Contacts of the helix formed by residues 110 - 136 (chain L) in PDB entry 4XLN
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 THR 110 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L LEU 6.1 0.2 - - - -
109L LEU* 1.3 78.5 - - - +
111L LEU* 1.3 74.1 + - + +
112L GLU* 3.4 10.3 + - - +
113L GLU* 3.5 26.2 + - - +
114L GLU* 3.1 19.6 + - - +
249L LYS* 5.4 2.5 - - - +
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Residues in contact with LEU 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349J PRO* 4.3 18.4 - - + -
110L THR* 1.3 82.9 - - - +
112L GLU* 1.3 62.4 - - - +
114L GLU* 3.2 6.7 + - - +
115L ILE* 2.9 35.6 + - + +
249L LYS* 4.0 31.2 - - + +
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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
----------------------------------------------------------
207J PHE* 3.5 35.4 - - + +
209J ARG* 3.9 26.8 + - - +
347J VAL* 5.3 4.5 - - - +
348J ALA 5.2 1.6 - - - -
349J PRO* 3.7 39.1 - - + +
391J ALA* 3.7 18.9 - - - +
110L THR* 3.4 8.8 + - - +
111L LEU* 1.3 78.3 - - - +
113L GLU* 1.3 66.0 + - + +
115L ILE* 3.3 1.7 + - - +
116L ASP* 2.9 24.6 + - - +
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Residues in contact with GLU 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207J PHE* 3.8 20.4 - - + -
108L LEU 4.2 10.5 - - - +
109L LEU* 4.0 17.9 - - + +
110L THR* 3.5 32.4 + - - +
111L LEU 3.5 0.4 - - - -
112L GLU* 1.3 77.1 - - + +
114L GLU* 1.3 57.4 + - - +
116L ASP* 3.6 2.4 - - - +
117L LEU* 2.9 38.5 + - + +
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Residues in contact with GLU 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109L LEU* 3.7 24.6 - - + +
110L THR 3.1 17.8 + - - +
111L LEU* 3.5 7.6 - - - +
113L GLU* 1.3 75.2 - - - +
115L ILE* 1.3 77.1 + - + +
117L LEU* 3.1 4.4 + - - +
118L ALA* 2.9 24.4 + - + +
202L LEU* 5.2 5.4 - - + +
206L ASN* 4.4 4.0 - - - +
242L PHE* 5.6 6.0 - - + -
248L PHE 4.8 1.8 - - - +
249L LYS* 3.2 41.1 - - - +
250L PHE* 3.2 34.0 + - + +
30R T 3.9 6.9 - - - +
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Residues in contact with ILE 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349J PRO* 4.1 21.3 - - + +
350J HIS* 4.9 12.1 - - - +
351J MET 5.7 2.0 - - - +
352J ASN* 5.9 4.5 - - - +
371J ILE* 6.5 0.7 - - + -
111L LEU* 2.9 27.3 + - + +
112L GLU 3.8 3.4 - - - +
114L GLU* 1.3 87.6 - - + +
116L ASP* 1.3 58.4 + - - +
118L ALA* 3.4 2.7 + - - +
119L ARG* 2.9 30.6 + - + +
242L PHE* 6.3 1.1 - - + -
244L TYR* 3.7 42.7 - - + +
247L ARG* 6.0 6.1 - - - -
248L PHE 5.9 2.5 - - - +
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Residues in contact with ASP 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207J PHE* 3.4 32.0 - - + -
352J ASN* 6.1 2.2 - - + -
112L GLU 2.9 17.3 + - - +
113L GLU* 3.6 3.1 - - - +
115L ILE* 1.3 77.1 - - - +
117L LEU* 1.3 61.4 + - - +
119L ARG* 3.1 31.0 + - - +
120L LYS* 2.9 47.9 + - - +
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Residues in contact with LEU 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109L LEU* 3.7 28.9 - - + -
113L GLU* 2.9 22.3 + - + +
114L GLU* 3.4 5.4 - - - +
116L ASP* 1.3 79.6 - - - +
118L ALA* 1.3 63.8 - - - +
120L LYS* 3.1 15.1 + - - +
121L VAL* 2.9 27.9 + - - +
198L ALA* 3.6 31.7 - - + +
201L HIS* 4.0 18.2 - - + +
202L LEU* 3.9 29.4 - - + +
205L ALA* 5.2 1.1 - - + -
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Residues in contact with ALA 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L GLU* 2.9 15.8 + - + +
115L ILE 3.9 1.1 - - - +
117L LEU* 1.3 75.7 - - - +
