Contacts of the helix formed by residues 112 - 137 (chain B) in PDB entry 5X6E
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 HIS 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLN* 5.4 5.6 - - + -
7B GLU* 3.6 31.6 + - + +
8B PHE* 3.3 45.3 - + + -
11B TYR* 3.4 41.7 - + + +
108B LYS* 3.0 17.8 - - - +
109B ASN* 4.0 10.8 + - - -
111B THR* 1.3 90.1 - - + +
113B PHE* 1.3 65.1 + - - +
115B TYR* 3.7 10.4 - - - +
116B VAL* 3.4 6.1 - - - +
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Residues in contact with PHE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 3.0 46.0 - + - -
114A PHE* 3.7 25.6 - + - -
117A PHE* 4.3 20.9 - + + -
106B LEU* 3.3 45.3 - - + -
108B LYS* 2.9 5.1 - - - +
109B ASN 4.4 0.2 - - - +
110B LEU* 3.4 25.4 - - + +
111B THR 3.2 0.8 - - - -
112B HIS* 1.3 74.5 - - - +
114B PHE* 1.3 63.9 + + + +
115B TYR 2.6 4.6 + - - -
116B VAL* 2.3 39.5 + - + +
117B PHE* 3.2 27.9 + + + -
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 4.2 26.4 - - + +
75A ASP* 3.9 20.5 - - + +
103A LYS* 3.8 49.1 - - + -
106A LEU* 5.0 0.7 - - + -
107A SER* 4.5 9.2 - - - -
113A PHE* 3.7 29.2 - + - -
110B LEU* 3.3 26.5 + - + +
111B THR* 3.8 8.9 + - - +
112B HIS 3.6 0.4 - - - -
113B PHE* 1.3 87.8 - + + +
115B TYR* 1.3 55.5 + - - +
116B VAL 3.4 0.2 - - - -
117B PHE* 4.4 3.9 - - - +
118B GLN* 3.0 27.5 + - - +
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Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASP* 5.5 1.1 - - - -
2B ASN* 5.6 1.3 - - - -
3B ALA 4.3 4.0 - - - -
4B GLN* 2.9 50.5 - - + +
5B ALA* 3.5 20.9 - - + +
8B PHE* 4.1 29.8 - + - -
40B PHE* 4.0 9.8 - + - -
66B ALA* 3.7 24.3 + - - +
67B PHE* 4.3 2.3 + - - -
68B VAL* 4.4 5.8 - - + -
111B THR 4.0 6.1 + - - +
112B HIS* 3.7 13.9 + - - +
113B PHE 2.6 4.8 + - - -
114B PHE* 1.3 74.2 - - - +
116B VAL* 1.3 54.5 + - + +
118B GLN* 3.5 15.8 - - - +
119B THR* 2.4 50.6 + - + +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE* 4.4 20.2 - - + -
8B PHE* 3.9 22.4 - - + -
68B VAL* 4.7 20.4 - - + -
70B MET* 5.4 4.7 - - + -
106B LEU* 4.2 22.2 - - + -
112B HIS 3.4 14.4 - - - +
113B PHE* 2.3 32.2 + - + +
115B TYR* 1.3 67.7 - - + +
117B PHE* 1.3 62.7 + - - +
119B THR* 3.3 15.9 + - - -
120B LEU* 3.4 16.2 + - + +
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A MET* 3.6 20.9 - - - -
74A ILE* 3.4 29.8 - - + -
102A LEU* 6.2 0.2 - - + -
106A LEU* 6.3 1.8 - - + -
113A PHE* 4.7 6.1 - + - -
116A VAL* 4.0 25.1 - - + -
117A PHE* 3.9 37.0 - + + -
120A LEU* 3.4 26.1 - - + +
113B PHE* 3.2 27.0 + + + -
114B PHE* 4.4 6.1 - - - +
116B VAL* 1.3 75.3 - - - +
118B GLN* 1.3 66.2 + - - +
120B LEU 3.3 1.9 + - - -
121B GLN* 3.1 44.9 + - - +
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 4.5 12.5 - - + -
