Contacts of the helix formed by residues 104 - 134 (chain L) in PDB entry 1LWU
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 ALA 104 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100L VAL 3.1 17.4 + - - +
101L SER* 3.5 10.8 - - - +
103L ASP* 1.3 77.9 - - - +
105L GLN* 1.3 63.3 + - + +
106L ILE 3.2 1.3 - - - -
107L GLN* 3.5 6.7 + - - +
108L GLU* 3.1 25.0 + - - +
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Residues in contact with GLN 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186K LEU* 2.9 47.1 + - + +
187K ARG* 5.0 15.9 + - - +
190K LYS* 5.0 15.3 - - + +
101L SER* 3.3 18.2 + - - +
102L HIS* 4.1 4.6 + - - +
104L ALA* 1.3 77.6 - - + +
106L ILE* 1.3 57.6 + - - +
108L GLU* 3.2 23.7 + - - +
109L LEU* 2.8 38.0 + - + +
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Residues in contact with ILE 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J GLN* 3.6 28.3 - - + -
125J GLN* 3.5 28.5 - - + +
126J LEU* 3.2 36.6 - - + -
129J LEU* 4.5 6.9 - - + +
186K LEU* 4.6 6.7 - - + -
102L HIS* 3.1 22.4 - - + +
103L ASP* 4.2 10.5 - - - +
104L ALA 3.2 0.2 - - - -
105L GLN* 1.3 77.0 - - - +
107L GLN* 1.3 66.1 + - - +
109L LEU* 3.2 7.2 + - - +
110L SER* 3.1 28.3 + - - +
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Residues in contact with GLN 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L ASP* 4.2 10.4 + - - +
104L ALA* 3.5 10.5 + - - +
106L ILE* 1.3 81.4 - - - +
108L GLU* 1.3 60.9 + - - +
110L SER* 4.6 5.5 + - - -
111L GLU* 3.4 21.5 + - + +
114L ARG* 3.8 21.4 + - - +
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Residues in contact with GLU 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190K LYS* 2.9 43.4 + - - -
104L ALA 3.1 14.2 + - - +
105L GLN* 3.2 32.5 + - - +
107L GLN* 1.3 79.5 - - - +
109L LEU* 1.3 59.3 + - + +
111L GLU* 3.8 5.6 + - - +
112L MET* 3.3 33.5 + - + +
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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
----------------------------------------------------------
129J LEU* 3.4 29.6 - - + -
186K LEU* 4.2 15.0 - - + -
189K MET* 3.1 37.7 - - + +
190K LYS* 3.5 40.4 - - + +
193K LEU* 3.6 10.1 - - + +
105L GLN* 2.8 23.3 + - + +
106L ILE 3.2 1.3 + - - +
108L GLU* 1.3 78.6 - - + +
110L SER* 1.3 55.1 + - - +
111L GLU 3.0 1.8 - - - -
112L MET* 2.8 9.5 + - - +
113L TRP* 2.7 37.1 + - - +
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Residues in contact with SER 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J LEU* 4.0 16.2 - - - +
106L ILE* 3.1 19.7 + - - +
107L GLN* 4.2 7.9 + - - -
108L GLU 3.6 0.2 - - - -
109L LEU* 1.3 77.7 - - - +
111L GLU* 1.3 52.0 + - - +
113L TRP* 3.9 11.9 - - - +
114L ARG* 2.6 53.9 + - - +
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Residues in contact with GLU 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107L GLN* 3.4 13.1 + - - +
108L GLU* 3.9 6.3 - - - +
109L LEU 3.0 0.8 - - - -
110L SER* 1.3 75.8 - - - +
112L MET* 1.3 65.0 + - - +
114L ARG* 3.2 35.3 + - - +
115L VAL* 3.0 50.2 + - + +
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Residues in contact with MET 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190K LYS* 4.1 15.9 - - + +
