Contacts of the helix formed by residues 116 - 143 (chain A) in PDB entry 4TLG
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 SER 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.2 3.6 - - - -
115A ALA* 1.3 78.2 - - - +
117A LYS* 1.3 63.9 + - - +
118A GLN* 3.5 20.2 + - - +
119A ASP* 3.0 36.2 + - - +
120A MET* 3.1 25.3 + - - +
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Residues in contact with LYS 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.8 19.4 - - + +
116A SER* 1.3 71.9 - - - +
118A GLN* 1.3 71.1 + - - +
120A MET* 3.2 4.1 + - - +
121A ILE* 2.9 40.0 + - + +
166A PRO 5.8 1.6 - - - +
169A GLU* 5.4 4.9 - - + +
170A VAL* 4.2 25.8 - - + +
173A GLN* 3.4 33.0 + - - +
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER* 3.1 20.1 - - - +
117A LYS* 1.3 94.0 + - - +
119A ASP* 1.3 61.0 + - - +
121A ILE* 3.5 5.5 + - - +
122A ARG* 2.9 29.9 + - - +
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Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 3.6 22.9 - - + -
77A PRO* 3.3 28.4 - - + +
80A ILE* 3.5 21.7 - - + +
115A ALA* 5.0 0.2 - - - +
116A SER* 3.0 28.7 + - - +
118A GLN* 1.3 75.9 - - - +
120A MET* 1.3 60.6 + - - +
122A ARG* 4.3 3.2 - - - -
123A LYS* 2.9 29.5 + - - +
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Residues in contact with MET 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 4.1 14.1 - - + -
84A ASP* 4.0 7.4 - - - +
108A PRO* 4.5 15.7 - - + -
111A LEU* 3.8 35.2 - - + +
112A LEU* 3.5 35.4 - - + -
115A ALA* 5.4 0.7 - - + -
116A SER 3.1 15.3 + - - +
117A LYS* 3.6 8.5 - - - +
119A ASP* 1.3 75.0 - - - +
121A ILE* 1.3 63.0 + - - +
123A LYS* 3.5 2.0 + - - +
124A ARG* 2.8 62.4 + - - +
170A VAL* 4.6 17.0 - - + -
171A TYR* 6.1 0.2 - - + -
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 2.9 31.5 + - + +
118A GLN* 3.9 5.8 - - - +
120A MET* 1.3 73.7 - - - +
122A ARG* 1.3 60.5 + - - +
124A ARG* 3.0 7.7 + - - +
125A ILE* 2.9 39.4 + - + +
170A VAL* 3.5 36.8 - - + +
173A GLN* 4.3 15.7 - - + +
174A PHE* 4.0 22.9 - - + +
177A ILE* 3.6 25.6 - - + -
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLN* 2.8 56.1 + - - +
67A ASP* 4.1 15.8 + - - +
68A LEU* 4.5 0.4 - - - +
70A ASN 5.6 0.2 - - - -
71A ILE* 3.5 28.7 - - + +
74A TRP* 3.5 51.2 - - + +
118A GLN 2.9 19.3 + - - +
119A ASP* 3.8 7.0 - - - +
121A ILE* 1.3 76.4 - - - +
123A LYS* 1.3 57.8 + - - +
125A ILE* 3.4 11.1 + - + +
126A LYS* 2.9 30.0 + - - +
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Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 3.7 10.9 - - + -
76A PRO* 5.0 5.2 - - + -
80A ILE* 3.9 24.0 - - + +
84A ASP* 2.9 39.4 + - - +
85A SER 2.7 29.4 + - - -
86A GLY 6.1 0.2 - - - -
99A TYR* 3.9 13.2 + - - -
119A ASP 2.9 17.1 + - - +
120A MET 3.6 4.9 - - - +
121A ILE 3.2 0.2 - - - -
122A ARG* 1.3 76.8 - - - +
124A ARG* 1.3 72.2 + - + +
126A LYS* 3.3 9.6 - - + +
127A VAL* 3.1 32.3 + - + +
171A TYR* 5.9 0.2 + - - -
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Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASP* 2.9 42.4 + - - -
106A LEU* 3.7 23.4 - - - +
120A MET* 2.8 50.3 + - - +
121A ILE* 3.0 8.7 + - - +
123A LYS* 1.3 87.4 - - + +
125A ILE* 1.3 64.6 + - - +
127A VAL* 3.3 10.7 + - + +
128A CYS* 3.1 24.8 + - - -
170A VAL* 4.4 7.4 - - - +
171A TYR* 3.2 37.5 + - + +
174A PHE* 3.5 39.5 - - + -