74A ILE* 5.6 0.8 - - - +
75A ASP* 4.0 20.4 - - - +
76A THR* 6.0 4.9 - - + +
4B GLN* 6.2 0.4 - - - +
114B PHE 3.0 21.1 + - - +
115B TYR* 3.5 23.2 - - + +
117B PHE* 1.3 80.2 - - - +
119B THR* 1.3 61.6 + - - +
121B GLN* 3.2 12.7 + - - +
122B LYS* 2.8 74.8 + - + +
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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
----------------------------------------------------------
67B PHE* 3.3 31.2 - - + -
68B VAL* 3.4 46.6 - - + +
115B TYR* 2.4 33.5 + - - +
116B VAL* 3.5 9.7 + - - -
117B PHE 3.3 0.4 - - - -
118B GLN* 1.3 85.5 + - - +
120B LEU* 1.3 64.0 + - + +
122B LYS* 3.2 8.8 - - - +
123B GLN* 3.2 15.1 + - - +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE* 3.5 32.3 - - + -
120A LEU* 3.5 21.1 - - + -
121A GLN* 4.4 27.4 - - + +
124A VAL* 4.3 15.9 - - + -
68B VAL* 4.7 14.6 - - + +
70B MET* 4.4 18.8 - - + +
116B VAL* 3.4 11.6 + - + +
117B PHE 3.3 2.8 + - - +
118B GLN 3.2 0.2 - - - -
119B THR* 1.3 77.8 - - + +
121B GLN* 1.3 61.5 + - - +
122B LYS 3.1 1.3 - - - -
123B GLN* 3.0 12.8 + - - +
124B VAL* 2.8 35.5 + - - +
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Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A MET* 3.5 22.2 + - - +
72A GLY 2.9 27.7 + - - -
73A PHE* 3.4 18.7 - - + +
74A ILE* 2.8 35.3 + - - +
80A VAL* 4.2 5.9 - - + +
120A LEU* 4.0 10.1 - - + +
117B PHE* 3.1 35.2 + - + +
118B GLN* 3.2 10.4 + - - +
120B LEU* 1.3 76.0 - - - +
122B LYS* 1.3 57.4 + - - +
124B VAL* 4.2 6.0 - - - +
125B SER* 2.5 34.8 + - - -
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 4.0 10.3 - - + -
67B PHE* 4.2 15.0 - - + -
118B GLN* 2.8 49.7 + - - +
119B THR 3.2 12.6 - - - +
120B LEU 3.1 0.2 - - - -
121B GLN* 1.3 78.5 - - - +
123B GLN* 1.3 54.2 + - - +
125B SER* 4.6 0.9 - - - -
126B TYR 3.3 9.5 + - - -
224B TRP* 3.1 30.1 + - + -
228B ALA* 3.6 25.6 - - + +
229B CYS* 4.0 21.4 - - - +
301B GSH 3.1 30.2 + - - -
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Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 4.7 14.8 - - + +
128A LEU* 3.6 21.0 - - - +
61B GLN* 3.3 14.0 + - - +
63B TYR* 2.9 30.0 + - - -
67B PHE* 3.6 18.0 - - - -
68B VAL 4.5 4.6 + - - -
69B ILE* 5.7 1.2 - - - +
119B THR 3.2 9.6 + - - +
120B LEU* 3.0 18.4 + - - +
122B LYS* 1.3 75.3 - - - +
124B VAL* 1.3 55.1 + - - +
125B SER 3.2 1.8 - - - -
126B TYR* 2.8 2.0 + - + +
127B SER* 2.6 44.0 + - - +
301B GSH 3.5 21.8 - - - -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 3.8 24.9 - - + +
123A GLN* 3.9 31.6 - - + +
124A VAL* 3.5 28.5 - - + +
127A SER* 5.2 2.6 + - - +
120B LEU 2.8 24.1 + - - +
121B GLN* 4.2 5.2 - - - +
123B GLN* 1.3 71.5 - - - +
125B SER* 1.3 59.0 + - - +
127B SER* 3.9 5.5 - - - -
128B LEU* 3.0 43.1 + - + +
