Contacts of the helix formed by residues 108 - 129 (chain B) in PDB entry 4HHM
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 ASP 108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A ARG* 2.9 49.5 + - - +
337A GLN* 3.7 6.2 - - - +
365A ALA 5.7 0.5 - - - +
368A ARG* 2.8 29.5 + - - +
370A MET* 3.9 9.1 - - - +
106B ALA* 3.2 1.8 - - + +
107B ASN* 1.3 75.4 - - - +
109B ARG* 1.3 64.9 + - - +
110B ASP* 3.3 16.6 - - - +
111B VAL* 3.1 24.8 + - + +
112B ARG* 3.2 15.2 + - - +
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Residues in contact with ARG 109 (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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337A GLN* 2.8 23.7 - - + +
340A GLU* 4.5 15.5 - - - +
341A PRO 3.0 23.5 + - - -
342A THR* 3.4 12.7 + - - +
344A ALA* 4.5 8.5 - - - +
345A ASP* 4.5 6.3 + - - +
107B ASN 3.4 2.4 + - - -
108B ASP* 1.3 70.8 - - - +
110B ASP* 1.3 64.1 + - - +
112B ARG* 2.9 38.2 + - - +
113B ARG* 3.0 52.2 + - - +
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A GLN* 4.5 1.6 - - - +
355A THR 5.6 1.8 - - - +
356A ALA* 5.3 1.9 - - - +
360A PHE* 3.2 31.2 - - + -
365A ALA* 4.5 0.3 - - - +
368A ARG* 3.0 26.9 + - - -
108B ASP* 3.3 19.8 - - - +
109B ARG* 1.3 77.3 - - - +
111B VAL* 1.3 72.9 + - - +
113B ARG* 3.5 11.0 + - - +
114B TYR* 3.1 27.7 + - - +
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Residues in contact with VAL 111 (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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360A PHE* 4.4 7.2 - - + -
365A ALA* 4.6 2.0 - - + +
368A ARG* 4.5 6.5 - - - +
98B VAL* 3.7 38.1 - - + +
99B PHE* 3.9 13.0 - - + -
102B GLY 3.8 7.0 - - - +
103B ALA 4.4 0.4 - - - +
106B ALA* 3.5 22.0 - - + -
108B ASP* 3.4 20.6 - - + +
109B ARG 3.1 0.4 - - - -
110B ASP* 1.3 92.4 + - - +
112B ARG* 1.3 66.2 + - - +
114B TYR* 3.3 4.6 + - - +
115B ALA* 2.9 22.3 + - - +
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Residues in contact with ARG 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A GLN 2.9 15.2 + - - -
338A LEU* 3.9 4.9 - - - +
340A GLU 2.8 27.1 + - - -
342A THR* 2.9 32.3 + - + +
103B ALA 3.2 20.4 - - - +
104B PHE* 3.1 24.1 - - - +
105B THR* 4.3 0.2 - - - +
106B ALA 2.8 44.8 + - - +
107B ASN 2.9 21.2 + - - -
108B ASP 3.6 2.0 - - - +
109B ARG* 2.9 33.8 + - - +
111B VAL* 1.3 76.6 - - - +
113B ARG* 1.3 61.2 + - - +
115B ALA* 3.3 5.0 + - - +
116B LEU* 3.2 24.1 + - - +
157B ARG* 3.5 15.2 - - - +
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A THR* 2.9 41.5 + - + +
343A ALA* 3.5 6.7 - - - +
345A ASP* 3.0 31.9 + - - -
350A LEU* 3.5 39.2 - - + +
353A ASP* 3.0 28.4 + - - +
355A THR* 5.6 0.6 + - - -
356A ALA* 4.2 12.2 - - + +
109B ARG* 3.0 54.8 + - - +
110B ASP* 3.9 9.6 - - - +
112B ARG* 1.3 75.9 - - - +
114B TYR* 1.3 63.2 + - - +
116B LEU* 3.2 14.3 + - - +
117B ARG* 3.2 17.2 + - - +
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Residues in contact with TYR 114 (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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356A ALA 3.2 24.0 + - - +
357A TYR* 3.9 32.8 - + - -
360A PHE* 3.5 30.1 - + + -
362A VAL* 3.9 20.4 - - + +
61B PHE* 3.2 31.0 - + - -
98B VAL* 4.4 5.8 - - + -
99B PHE* 3.4 37.9 - + - -
110B ASP 3.1 18.2 + - - +
111B VAL 3.6 3.1 - - - +
113B ARG* 1.3 76.1 - - - +
115B ALA* 1.3 62.8 + - - +
117B ARG* 3.1 4.3 + - - +
118B LYS* 3.0 37.9 + - + +
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Residues in contact with ALA 115 (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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93B LEU* 4.0 12.8 - - + +
99B PHE* 4.2 5.6 - - + -
103B ALA* 3.8 35.2 - - + +