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Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 3.7 31.4 - - + -
66A GLN* 5.1 5.8 - - + +
68A LEU* 3.5 32.1 - - + -
71A ILE* 3.9 4.3 - - + -
121A ILE* 2.9 35.4 + - + +
122A ARG* 3.7 10.1 - - + +
124A ARG* 1.3 72.1 - - - +
126A LYS* 1.3 66.8 + - - +
128A CYS* 3.1 11.5 + - - +
129A GLU* 3.0 22.2 + - + +
174A PHE* 5.1 3.1 - - + -
177A ILE* 4.2 18.2 - - + -
182A TYR* 3.5 18.6 - - + +
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 3.4 39.7 - - + +
72A VAL* 3.7 19.0 + - - +
74A TRP* 2.7 36.7 + - + +
75A GLN* 4.1 12.7 + - - +
76A PRO* 4.5 8.0 - - + +
122A ARG 2.9 15.1 + - - +
123A LYS* 3.3 13.2 - - + +
124A ARG 3.3 0.2 - - - -
125A ILE* 1.3 77.0 - - - +
127A VAL* 1.3 57.0 + - + +
129A GLU* 3.3 2.6 + - - +
130A LEU* 2.8 53.7 + - + +
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Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 4.7 2.7 - - + -
99A TYR* 3.5 55.2 - - + +
123A LYS* 3.1 24.7 + - + +
124A ARG* 3.4 11.7 - - - +
125A ILE 3.3 0.2 - - - -
126A LYS* 1.3 77.3 - - + +
128A CYS* 1.3 58.7 + - - +
130A LEU* 3.2 13.7 + - + +
131A LEU* 2.9 40.2 + - + +
151A MET* 6.3 0.9 - - - -
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Residues in contact with CYS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG 3.1 19.2 + - - -
125A ILE* 3.1 9.2 + - - +
127A VAL* 1.3 78.9 - - - +
129A GLU* 1.3 59.2 + - - +
131A LEU* 3.3 1.5 + - - -
132A LEU* 3.0 33.8 + - - +
174A PHE* 3.9 15.0 - - - -
178A LEU* 3.8 18.8 - - - -
182A TYR* 3.8 24.7 - - + -
513A EDO 3.4 32.3 - - - -
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Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO* 6.1 0.3 - - - +
63A ARG* 2.8 42.6 + - - -
68A LEU* 4.0 7.5 - - + +
71A ILE* 3.7 25.8 - - + -
72A VAL* 4.3 10.6 - - + +
125A ILE* 3.0 18.4 + - + +
126A LYS 3.7 6.5 - - - +
128A CYS* 1.3 72.6 - - - +
130A LEU* 1.3 59.9 + - - +
132A LEU* 3.3 12.1 + - - +
133A HIS* 3.0 28.9 + - - +
182A TYR* 2.6 31.2 + - - +
502A EDO 5.5 0.2 - - - -
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL* 3.7 32.1 - - + +
88A LEU* 4.2 29.2 - - + +
126A LYS* 2.8 45.8 + - + +
127A VAL* 3.6 9.6 - - + +
129A GLU* 1.3 71.6 - - - +
131A LEU* 1.3 58.0 + - - +
133A HIS* 3.4 13.0 + - + +
134A GLU* 2.9 28.8 + - - +
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.6 28.3 - - + -
97A PRO* 4.0 15.7 - - + +
98A VAL 4.6 1.3 - - - +
99A TYR* 3.9 21.3 - - + -
127A VAL* 2.9 36.5 + - + +
128A CYS* 3.6 4.9 - - - +
129A GLU 3.3 0.2 - - - -
130A LEU* 1.3 77.0 - - - +
132A LEU* 1.3 56.7 + - - +
134A GLU* 3.2 5.3 + - - +
135A CYS* 2.9 33.3 + - - -
149A ALA* 4.0 25.8 - - + -
151A MET* 5.0 8.1 - - + -
513A EDO 3.8 22.4 - - - +
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ARG* 5.0 3.4 - - - +
128A CYS 3.0 17.0 + - - +
129A GLU* 3.7 12.1 - - - +
131A LEU* 1.3 72.7 - - - +
133A HIS* 1.3 65.0 + - - +
135A CYS* 3.2 11.0 + - + +
136A GLU* 3.1 26.9 + - - +
147A GLU 4.9 9.0 - - - +
148A MET* 6.3 0.2 - - - -
182A TYR* 3.7 23.6 - - + -
185A THR* 4.0 16.6 - - + -
502A EDO 3.4 36.8 - - - +
513A EDO 3.9 17.5 - - - +
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Residues in contact with HIS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL* 5.4 7.9 - - + -
129A GLU 3.0 12.9 + - - +
130A LEU* 3.5 15.5 - - + +
132A LEU* 1.3 75.4 - - - +