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Residues in contact with SER 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 4.2 2.1 - - - -
80A VAL* 3.2 44.1 - - - +
83A TYR* 4.3 5.6 + - - -
121B GLN 2.5 24.0 + - - -
122B LYS* 4.8 0.4 - - - -
123B GLN 3.2 0.2 - - - -
124B VAL* 1.3 79.0 - - - +
126B TYR* 1.3 56.5 + - - +
128B LEU* 4.0 7.7 - - - +
129B ALA* 3.2 21.7 + - - +
224B TRP* 3.2 27.5 - - - -
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Residues in contact with TYR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLN* 3.7 37.5 - - + -
122B LYS 3.3 13.4 + - - +
123B GLN* 2.8 10.2 + - - +
125B SER* 1.3 75.8 - - - +
127B SER* 1.3 63.7 + - - +
128B LEU 3.3 0.2 - - - -
129B ALA* 3.3 2.9 + - - +
130B LYS* 2.9 51.6 + - + +
149B ILE* 3.2 30.0 - - + +
221B LEU* 4.2 17.5 - - + -
224B TRP* 3.2 41.1 - + + +
225B PHE* 4.8 1.8 - + - -
301B GSH 3.0 38.8 + - + -
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 5.0 2.5 + - - -
127A SER* 3.7 31.1 - - - -
128A LEU* 4.1 17.5 - - - +
131A PHE* 5.7 4.5 - - - +
61B GLN* 4.5 3.3 + - - -
123B GLN* 2.6 32.1 + - - +
124B VAL* 3.9 5.3 - - - -
126B TYR* 1.3 76.0 - - - +
128B LEU* 1.3 57.6 + - - +
130B LYS* 3.4 6.0 + - - +
131B PHE* 2.9 31.6 + - - +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 4.2 18.8 - - + -
60A LEU* 3.8 34.1 - - + +
61A GLN* 4.5 15.7 - - - +
83A TYR* 3.6 33.1 + - + +
123A GLN* 4.6 3.8 - - - +
127A SER* 4.9 8.7 - - - +
124B VAL* 3.0 36.4 + - + +
125B SER* 4.0 4.5 - - - +
127B SER* 1.3 77.8 - - - +
129B ALA* 1.3 60.5 + - - +
131B PHE* 3.6 9.5 + - + +
132B ASN* 3.1 23.9 + - - +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TYR* 3.6 9.6 + - - +
125B SER 3.2 18.1 + - - +
126B TYR* 3.3 4.9 + - - +
128B LEU* 1.3 78.3 - - - +
130B LYS* 1.3 61.7 + - - +
132B ASN* 3.6 1.6 + - - +
133B ASP* 3.3 31.2 + - - +
220B LYS* 3.5 31.1 - - - +
221B LEU* 3.9 12.1 - - + -
224B TRP* 4.2 8.7 - - + -
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PHE* 4.0 19.5 - - + -
59B ASN 4.8 0.4 + - - -
60B LEU 2.7 29.6 + - - +
61B GLN* 4.1 5.5 - - - +
126B TYR* 2.9 49.5 + - + +
127B SER* 3.7 6.3 - - - +
129B ALA* 1.3 74.6 - - - +
131B PHE* 1.3 63.8 + - - +
133B ASP 3.6 0.2 + - - -
134B PHE* 3.1 65.7 + - + +
146B GLN* 3.5 19.3 + - - +
149B ILE* 4.0 3.6 - - + -
177B SER 4.7 2.3 + - - -
221B LEU* 3.8 15.2 - - + +
301B GSH 4.4 1.6 + - - -
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Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A MET* 4.0 13.1 - - + +
59A ASN 4.3 3.6 - - - -
60A LEU* 3.3 41.1 - - + -
127A SER 6.0 1.6 - - - +
130A LYS* 3.4 28.5 - - + -
131A PHE* 4.5 23.9 - + + -
134A PHE* 3.4 35.4 - + + -
177A SER 4.4 4.7 - - - -
127B SER 2.9 19.2 + - - +
128B LEU* 3.8 10.5 - - + +
129B ALA 3.4 0.2 - - - -