119L ARG* 1.3 58.2 + - - +
121L VAL* 3.1 10.2 + - - +
122L GLU* 2.9 34.5 + - + +
202L LEU* 4.2 11.1 - - + +
242L PHE* 4.3 18.2 - - + +
244L TYR* 3.7 32.1 - - + -
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Residues in contact with ARG 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352J ASN* 3.4 49.2 + - - +
353J VAL 5.4 3.8 + - - -
115L ILE* 2.9 20.8 + - + +
116L ASP* 3.1 30.5 + - - +
118L ALA* 1.3 75.7 - - - +
120L LYS* 1.3 61.9 + - - +
122L GLU* 3.6 1.4 + - - +
123L GLU* 2.9 71.5 + - + +
244L TYR* 3.2 37.1 - - + +
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Residues in contact with LYS 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L ASP* 2.9 38.8 + - - +
117L LEU* 3.1 11.5 + - - +
119L ARG* 1.3 80.4 - - - +
121L VAL* 1.3 56.9 + - - +
123L GLU* 3.6 13.8 - - - +
124L GLY 2.9 21.5 + - - -
191L ILE* 4.6 1.5 - - - +
194L GLU* 3.8 34.4 + - + +
195L GLY* 3.2 20.1 + - - +
198L ALA* 3.7 24.2 - - + +
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Residues in contact with VAL 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117L LEU 2.9 22.2 + - - +
118L ALA* 3.1 10.7 + - - +
120L LYS* 1.3 74.4 - - - +
122L GLU* 1.3 64.6 + - + +
124L GLY* 2.8 19.1 + - - -
125L MET* 2.9 36.3 + - + +
143L ARG* 5.6 0.7 - - - +
195L GLY* 3.6 12.3 - - - +
198L ALA* 3.7 4.5 - - + +
199L ARG* 3.6 43.1 - - + +
202L LEU* 4.6 7.0 - - + -
239L VAL* 5.5 7.9 - - + +
240L GLU* 6.2 1.8 - - - -
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Residues in contact with GLU 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118L ALA* 2.9 17.7 + - + +
119L ARG 4.1 2.7 - - - +
121L VAL* 1.3 78.8 - - + +
123L GLU* 1.3 57.5 + - - +
125L MET* 3.3 12.8 + - - +
126L GLU* 2.9 52.0 + - - +
242L PHE 3.5 22.3 - - - +
243L GLU* 3.6 12.3 - - - +
244L TYR* 3.2 40.2 + - + +
245L LYS* 4.3 11.6 - - - +
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Residues in contact with GLU 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119L ARG* 2.9 59.9 + - + +
120L LYS* 3.6 10.2 - - - +
122L GLU* 1.3 76.9 - - - +
124L GLY* 1.3 58.7 + - - +
126L GLU* 3.5 5.9 + - - +
127L ALA* 2.9 29.5 + - - +
188L TYR* 5.8 0.3 - - - -
191L ILE* 3.8 16.8 - - + +
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Residues in contact with GLY 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120L LYS 2.9 10.0 + - - -
121L VAL 2.8 9.2 + - - -
123L GLU* 1.3 77.4 - - - +
125L MET* 1.3 54.7 + - - -
127L ALA* 3.1 4.7 - - - +
128L ILE* 2.9 32.8 + - - +
191L ILE* 3.6 22.4 - - - +
192L ALA* 3.7 13.4 - - - -
195L GLY* 4.3 1.6 - - - -
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Residues in contact with MET 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L VAL* 2.9 36.6 + - + +
122L GLU* 3.8 12.3 - - - +
124L GLY* 1.3 73.9 - - - +
126L GLU* 1.3 61.9 + - + +
128L ILE* 3.1 15.3 + - - +
129L LYS* 2.9 24.1 + - - +
139L GLN* 5.2 0.7 - - - +
143L ARG* 3.5 39.7 - - - +
240L GLU* 4.8 25.6 - - + +
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Residues in contact with GLU 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122L GLU* 2.9 39.3 + - - +
123L GLU* 4.1 5.6 - - - +
125L MET* 1.3 73.7 - - + +
127L ALA* 1.3 67.2 + - - +
129L LYS* 3.0 17.8 + - + +
130L LYS* 3.0 25.6 + - - +
188L TYR* 5.5 1.1 - - - -
245L LYS* 5.4 5.5 + - - -
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Residues in contact with ALA 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123L GLU 2.9 16.5 + - - +
124L GLY* 3.1 12.3 - - - +
126L GLU* 1.3 76.9 - - - +
128L ILE* 1.3 56.6 + - - +
130L LYS* 3.3 3.6 + - - +