134A GLU* 1.3 61.4 + - - +
136A GLU* 3.2 11.4 + - + +
137A LEU* 3.0 66.9 + - + +
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 4.4 12.2 - - + +
91A TYR* 2.4 34.0 + - + -
97A PRO* 3.8 24.7 - - + -
130A LEU 2.9 16.3 + - - +
131A LEU* 3.2 7.6 + - - +
133A HIS* 1.3 81.2 - - - +
135A CYS* 1.3 55.7 + - - +
137A LEU* 3.3 23.1 + - - +
138A GLN* 2.9 38.3 + - - +
141A LYS* 5.0 4.5 + - - -
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Residues in contact with CYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A PRO* 3.8 14.1 - - - -
131A LEU 2.9 19.8 + - - -
132A LEU* 3.2 17.4 + - + +
134A GLU* 1.3 75.7 - - - +
136A GLU* 1.3 58.1 + - + +
138A GLN* 3.4 3.5 + - - +
139A THR* 2.9 32.7 + - - -
146A ILE* 3.4 23.6 - - - +
147A GLU 4.2 4.5 - - - -
148A MET* 3.6 39.0 - - - -
149A ALA* 4.4 1.6 - - - -
513A EDO 5.5 0.9 - - - -
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Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO 5.1 2.2 - - - +
32A ASN* 2.9 30.5 + - - +
132A LEU 3.1 15.2 + - - +
133A HIS* 3.2 12.5 + - - +
135A CYS* 1.3 74.8 - - + +
137A LEU* 1.3 66.5 + - - +
139A THR* 3.3 8.2 + - - +
140A GLN* 3.0 32.0 + - + +
145A LYS* 3.6 11.8 + - - -
146A ILE 6.0 0.2 - - - -
508A EDO 3.0 21.2 + - - -
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A HIS* 3.0 51.7 + - + +
134A GLU* 3.7 28.0 - - - +
136A GLU* 1.3 77.6 - - + +
138A GLN* 1.3 57.1 + - - +
140A GLN* 3.2 9.4 + - + +
141A LYS* 2.9 53.8 + - - +
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Residues in contact with GLN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 3.5 40.2 + - + +
95A GLY* 2.8 39.0 + - - +
97A PRO* 4.8 2.5 - - + -
134A GLU* 2.9 23.7 + - - +
135A CYS 3.6 4.5 - - - +
137A LEU* 1.3 73.1 - - - +
139A THR* 1.3 58.5 + - - +
141A LYS* 3.9 21.2 + - - +
142A LEU* 2.8 50.3 + - - +
146A ILE* 3.9 13.5 - - + -
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Residues in contact with THR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A CYS 2.9 20.2 + - - -
136A GLU* 3.4 13.8 - - - -
138A GLN* 1.3 75.0 - - - +
140A GLN* 1.3 63.9 + - - +
143A GLY* 2.9 30.0 + - - -
144A ARG* 3.3 20.5 + - - +
145A LYS* 3.8 12.7 + - + +
146A ILE* 2.9 25.0 + - - +
508A EDO 3.9 29.4 - - - +
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Residues in contact with GLN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU* 3.0 21.5 + - + +
137A LEU* 3.2 12.1 + - + +
139A THR* 1.3 79.9 - - - +
141A LYS* 1.3 64.2 + - + +
143A GLY* 3.9 5.9 + - - -
508A EDO 4.3 23.2 + - - -
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 5.2 2.6 + - - -
134A GLU* 5.0 6.5 + - - -
137A LEU* 2.9 39.6 + - - +
138A GLN* 3.8 23.8 + - - +
140A GLN* 1.3 81.4 - - + +
142A LEU* 1.3 65.1 + - + +
143A GLY 3.5 0.6 + - - -
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU 4.0 4.5 - - - +
95A GLY* 4.2 2.9 - - - -
138A GLN* 2.8 42.8 + - - +
141A LYS* 1.3 83.7 - - + +
143A GLY* 1.3 62.3 + - - +
144A ARG* 3.3 43.8 + - + +
146A ILE* 4.0 20.6 - - + -
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Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A THR* 2.9 12.4 + - - -
140A GLN 3.9 5.3 + - - -
141A LYS 3.5 2.4 - - - -
142A LEU* 1.3 77.3 - - - +
144A ARG* 1.3 59.1 + - - +
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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