104B PHE* 3.9 10.5 - - + -
111B VAL 2.9 14.1 + - - +
112B ARG 3.3 10.8 - - - +
114B TYR* 1.3 77.1 - - - +
116B LEU* 1.3 62.2 + - - +
118B LYS* 3.5 2.5 + - - +
119B THR* 3.1 27.7 + - - -
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Residues in contact with LEU 116 (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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342A THR* 3.8 24.0 - - + -
350A LEU* 3.9 17.3 - - + -
104B PHE* 3.6 25.1 - - + -
112B ARG 3.2 6.3 + - - +
113B ARG* 3.2 7.9 + - - +
115B ALA* 1.3 78.3 - - - +
117B ARG* 1.3 57.6 + - - +
119B THR* 3.3 2.1 + - - -
120B ILE* 2.8 40.7 + - + +
161B ALA* 3.7 31.0 - - + +
164B LEU* 3.4 31.4 - - + -
165B LEU* 4.2 11.9 - - + -
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Residues in contact with ARG 117 (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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350A LEU* 3.3 30.9 + - + -
351A LEU* 3.2 40.9 + - - +
353A ASP 3.1 26.5 + - - -
356A ALA* 3.7 14.4 - - + +
357A TYR* 3.4 45.6 - - + +
358A GLU* 4.0 10.9 + - - -
113B ARG 3.2 11.6 + - - +
114B TYR 3.1 5.9 + - - +
116B LEU* 1.3 77.1 - - - +
118B LYS* 1.3 57.7 + - - +
120B ILE* 3.5 6.1 + - - +
121B ARG* 3.0 29.3 + - - +
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Residues in contact with LYS 118 (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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357A TYR* 4.3 12.9 - - + +
55B ASP* 2.7 32.9 + - - +
56B ASP* 3.3 17.1 + - - -
61B PHE* 3.9 28.9 - - - -
91B THR* 4.3 2.2 - - + -
92B ASN 3.1 24.1 + - - +
93B LEU* 3.8 16.2 - - + -
96B HIS* 6.1 0.2 - - - -
99B PHE* 4.1 6.7 - - + -
114B TYR* 3.0 38.9 + - + +
115B ALA 3.7 5.4 - - - +
117B ARG* 1.3 74.4 - - - +
119B THR* 1.3 66.5 + - - +
121B ARG* 3.4 11.0 + - - +
122B ASN* 3.4 13.0 + - - +
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Residues in contact with THR 119 (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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91B THR* 3.4 22.8 + - - +
93B LEU* 3.3 24.0 - - + +
104B PHE* 3.8 7.5 - - + -
115B ALA 3.1 18.4 + - - -
116B LEU 3.7 3.8 - - - -
118B LYS* 1.3 76.3 - - - +
120B ILE* 1.3 63.1 + - - +
122B ASN 3.1 11.4 + - - -
123B ILE* 3.1 14.0 + - + +
134B TYR* 3.6 16.9 + - + -
165B LEU* 3.9 31.2 - - + -
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Residues in contact with ILE 120 (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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347A LEU* 4.2 19.1 - - + -
350A LEU* 5.2 2.7 - - + -
351A LEU* 4.0 26.0 - - + -
116B LEU* 2.8 33.4 + - + +
117B ARG* 3.8 8.1 - - - +
119B THR* 1.3 74.7 - - - +
121B ARG* 1.3 61.9 + - - +
123B ILE* 3.3 20.4 + - - +
124B ASP* 3.5 11.1 + - - +
164B LEU* 5.4 2.9 - - + +
165B LEU* 3.5 22.7 - - + -
168B TYR* 3.5 39.9 - - + +
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Residues in contact with ARG 121 (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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357A TYR* 3.3 41.7 + - + +
63B ALA 4.7 7.9 + - - -
64B SER* 5.8 0.2 - - - +
65B ASP* 3.8 30.5 + - - +
68B ARG* 3.3 59.4 + - - +
117B ARG 3.0 18.2 + - - +
118B LYS 3.9 4.5 - - - +
119B THR 3.2 0.8 - - - -
120B ILE* 1.3 79.1 - - - +
122B ASN* 1.3 60.9 + - - +
123B ILE 3.6 0.3 + - - -
124B ASP* 3.7 12.9 + - + +
125B LEU 3.6 9.4 + - - -
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Residues in contact with ASN 122 (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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53B PHE* 3.7 9.8 - - - -
55B ASP* 3.4 31.0 - - + +
59B ILE* 5.4 0.2 - - - +
68B ARG* 4.6 3.5 + - - +
89B ALA* 4.4 4.6 - - - +