131L LEU* 2.9 34.2 + - - +
188L TYR* 3.4 48.6 - - + +
191L ILE* 3.9 9.0 - - + -
192L ALA 4.1 0.9 - - - +
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Residues in contact with ILE 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124L GLY 2.9 21.8 + - - +
125L MET* 3.1 9.2 + - - +
127L ALA* 1.3 76.1 - - - +
129L LYS* 1.3 57.7 + - - +
131L LEU* 3.6 8.9 - - + -
132L SER* 2.9 28.1 + - - -
139L GLN* 3.5 33.0 - - + +
142L ILE* 4.3 11.4 - - + +
143L ARG* 3.8 51.4 - - + +
146L VAL* 5.1 5.2 - - + -
192L ALA* 3.8 19.3 - - + +
196L GLU* 5.1 6.7 - - + -
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Residues in contact with LYS 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125L MET 2.9 9.8 + - - +
126L GLU* 3.0 23.8 + - + +
128L ILE* 1.3 76.7 - - - +
130L LYS* 1.3 59.5 + - + +
132L SER* 3.3 14.9 - - - -
133L GLU* 3.5 23.2 + - - +
139L GLN* 3.3 24.1 + - - +
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Residues in contact with LYS 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126L GLU 3.0 14.1 + - - +
127L ALA 3.8 6.5 - - - +
129L LYS* 1.3 72.9 - - + +
131L LEU* 1.3 58.3 + - - +
132L SER 3.0 4.3 - - - -
133L GLU* 2.9 23.7 + - - +
134L ALA* 2.9 24.0 + - - +
185L LEU* 5.4 4.5 - - + +
188L TYR* 3.4 45.7 + - + +
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Residues in contact with LEU 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127L ALA 2.9 21.3 + - - +
128L ILE* 3.3 10.1 + - - +
130L LYS* 1.3 75.0 - - - +
132L SER* 1.3 60.2 + - - +
133L GLU 3.3 0.2 - - - -
134L ALA* 3.3 27.8 + - + +
135L THR* 3.6 8.0 + - - -
142L ILE* 3.4 29.3 - - + +
146L VAL* 6.5 0.2 - - + -
178L LEU* 4.2 14.3 - - + +
181L LEU* 4.8 2.2 - - + -
185L LEU* 3.6 29.6 - - + +
186L LYS* 5.6 0.2 - - - -
188L TYR* 3.5 33.4 - - + +
189L LEU* 3.6 14.4 - - + +
192L ALA* 4.5 6.1 - - + -
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Residues in contact with SER 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128L ILE 2.9 10.7 + - - -
129L LYS 3.3 13.2 - - - -
130L LYS 3.0 0.2 - - - -
131L LEU* 1.3 79.3 - - - +
133L GLU* 1.3 59.2 + - - +
136L GLY* 3.1 8.3 + - - -
137L LEU 2.3 54.7 + - - +
138L ASP 3.8 5.6 - - - -
139L GLN* 3.1 28.6 + - - -
142L ILE* 3.9 7.0 - - - -
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Residues in contact with GLU 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129L LYS* 3.5 32.8 + - - +
130L LYS* 2.9 22.5 + - - +
132L SER* 1.3 75.8 - - - +
134L ALA* 1.3 67.3 + - - +
136L GLY* 3.9 5.6 + - - -
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Residues in contact with ALA 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130L LYS 2.9 7.8 + - - +
131L LEU* 3.3 24.9 - - + +
132L SER 3.2 0.2 - - - -
133L GLU* 1.3 80.3 - - - +
135L THR* 1.3 62.5 + - + +
178L LEU* 4.7 0.4 - - + -
181L LEU* 3.7 27.5 - - + +
185L LEU* 4.0 19.8 - - + +
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Residues in contact with THR 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131L LEU 3.6 5.9 + - - -
134L ALA* 1.3 77.7 - - - +
136L GLY* 1.3 61.2 + - - +
137L LEU* 3.3 30.1 - - - +
177L LYS* 3.5 39.2 - - + +
178L LEU* 3.5 31.8 - - + +
180L SER* 5.3 0.2 - - - +
181L LEU* 3.9 13.7 - - + -
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Residues in contact with GLY 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132L SER 3.1 12.1 + - - -
133L GLU* 3.9 5.0 + - - -
134L ALA 3.4 3.6 + - - -
135L THR* 1.3 80.1 - - - +
137L LEU* 1.3 64.0 + - - +
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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