110L ARG* 2.7 30.3 + - - +
139L ILE* 3.7 13.0 - - + +
142L HIS* 4.0 24.7 - - + -
143L ILE* 3.8 19.1 - - + +
146L PHE* 4.3 15.5 - - + -
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Residues in contact with GLU 107 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L VAL* 2.8 29.0 + - + +
104L GLY* 3.6 12.7 - - - +
106L LEU* 1.3 76.7 - - - +
108L LEU* 1.3 62.2 - - - +
110L ARG* 3.1 25.3 + - - +
111L ASP* 3.0 31.5 + - - +
143L ILE* 3.9 18.9 - - + +
147L LYS* 3.3 23.2 + - - -
154L PRO 4.3 5.0 - - - +
156L GLU* 3.4 25.9 - - - +
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Residues in contact with LEU 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L ASN* 4.2 0.2 - - - +
83L SER* 3.7 30.1 - - - +
84L VAL* 4.0 23.8 - - + -
85L GLU 5.3 0.9 - - - +
104L GLY 2.9 13.7 + - - +
105L THR* 3.2 10.5 + - - +
107L GLU* 1.3 77.0 - - - +
109L LEU* 1.3 65.6 + - + +
111L ASP* 3.3 6.8 + - - +
112L GLU* 2.9 57.6 + - + +
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Residues in contact with LEU 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L GLN* 3.7 23.1 - - - +
19L ASN* 4.1 22.2 - - + +
20L LEU* 4.3 13.9 - - + -
23L PHE* 3.6 39.0 - - + -
53L PHE* 4.6 7.9 - - + -
84L VAL* 4.4 1.1 - - + -
105L THR* 2.9 22.6 + - + +
106L LEU* 3.6 8.1 - - + +
108L LEU* 1.3 77.2 - - + +
110L ARG* 1.3 57.8 - - - +
112L GLU* 3.2 1.8 + - - -
113L TYR* 2.7 50.1 + - + +
139L ILE* 4.2 13.0 - - + -
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Residues in contact with ARG 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106L LEU 2.7 13.7 + - - +
107L GLU* 3.4 33.4 + - - +
109L LEU* 1.3 78.7 - - - +
111L ASP* 1.3 86.7 + - - +
113L TYR* 3.3 6.1 + - - +
114L LYS* 2.9 28.4 + - + +
136L LYS* 4.1 21.4 - - + +
139L ILE* 3.9 15.8 - - + +
140L ASP* 3.1 27.8 - - - +
143L ILE* 3.8 19.6 - - + +
154L PRO 5.0 0.4 + - - -
155L LEU* 3.7 27.6 - - - +
156L GLU* 5.5 2.4 + - - -
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Residues in contact with ASP 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107L GLU* 3.0 21.9 + - - +
108L LEU* 3.8 5.7 - - - +
109L LEU 3.2 0.2 - - - -
110L ARG* 1.3 112.2 + - - +
112L GLU* 1.3 61.5 + - + +
114L LYS* 3.2 16.7 - - - +
115L GLN* 2.9 26.9 + - - +
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Residues in contact with GLU 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L PHE* 3.1 12.0 - - + -
15L HIS* 3.0 10.2 + - - -
16L GLN* 3.0 19.0 + - - +
19L ASN* 2.9 21.8 + - - -
83L SER* 2.4 27.4 + - - -
108L LEU* 2.9 35.9 + - + +
109L LEU* 3.9 3.8 - - - +
111L ASP* 1.3 74.1 - - + +
113L TYR* 1.3 67.8 + - - +
115L GLN* 2.9 20.8 + - + +
116L GLY 3.0 10.0 + - - -
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Residues in contact with TYR 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L PHE* 3.9 9.1 - + - -
16L GLN* 3.5 33.7 - - + +
20L LEU* 3.5 24.8 - - - +
56L GLN* 3.0 19.2 + - - -
60L VAL* 4.8 1.2 - - + +
109L LEU* 2.7 35.1 + - + +
110L ARG* 3.6 5.8 - - - +
112L GLU* 1.3 72.8 - - - +
114L LYS* 1.3 54.3 + - - +
116L GLY 2.9 2.4 + - - -
117L ILE* 2.5 47.3 + - + +
132L LEU* 4.0 20.2 - - + +
135L PHE* 3.4 41.1 - + + -
136L LYS* 4.2 7.0 - - + -
139L ILE* 3.9 15.9 - - + -
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Residues in contact with LYS 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G GLY* 3.7 14.7 + - - -
126G ASP* 2.4 37.5 + - - +