193K LEU* 3.7 30.1 - - + +
194K GLU* 3.5 34.5 - - + +
197K ARG* 4.7 6.5 - - + +
108L GLU* 3.3 35.0 + - + +
109L LEU* 2.8 12.0 + - + +
111L GLU* 1.3 81.7 - - - +
113L TRP* 1.3 57.5 + - - +
115L VAL* 3.8 5.2 + - - +
116L ASN* 2.8 31.1 + - - +
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Residues in contact with TRP 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J LEU* 4.6 7.9 - - + -
132J ASN* 3.2 54.9 + - + +
133J ILE* 4.0 19.7 - - + -
135J THR* 5.5 1.3 - - - -
136J GLN* 2.9 51.2 + - - +
193K LEU* 3.8 12.3 - - + -
109L LEU 2.7 18.9 + - - +
110L SER* 4.0 11.2 - - - +
112L MET* 1.3 73.3 - - - +
114L ARG* 1.3 89.1 + - + +
115L VAL 3.3 0.2 - - - -
116L ASN* 3.1 2.2 + - - -
117L GLN* 3.0 44.0 + - + +
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Residues in contact with ARG 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107L GLN* 3.8 22.4 + - - +
110L SER* 2.6 32.9 + - - +
111L GLU* 3.2 49.9 + - - +
112L MET 3.4 0.2 - - - -
113L TRP* 1.3 93.5 - - + +
115L VAL* 1.3 66.7 + - + +
117L GLN* 3.2 7.9 + - + +
118L GLN* 3.2 27.3 + - - +
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Residues in contact with VAL 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197K ARG* 6.1 4.0 - - + -
111L GLU* 3.0 42.3 + - + +
112L MET* 3.9 7.9 - - - +
114L ARG* 1.3 75.6 - - - +
116L ASN* 1.3 55.3 + - - +
118L GLN* 3.0 23.7 + - - +
119L PHE* 2.7 35.6 + - + +
122L ARG* 4.9 8.2 + - - +
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Residues in contact with ASN 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136J GLN* 2.9 32.5 + - - +
193K LEU* 3.4 23.0 + - - +
196K LEU* 3.4 22.8 - - - +
197K ARG* 3.7 15.7 - - - +
200K MET* 3.5 21.2 - - + +
112L MET* 2.8 20.5 + - - +
113L TRP* 3.1 3.5 + - - +
115L VAL* 1.3 78.9 - - - +
117L GLN* 1.3 54.8 + - - +
119L PHE* 3.0 2.7 + - - +
120L VAL* 2.7 37.5 + - - +
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Residues in contact with GLN 117 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J THR* 5.8 1.4 + - - -
136J GLN* 3.3 26.2 + - - +
139J GLN* 3.7 20.6 + - - +
113L TRP* 3.0 55.2 + - + +
114L ARG* 3.2 8.7 + - + +
116L ASN* 1.3 75.3 - - - +
118L GLN* 1.3 60.9 + - + +
120L VAL* 2.8 25.8 - - - +
121L THR* 3.0 10.8 + - - -
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Residues in contact with GLN 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L ARG* 3.2 14.6 - - - +
115L VAL* 3.0 32.9 + - + +
116L ASN 3.0 0.2 - - - -
117L GLN* 1.3 76.4 - - + +
119L PHE* 1.3 56.6 + - - +
121L THR* 2.9 8.2 + - - -
122L ARG* 2.8 40.7 + - - +
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Residues in contact with PHE 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197K ARG* 4.1 16.2 - - + -
200K MET* 2.9 66.4 - - + -
201K GLN* 3.3 29.2 - - - -
204K GLU* 3.8 13.7 - - + -
115L VAL* 2.7 20.1 + - + +
116L ASN* 3.0 9.4 + - - +
118L GLN* 1.3 73.1 - - - +
120L VAL* 1.3 64.3 + - - +
122L ARG* 3.2 43.9 + - - +
123L LEU* 2.8 26.6 + - + +
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Residues in contact with VAL 120 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136J GLN* 5.8 0.9 - - + -
139J GLN* 3.1 42.6 - - + +
140J ILE* 3.4 31.2 - - + -
143J VAL* 4.6 14.1 - - + +
