Contacts of the helix formed by residues 118 - 148 (chain A) in PDB entry 4GCK
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 GLN 118 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 3.6 25.5 + - + +
114A LEU 4.9 2.1 - - - +
117A GLU* 1.3 75.8 + - - +
119A ASP* 1.3 69.4 + - - +
120A ARG* 4.0 27.5 + - - +
121A LEU* 2.8 32.2 + - + +
122A GLN* 4.0 1.6 + - - +
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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
----------------------------------------------------------
114A LEU 5.7 0.4 - - - +
117A GLU 4.1 5.7 - - - +
118A GLN* 1.3 74.9 + - - +
120A ARG* 1.3 62.9 + - - +
121A LEU 3.2 0.7 + - - -
122A GLN* 3.2 18.3 + - - +
123A GLY* 3.3 7.8 + - - -
29B SER* 4.2 20.6 + - - +
30B GLN* 4.1 17.2 - - - +
177B GLU* 5.7 0.3 - - - +
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Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 3.1 25.8 - - - +
57A ARG* 3.8 8.1 - - - +
60A ASP* 2.4 41.4 + - - -
118A GLN* 2.9 20.6 + - + +
119A ASP* 1.3 79.2 - - - +
121A LEU* 1.3 62.4 + - - +
123A GLY* 3.0 5.4 + - - +
124A ARG* 3.0 30.6 + - + +
127A GLN* 5.4 0.3 + - - -
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Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 4.0 9.9 - - + +
59A PHE* 3.8 17.5 - - + -
60A ASP* 3.5 47.1 - - - +
63A ILE* 3.7 17.0 - - + +
114A LEU* 3.9 17.9 - - + -
117A GLU* 3.6 31.2 - - + -
118A GLN* 2.8 23.0 + - + +
120A ARG* 1.3 81.0 - - - +
122A GLN* 1.3 65.9 + - - +
124A ARG* 3.0 17.4 + - + +
125A ILE* 3.1 10.7 + - - +
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Residues in contact with GLN 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A THR 4.7 0.2 - - - -
111A GLY* 3.3 27.5 + - - +
114A LEU* 3.7 25.3 - - + +
115A MET* 6.2 3.4 - - - -
118A GLN 4.0 1.0 + - - -
119A ASP* 3.2 13.3 + - - +
121A LEU* 1.3 77.7 - - - +
123A GLY* 1.3 57.9 + - - +
125A ILE* 3.1 12.6 + - - +
126A ASN* 2.8 50.2 + - - +
112B HIS* 5.5 0.7 + - - -
175B ARG* 4.0 20.6 + - - +
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Residues in contact with GLY 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASP 3.3 6.4 + - - -
120A ARG* 3.0 11.4 + - - -
122A GLN* 1.3 80.7 - - - +
124A ARG* 1.3 60.2 + - - +
126A ASN* 3.3 10.7 + - - +
127A GLN* 3.0 33.6 + - - +
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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
----------------------------------------------------------
60A ASP* 3.1 55.2 + - - +
63A ILE* 3.9 25.2 - - + +
64A GLU* 3.1 29.7 + - - +
67A GLU* 4.0 18.1 + - - -
120A ARG* 3.0 19.5 + - + +
121A LEU* 3.0 14.3 + - + +
123A GLY* 1.3 76.6 - - - +
125A ILE* 1.3 62.6 + - - +
127A GLN* 3.1 20.7 + - - +
128A LEU* 3.0 21.9 + - - +
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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
----------------------------------------------------------
63A ILE* 4.0 22.7 - - + -