130B LYS* 1.3 76.8 - - - +
132B ASN* 1.3 62.2 + - - +
134B PHE* 4.2 1.4 - - + +
135B SER* 3.0 47.2 + - - -
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Residues in contact with ASN 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A SER* 3.2 34.0 + - - -
58A MET* 3.6 27.1 - - - +
60A LEU* 3.8 10.6 - - + +
128B LEU 3.1 18.2 + - - +
129B ALA 3.8 5.4 - - - +
130B LYS 3.2 0.2 - - - -
131B PHE* 1.3 79.8 - - - +
133B ASP* 1.3 75.0 + - - +
135B SER* 4.1 1.2 - - - -
136B ILE* 3.3 36.2 + - - +
219B PRO* 5.2 1.0 - - - +
220B LYS* 3.8 17.3 - - + +
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA 3.3 9.4 + - - +
130B LYS 4.4 0.7 - - - +
132B ASN* 1.3 85.7 - - - +
134B PHE* 1.3 65.9 + - + +
136B ILE* 3.6 16.7 - - - +
137B ASN 4.0 4.7 + - - -
141B GLY* 4.1 15.3 - - - +
217B TYR 4.3 3.3 - - - +
218B ALA* 3.3 25.4 - - + -
219B PRO* 3.3 9.0 - - - +
220B LYS* 3.2 18.4 + - - -
221B LEU* 2.6 48.0 + - + +
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Residues in contact with PHE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PHE* 3.4 33.9 - + + -
135A SER* 5.1 3.1 - - - -
139A LYS* 5.8 0.2 - - - -
130B LYS* 3.1 55.1 + - + +
131B PHE* 4.2 3.8 - - + +
133B ASP* 1.3 84.5 - - + +
135B SER* 1.3 61.0 + - - +
138B GLY* 3.2 24.8 + - - +
141B GLY 4.7 0.9 - - - -
142B SER* 3.2 51.9 + - - +
145B GLY* 4.4 5.4 - - - -
146B GLN* 4.2 15.3 - - + -
177B SER 3.7 16.6 - - - -
178B SER* 4.1 6.5 - - - -
179B GLY 5.7 0.2 - - - -
221B LEU* 4.4 4.3 - - + -
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Residues in contact with SER 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A MET* 3.6 21.1 - - - -
134A PHE* 4.9 4.6 - - - +
139A LYS* 3.7 15.2 + - - +
179A GLY* 3.1 34.0 - - - +
131B PHE* 3.0 37.8 + - - -
132B ASN 4.1 0.7 - - - -
133B ASP 3.4 0.2 - - - -
134B PHE* 1.3 81.0 - - - +
136B ILE* 1.3 61.4 + - - +
138B GLY 4.3 1.5 + - - -
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Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 5.8 14.4 - - + -
57A ILE 5.6 2.2 - - - +
58A MET* 4.4 25.6 - - + -
139A LYS* 5.7 0.7 + - - -
179A GLY 4.8 3.9 - - - +
132B ASN* 3.3 32.8 - - - +
133B ASP* 3.6 20.0 - - - +
135B SER* 1.3 80.8 - - - +
137B ASN* 1.3 80.9 + - - +
138B GLY 3.5 1.0 + - - -
217B TYR 5.1 0.2 - - - +
219B PRO* 4.7 13.5 - - + -
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASP 4.0 3.1 + - - +
136B ILE* 1.3 101.7 + - + +
138B GLY* 1.3 61.2 + - - +
140B LEU* 3.8 9.0 + - - +
141B GLY* 3.0 33.3 + - - +
216B ARG 5.2 1.4 - - - +
217B TYR* 3.9 37.4 + - + +
219B PRO* 5.6 0.3 - - - +
17D T 4.2 2.1 + - - -
----------------------------------------------------------
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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