90B THR 2.9 23.2 + - - +
118B LYS 3.4 8.5 + - - +
119B THR 3.1 4.2 + - - +
121B ARG* 1.3 76.6 - - - +
123B ILE* 1.3 60.4 + - - +
124B ASP 3.3 0.4 - - - -
125B LEU* 3.6 24.7 - - - +
126B ALA* 2.8 26.9 + - - +
134B TYR* 2.8 31.6 + - - +
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Residues in contact with ILE 123 (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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119B THR* 3.1 16.8 + - + +
120B ILE* 3.5 11.4 - - - +
121B ARG 3.2 0.2 - - - -
122B ASN* 1.3 77.5 - - - +
124B ASP* 1.3 65.6 + - - +
126B ALA* 3.2 7.5 + - - +
127B VAL* 3.0 27.2 + - + +
134B TYR* 4.0 18.6 - - + -
165B LEU* 4.0 20.9 - - + -
168B TYR* 4.4 7.9 - - + -
169B VAL* 4.2 13.7 - - + -
174B TYR* 4.1 23.3 - - + -
176B ILE* 4.8 8.1 - - + -
178B PHE* 3.7 31.2 - - + -
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Residues in contact with ASP 124 (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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120B ILE* 3.5 11.1 + - - +
121B ARG* 3.7 13.8 + - + +
123B ILE* 1.3 78.4 - - - +
125B LEU* 1.3 55.8 + - - +
127B VAL* 3.4 2.6 + - - +
128B GLU* 2.9 29.7 + - - +
168B TYR* 2.6 31.0 + - - -
174B TYR* 2.9 32.3 + - - +
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Residues in contact with LEU 125 (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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53B PHE* 4.4 11.4 - - + -
58B LEU* 4.8 2.2 - - + -
59B ILE* 3.4 33.0 - - + -
68B ARG* 4.0 18.8 - - - +
72B VAL* 3.8 24.0 - - + -
121B ARG 3.6 2.0 + - - -
122B ASN* 3.5 25.3 + - - +
123B ILE 3.2 0.4 - - - -
124B ASP* 1.3 78.3 - - - +
126B ALA* 1.3 67.2 + - - +
128B GLU* 3.0 27.4 + - - +
129B LEU* 2.8 42.8 + - + +
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Residues in contact with ALA 126 (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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53B PHE* 5.2 2.7 - - - -
89B ALA* 3.8 25.6 - - + -
122B ASN* 2.8 18.9 + - - +
123B ILE* 3.3 7.0 - - - +
125B LEU* 1.3 77.3 - - - +
127B VAL* 1.3 57.2 + - - +
129B LEU* 3.2 4.4 + - - +
130B GLY 3.1 7.8 + - - -
131B ALA* 2.9 34.4 + - + +
134B TYR* 3.9 14.1 - - + -
176B ILE* 4.1 10.3 - - + -
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Residues in contact with VAL 127 (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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123B ILE 3.0 13.8 + - - +
124B ASP 3.7 6.5 - - - +
126B ALA* 1.3 73.2 - - - +
128B GLU* 1.3 67.2 + - - +
130B GLY* 2.9 14.6 + - - +
131B ALA 4.1 6.5 - - - +
174B TYR* 3.8 50.5 - - + -
175B ASP 5.5 3.6 - - - +
176B ILE* 4.2 18.8 - - + -
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ARG* 5.7 1.6 + - - -
69B GLU* 4.3 14.6 - - - +
72B VAL* 4.5 5.5 - - - +
76B ARG* 2.7 47.4 + - - +
124B ASP 2.9 14.8 + - - +
125B LEU* 3.0 30.7 + - + +
127B VAL* 1.3 78.8 - - - +
129B LEU* 1.3 59.0 + - - +
130B GLY 3.6 0.3 + - - -
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Residues in contact with LEU 129 (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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53B PHE* 3.7 35.4 - - + -
58B LEU* 4.3 12.1 - - + -
72B VAL* 5.2 5.4 - - + +
75B PHE* 4.6 10.5 - - + -
76B ARG* 4.0 38.8 - - + +
79B LEU* 4.8 12.8 - - + +
86B VAL* 4.3 23.8 + - + +
125B LEU* 2.8 34.6 + - + +
126B ALA* 3.7 4.5 - - - +
128B GLU* 1.3 76.0 - - - +
130B GLY* 1.3 59.5 + - - +
131B ALA 3.5 0.7 + - - -
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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) + - + + + + + -
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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