66A ILE* 4.8 3.8 - - + -
108A ILE* 3.9 21.8 - - + +
109A LEU* 3.5 28.3 - - + +
114A LEU* 3.8 24.5 - - + -
121A LEU 3.1 8.0 + - - +
122A GLN* 3.5 19.3 - - - +
124A ARG* 1.3 76.2 - - - +
126A ASN* 1.3 64.0 + - - +
128A LEU* 3.2 13.8 + - + +
129A PHE* 3.0 47.5 + - + -
175B ARG* 5.1 0.4 - - - -
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Residues in contact with ASN 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLN* 2.8 28.7 + - - +
123A GLY* 3.6 11.4 - - - +
125A ILE* 1.3 76.4 - - - +
127A GLN* 1.3 57.7 + - + +
129A PHE* 3.2 4.0 + - - +
130A GLU* 2.9 34.4 + - + +
175B ARG* 2.9 64.9 + - - +
176B SER* 4.6 4.3 - - - +
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Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 5.7 1.3 - - - +
120A ARG 5.4 0.4 + - - -
123A GLY 3.0 20.0 + - - +
124A ARG* 3.1 25.5 + - - +
126A ASN* 1.3 77.7 - - + +
128A LEU* 1.3 56.1 + - - +
130A GLU* 3.2 9.4 + - - +
131A ARG* 2.8 29.3 + - - +
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 5.3 3.6 - - + +
66A ILE* 3.6 32.1 - - + +
67A GLU* 3.7 34.7 + - + +
70A LEU* 4.5 5.6 - - + -
71A ILE* 3.6 29.2 - - + -
109A LEU* 4.3 15.5 - - + -
124A ARG 3.0 12.2 + - - +
125A ILE* 3.5 18.6 - - + +
126A ASN 3.2 0.2 - - - -
127A GLN* 1.3 77.0 - - - +
129A PHE* 1.3 59.0 + - + +
131A ARG* 3.2 6.0 + - + +
132A ILE* 2.9 43.2 + - + +
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Residues in contact with PHE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 5.9 5.2 - - + -
109A LEU* 3.3 48.5 - - + -
110A THR* 5.7 0.2 - - - -
125A ILE* 3.0 32.3 + - + -
126A ASN 3.6 5.8 - - - +
128A LEU* 1.3 78.0 - - + +
130A GLU* 1.3 58.6 + - - +
132A ILE* 3.3 12.9 + - + +
133A GLU* 2.8 30.1 + - - +
163A LEU* 3.6 28.1 - - + +
166A CYS* 6.3 0.4 - - + -
167A GLU* 4.1 24.5 - - + -
170A LEU* 5.2 9.4 - - + -
175B ARG* 3.5 46.2 - - - +
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASN* 2.9 22.1 + - + +
127A GLN* 3.2 11.0 + - - +
129A PHE* 1.3 76.2 - - - +
131A ARG* 1.3 53.9 + - - +
133A GLU* 3.7 17.7 - - - +
134A VAL* 2.7 46.5 + - + +
137A ARG* 5.1 4.9 + - - -
175B ARG* 4.6 6.8 + - - -
180B TYR* 2.5 37.2 + - - -
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Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 3.6 26.0 + - - +
71A ILE* 3.5 48.7 - - + +
127A GLN 2.8 13.8 + - - +
128A LEU* 3.4 12.1 - - - +
130A GLU* 1.3 75.9 - - - +
132A ILE* 1.3 57.8 + - - +
134A VAL* 3.1 9.7 + - + +
135A GLN* 2.9 35.1 + - + +
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Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 3.9 30.1 - - + -
71A ILE* 4.5 13.9 - - + -
74A ILE* 5.5 8.1 - - + -
91A ILE* 4.9 3.8 - - + -
95A ILE* 3.8 31.4 - - + -
109A LEU* 6.2 0.4 - - + -
128A LEU* 2.9 32.2 + - + +
129A PHE* 3.7 15.5 - - + +
131A ARG* 1.3 74.8 - - - +
133A GLU* 1.3 65.0 + - - +
135A GLN* 3.2 9.5 + - - +
136A LEU* 2.9 31.6 + - + +
163A LEU* 4.0 15.7 - - + -
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A PHE 2.8 16.3 + - - +