110L ARG* 2.9 14.2 + - + +
111L ASP* 3.2 15.3 - - - +
112L GLU 3.1 0.2 - - - -
113L TYR* 1.3 77.3 - - - +
115L GLN* 1.3 68.0 + - - +
117L ILE* 3.1 13.8 + - + +
118L GLU* 3.0 53.4 + - - +
136L LYS* 4.6 12.8 - - + +
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Residues in contact with GLN 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L PHE* 4.7 5.2 - - + -
111L ASP* 2.9 27.3 + - - +
112L GLU* 2.9 16.5 + - + +
114L LYS* 1.3 84.1 - - - +
116L GLY* 1.3 59.5 + - - +
118L GLU* 3.0 16.6 + - - +
119L LEU* 2.8 31.4 + - + +
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Residues in contact with GLY 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L PHE* 3.5 34.3 - - - -
112L GLU 3.0 7.3 + - - -
113L TYR 2.9 6.5 + - - -
115L GLN* 1.3 73.2 - - - +
117L ILE* 1.3 70.1 + - - +
119L LEU* 3.5 6.5 - - - +
120L THR* 2.9 26.2 + - - -
132L LEU* 4.0 6.5 - - - -
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Residues in contact with ILE 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G ASP* 3.8 32.8 - - + +
113L TYR 2.5 24.5 + - - +
114L LYS* 3.5 11.9 - - + +
115L GLN 3.1 0.2 - - - -
116L GLY* 1.3 74.3 - - - +
118L GLU* 1.3 64.3 + - - +
120L THR* 2.9 21.0 - - - +
121L ASP* 3.1 6.4 + - + +
129L ASN* 3.1 20.8 + - - +
132L LEU* 3.8 17.7 - - + +
133L ILE* 3.8 33.2 - - + +
136L LYS* 4.0 30.3 - - + -
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Residues in contact with GLU 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L LYS* 3.0 45.0 + - - +
115L GLN* 3.4 19.2 - - - +
117L ILE* 1.3 78.7 - - - +
119L LEU* 1.3 65.2 + - - +
121L ASP* 3.0 9.0 - - - +
122L LYS* 2.8 21.3 + - - +
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Residues in contact with LEU 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L VAL* 4.3 15.5 - - + +
8L ASP* 3.9 25.6 - - - +
9L THR* 4.5 2.9 - - - +
12L PHE* 4.0 20.4 - - + -
115L GLN* 2.8 19.3 + - + +
116L GLY* 3.5 5.2 - - - +
118L GLU* 1.3 76.3 - - - +
120L THR* 1.3 55.4 + - - +
121L ASP 2.8 0.4 - - - -
122L LYS* 2.9 11.6 + - + +
123L GLU* 2.8 63.6 + - + +
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Residues in contact with THR 120 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L THR* 4.1 13.4 + - - +
116L GLY* 2.9 13.0 + - - +
117L ILE* 2.9 11.7 - - - +
119L LEU* 1.3 82.6 - - - +
121L ASP* 1.3 55.5 - - - +
123L GLU* 3.8 1.5 - - - -
124L GLY 3.1 2.9 + - - -
125L ASP* 2.8 38.1 + - - +
128L THR* 3.5 29.3 - - - +
129L ASN* 2.9 47.8 + - + +
132L LEU* 4.5 4.3 - - + -
----------------------------------------------------------
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Residues in contact with ASP 121 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G ASP* 5.4 3.5 - - - +
117L ILE* 3.2 12.9 - - - +
118L GLU* 3.0 13.9 - - - +
119L LEU 2.8 0.2 - - - -
120L THR* 1.3 80.1 - - - +
122L LYS* 1.3 62.1 + - - +
123L GLU 2.9 1.1 - - - -
124L GLY* 2.8 21.5 + - - -
129L ASN* 4.0 12.7 + - - +
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Residues in contact with LYS 122 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118L GLU 2.8 12.7 + - - +
119L LEU* 2.9 15.2 + - + +
121L ASP* 1.3 75.7 - - - +
123L GLU* 1.3 62.2 + - + +
124L GLY 3.6 0.3 + - - -
----------------------------------------------------------
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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