200K MET* 3.4 6.9 - - + -
116L ASN 2.7 15.1 + - - +
117L GLN* 2.8 35.4 - - + +
119L PHE* 1.3 72.7 - - - +
121L THR* 1.3 59.6 + - - +
123L LEU* 3.3 5.8 + - + +
124L GLN* 2.7 29.8 + - + +
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Residues in contact with THR 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139J GLN* 5.3 0.5 + - - -
117L GLN 3.5 9.4 + - - -
118L GLN* 2.9 11.2 + - - +
120L VAL* 1.3 80.8 - - - +
122L ARG* 1.3 56.8 + - - +
123L LEU 2.7 6.5 + - - -
124L GLN* 2.6 30.1 + - + +
125L GLN* 3.1 13.3 + - + +
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Residues in contact with ARG 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204K GLU* 2.7 55.7 + - - +
115L VAL* 4.9 6.1 + - - +
118L GLN* 2.8 19.6 + - - +
119L PHE* 3.2 54.3 - - - +
121L THR* 1.3 76.3 - - - +
123L LEU* 1.3 52.3 + - - +
125L GLN* 4.2 8.1 + - - +
126L GLN* 2.7 36.5 + - - +
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Residues in contact with LEU 123 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J VAL* 4.1 8.4 - - + +
147J ILE* 4.1 14.4 - - + +
200K MET* 4.2 16.4 - - + +
203K MET* 3.4 42.6 - - + +
204K GLU* 3.2 42.8 - - + +
207K ILE* 4.3 4.7 - - + +
119L PHE* 2.8 18.8 + - + +
120L VAL* 3.4 6.7 - - + +
121L THR 2.7 1.4 + - - -
122L ARG* 1.3 76.3 - - - +
124L GLN* 1.3 57.3 + - - +
125L GLN 3.1 5.8 - - - -
126L GLN* 3.5 13.8 + - - +
127L LEU* 3.4 21.1 + - - +
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Residues in contact with GLN 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139J GLN* 4.9 12.9 + - - +
142J ARG* 6.2 1.8 - - - +
143J VAL* 3.7 27.0 - - + +
146J ASP* 4.9 3.3 - - - +
120L VAL* 2.7 16.6 + - + +
121L THR* 2.6 16.6 + - + +
123L LEU* 1.3 72.2 - - - +
125L GLN* 1.3 58.9 + - - +
127L LEU* 3.9 18.7 - - - +
128L VAL* 3.2 25.6 + - + +
131L ARG* 5.5 0.9 + - - -
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Residues in contact with GLN 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121L THR* 3.1 12.2 + - + +
122L ARG* 4.3 6.8 + - - +
123L LEU 3.1 0.4 - - - -
124L GLN* 1.3 78.6 - - - +
126L GLN* 1.3 76.6 + - - +
127L LEU 3.0 1.6 - - - -
128L VAL* 3.0 11.2 + - + +
129L ASP* 2.8 54.7 + - - +
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Residues in contact with GLN 126 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204K GLU* 2.6 59.2 + - - +
207K ILE* 3.4 26.2 - - + +
208K LYS* 4.4 19.5 - - - +
122L ARG* 2.7 32.4 + - - +
123L LEU* 3.5 14.0 + - - +
125L GLN* 1.3 89.5 - - - +
127L LEU* 1.3 57.1 + - - +
129L ASP* 3.6 5.4 - - - +
130L ILE* 2.9 30.0 + - - +
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Residues in contact with LEU 127 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J VAL* 5.1 3.1 - - + +
146J ASP* 3.3 32.1 - - + +
147J ILE* 3.8 18.2 - - + +
150J ALA* 3.6 30.7 - - + -
207K ILE* 4.2 3.8 - - - +
123L LEU 3.4 13.7 + - - +
124L GLN* 3.9 22.9 - - - +
125L GLN 3.0 0.6 - - - -
126L GLN* 1.3 74.9 - - - +
128L VAL* 1.3 56.3 + - - +
129L ASP 2.9 3.9 + - - -
130L ILE* 3.9 6.1 - - + -
131L ARG* 2.8 63.8 + - - +
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Residues in contact with VAL 128 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124L GLN* 3.2 21.1 - - + +