130A GLU* 3.7 19.2 - - - +
132A ILE* 1.3 76.4 - - - +
134A VAL* 1.3 63.4 + - - +
136A LEU* 3.1 8.8 + - - +
137A ARG* 2.9 48.0 + - - +
156A THR* 4.3 5.7 - - - +
159A ALA* 4.0 16.6 - - + +
160A SER* 3.5 19.3 + - - -
163A LEU* 3.4 14.8 - - + +
172B ARG* 2.9 39.1 + - - -
175B ARG* 5.0 0.2 + - - -
180B TYR* 5.8 0.2 - - - -
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 2.7 35.8 + - + +
131A ARG* 3.4 9.2 - - + +
133A GLU* 1.3 77.4 - - - +
135A GLN* 1.3 56.8 + - - +
137A ARG* 3.1 31.6 + - - +
138A GLN* 3.0 30.2 + - + +
141A ARG* 5.4 2.2 + - - +
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Residues in contact with GLN 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 4.2 20.2 - - + -
75A ASN* 4.3 10.5 + - - +
78A LEU* 3.3 31.6 - - - +
91A ILE* 5.4 1.8 - - + -
131A ARG* 2.9 20.2 + - + +
132A ILE* 3.2 11.6 + - - +
134A VAL* 1.3 73.9 - - + +
136A LEU* 1.3 68.7 + - + +
138A GLN* 3.2 25.1 + - - +
139A VAL* 3.0 26.1 + - - +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 4.3 9.9 - - + +
91A ILE* 3.7 41.3 - - + -
92A VAL* 5.7 4.9 - - + -
95A ILE* 5.8 1.6 - - + -
132A ILE* 2.9 24.7 + - + +
133A GLU* 3.2 15.5 - - - +
135A GLN* 1.3 78.6 - - + +
137A ARG* 1.3 63.3 + - - +
139A VAL* 3.3 6.4 + - - +
140A MET* 3.1 27.7 + - + +
159A ALA* 3.8 27.4 - - + +
162A LEU* 4.2 25.6 - - + -
163A LEU* 4.5 10.3 - - + +
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Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 5.1 5.3 + - - -
133A GLU* 2.9 41.0 + - - +
134A VAL* 3.1 44.4 - - - +
136A LEU* 1.3 74.3 - - - +
138A GLN* 1.3 57.4 - - - +
140A MET* 3.0 12.7 + - - +
141A ARG* 2.8 60.3 + - - +
155A GLU* 3.8 8.5 - - + +
156A THR* 3.3 34.3 + - - +
159A ALA* 3.6 18.2 - - + -
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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
----------------------------------------------------------
78A LEU* 5.4 4.4 - - - +
134A VAL* 3.0 18.5 + - + +
135A GLN* 3.6 31.0 + - - +
136A LEU 3.2 0.6 - - - -
137A ARG* 1.3 76.9 - - - +
139A VAL* 1.3 63.5 + - + +
141A ARG* 3.1 22.5 + - + +
142A GLU* 3.3 33.1 + - + +
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.7 30.7 - - + -
84A THR* 3.7 29.5 + - + +
87A ARG* 3.9 19.4 + - + +
88A LEU* 3.3 25.4 - - + -
91A ILE* 4.2 13.9 - - + -
135A GLN* 3.0 21.2 + - - +
136A LEU 3.5 7.4 - - - +
138A GLN* 1.3 76.0 - - - +
140A MET* 1.3 63.0 + - - +
142A GLU* 3.2 19.7 + - - +
143A LYS 3.8 0.5 + - - -
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Residues in contact with MET 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 4.6 0.4 - - - -
88A LEU* 4.3 12.3 - - + -
136A LEU 3.1 15.1 + - - +
137A ARG* 3.0 8.6 + - - +
139A VAL* 1.3 78.3 - - - +
141A ARG* 1.3 61.2 + - - +
142A GLU 3.1 1.4 + - - -
143A LYS* 3.3 18.2 + - - +
144A LYS 4.9 0.3 + - - -
150A GLY* 5.5 1.0 - - - -
151A TYR* 3.8 32.7 + - + -
155A GLU* 3.6 37.7 - - + +
158A LEU* 3.6 20.2 - - + -