125L GLN* 3.0 12.9 + - + +
127L LEU* 1.3 79.0 - - + +
129L ASP* 1.3 65.7 + - - +
131L ARG* 4.1 24.8 - - - +
132L GLN* 3.7 15.8 + - - +
----------------------------------------------------------
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Residues in contact with ASP 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211K LYS* 4.9 15.6 + - + +
125L GLN* 2.8 41.9 + - - +
126L GLN* 3.6 9.6 - - - +
127L LEU 2.9 0.8 + - - -
128L VAL* 1.3 79.4 - - - +
130L ILE* 1.3 57.5 + - - +
131L ARG 3.0 0.9 - - - -
132L GLN* 2.7 29.9 + - - +
133L THR* 2.9 15.6 + - + +
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Residues in contact with ILE 130 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J ILE* 6.2 0.4 - - + -
150J ALA* 4.4 10.0 - - + -
151J LEU* 4.0 21.3 - - + -
154J CYS* 4.0 3.1 - - - -
207K ILE* 3.8 18.8 - - + +
210K GLN* 4.5 4.3 - - + -
211K LYS* 4.1 33.5 - - + +
214K CYS* 4.5 0.4 - - - -
126L GLN 2.9 18.6 + - - +
127L LEU* 3.2 21.8 - - + +
129L ASP* 1.3 73.6 - - - +
131L ARG* 1.3 61.4 + - - +
133L THR* 3.2 16.6 - - + +
134L CYS* 2.9 50.2 + - - +
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Residues in contact with ARG 131 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J ASP* 4.4 15.2 + - - +
150J ALA* 4.5 15.2 - - + +
153J ALA* 5.7 2.9 - - - +
282K ASN* 4.5 19.7 + - + +
435K ARG* 4.7 9.3 - - - +
448K ASP* 4.8 6.3 + - - -
124L GLN* 5.5 1.2 + - - -
127L LEU* 2.8 58.1 + - + +
128L VAL* 4.1 24.0 - - - +
130L ILE* 1.3 75.3 - - - +
132L GLN* 1.3 59.9 + - - +
134L CYS* 3.7 4.6 + - - +
135L SER* 3.0 22.9 + - - -
----------------------------------------------------------
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Residues in contact with GLN 132 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128L VAL 3.7 9.7 + - - +
129L ASP* 2.7 16.9 + - - +
131L ARG* 1.3 71.0 - - - +
133L THR* 1.3 67.0 + - + +
134L CYS 3.0 1.6 - - - -
135L SER* 3.0 32.2 + - - -
136L ARG* 4.4 1.6 + - - +
----------------------------------------------------------
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Residues in contact with THR 133 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157J SER* 3.4 10.6 + - - -
158J CYS* 5.0 1.6 - - - -
211K LYS* 4.6 17.7 - - + +
214K CYS* 4.0 14.4 + - - +
129L ASP* 2.9 20.4 - - + +
130L ILE* 3.2 25.5 - - + +
132L GLN* 1.3 74.3 - - + +
134L CYS* 1.3 67.0 + - - +
135L SER 3.3 1.8 + - - -
136L ARG* 3.8 11.3 - - - +
----------------------------------------------------------
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Residues in contact with CYS 134 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150J ALA 4.9 0.4 - - - +
153J ALA* 3.6 20.4 - - + +
154J CYS* 2.0 59.9 - - - +
157J SER* 3.4 16.6 - - - -
158J CYS* 3.9 0.2 - - - -
214K CYS* 3.7 18.8 - - - -
281K SER* 5.7 0.5 - - - -
282K ASN* 5.1 3.5 + - - +
130L ILE* 2.9 22.6 + - - +
131L ARG* 3.9 5.2 - - - +
132L GLN 3.0 0.4 - - - -
133L THR* 1.3 79.5 - - - +
135L SER* 1.3 59.3 + - - +
136L ARG 3.5 1.3 - - - -
----------------------------------------------------------
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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