159A ALA* 3.6 22.0 - - + +
162A LEU* 3.3 33.7 - - + -
197A LEU* 4.4 5.6 - - + -
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Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 5.4 2.0 + - - +
137A ARG* 2.8 56.2 + - - +
138A GLN* 3.1 14.3 + - + +
140A MET* 1.3 74.6 - - - +
142A GLU* 1.3 60.2 + - + +
143A LYS 3.4 0.4 + - - -
144A LYS* 4.5 7.7 + - - +
145A MET* 5.0 2.8 + - - +
155A GLU* 2.8 35.2 + - + +
156A THR* 3.9 10.1 + - - -
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Residues in contact with GLU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 5.0 0.7 - - - +
87A ARG* 2.8 20.2 + - - +
138A GLN* 3.4 36.3 + - + +
139A VAL* 3.2 8.4 + - - +
140A MET 3.1 1.2 - - - -
141A ARG* 1.3 77.8 - - + +
143A LYS* 1.3 54.7 + - - +
144A LYS 3.3 2.7 - - - -
145A MET* 3.0 25.6 + - + +
146A ARG* 2.6 77.2 + - - +
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Residues in contact with LYS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 3.6 22.0 + - + +
85A THR* 5.7 3.6 - - - +
139A VAL 3.8 2.6 + - - -
140A MET 3.3 15.2 + - - +
142A GLU* 1.3 79.0 - - - +
144A LYS* 1.3 55.1 + - - +
146A ARG* 4.2 1.3 - - - -
147A GLU* 2.7 74.0 + - - +
148A GLY 3.7 0.3 + - - -
149A GLU* 3.3 19.2 + - - +
150A GLY* 4.0 10.9 + - - -
151A TYR* 3.5 46.9 - - + +
197A LEU 5.4 0.4 + - - -
198A GLN* 5.7 0.2 + - - -
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Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A MET 4.9 0.4 + - - -
141A ARG 4.5 7.0 + - - +
142A GLU 3.3 0.6 - - - -
143A LYS* 1.3 76.7 - - - +
145A MET* 1.3 59.5 + - - +
148A GLY* 2.7 44.8 + - - +
149A GLU* 3.6 10.9 + - - +
150A GLY* 3.6 19.3 - - - +
----------------------------------------------------------
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Residues in contact with MET 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG 5.0 1.3 + - - +
142A GLU* 3.0 34.5 + - + +
144A LYS* 1.3 81.4 - - - +
146A ARG* 1.3 84.1 + - - +
148A GLY 4.6 1.0 + - - -
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Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 3.8 46.5 + - - +
84A THR* 4.2 7.6 - - - +
87A ARG* 3.3 23.6 - - - +
142A GLU* 2.6 63.5 + - - +
143A LYS* 3.7 5.6 - - - +
145A MET* 1.3 92.6 - - - +
147A GLU* 1.3 65.0 + - + +
----------------------------------------------------------
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP* 3.9 17.3 - - - +
84A THR* 3.9 13.5 + - - -
85A THR* 5.0 3.3 + - - -
143A LYS* 2.7 61.5 + - + +
146A ARG* 1.3 80.4 - - + +
148A GLY* 1.3 57.4 + - - +
149A GLU 3.4 3.6 + - - +
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Residues in contact with GLY 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LYS* 2.7 35.9 + - - +
145A MET 4.6 1.0 + - - -
146A ARG 3.8 0.8 - - - -
147A GLU* 1.3 72.8 - - - +
149A GLU* 1.3 60.1 + - - +
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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