Contacts of the helix formed by residues 117 - 144 (chain A) in PDB entry 4CKG
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 LEU 117 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 3.8 26.0 - - + +
31A LEU* 6.0 5.2 - - + -
32A GLU* 4.2 22.7 - - + +
35A LEU* 5.4 8.5 - - + -
112A LEU 4.2 4.3 + - - +
113A VAL* 4.4 13.4 + - + +
115A GLU 3.3 0.4 - - - -
116A GLY* 1.4 82.3 - - - +
118A ARG* 1.4 57.8 + - - +
119A GLY 3.6 1.6 - - - -
120A PHE* 3.8 20.9 + - + +
121A ARG* 3.0 70.3 + - + +
180A ILE* 4.6 20.6 - - + -
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Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LYS* 3.5 19.4 + - - +
115A GLU* 2.6 68.0 + - - +
117A LEU* 1.4 75.0 - - - +
119A GLY* 1.3 59.5 + - - +
121A ARG* 3.5 3.9 + - - +
122A GLU* 3.0 31.5 + - + +
125C ARG* 4.9 8.1 - - - +
129C ARG* 0.6 191.9 - - - +
169C ARG* 4.6 7.3 - - - +
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Residues in contact with GLY 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU 4.7 1.0 + - - -
116A GLY 5.4 0.6 - - - -
117A LEU 3.6 0.4 - - - -
118A ARG* 1.3 77.8 - - - +
120A PHE* 1.3 59.1 + - - +
122A GLU* 3.8 6.2 + - - +
123A ALA* 3.1 27.5 + - - +
176A GLN* 3.9 20.3 + - - -
129C ARG* 5.5 1.3 - - - -
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Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 5.1 0.7 - - + -
25A GLU* 5.6 8.1 - - - -
28A VAL* 4.2 24.5 - - + -
116A GLY 5.5 2.0 + - - +
117A LEU* 3.8 29.3 + - + +
118A ARG 3.5 0.2 - - - -
119A GLY* 1.3 73.4 - - - +
121A ARG* 1.3 61.0 + - + +
123A ALA* 3.2 3.7 + - + +
124A ARG* 2.9 29.8 + - + +
173A TYR* 3.4 63.5 - + - -
176A GLN* 3.8 34.7 + - + +
177A ILE* 3.5 27.1 - - + -
180A ILE* 5.3 6.1 - - + -
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 5.6 6.1 + - - +
28A VAL* 3.9 23.4 - - - +
29A SER* 4.5 9.9 + - - -
32A GLU* 2.6 48.0 + - - +
113A VAL 6.0 0.4 + - - -
117A LEU* 3.0 48.0 + - + +
118A ARG* 4.0 4.3 - - - +
120A PHE* 1.3 76.1 - - + +
122A GLU* 1.4 59.0 + - - +
124A ARG* 3.3 14.0 + - + +
125A ARG* 2.9 27.5 + - - +
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ARG* 3.0 21.9 + - + +
119A GLY* 3.9 7.2 - - - +
121A ARG* 1.4 74.4 - - + +
123A ALA* 1.3 60.4 + - - +
125A ARG* 2.6 37.7 + - - +
126A ASP* 3.5 16.8 + - - +
122C GLU* 1.6 23.8 - - - +
125C ARG* 1.6 45.9 + - - +
129C ARG* 5.7 0.9 - - - +
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLY 3.1 19.6 + - - +
120A PHE* 3.2 8.7 + - + +
122A GLU* 1.3 71.5 - - - +
124A ARG* 1.4 58.0 + - - +
125A ARG 3.5 0.2 + - - -
126A ASP* 3.8 3.0 + - - +
127A PHE* 3.0 32.1 + - - +
169A ARG* 5.1 2.6 - - - +
172A ASP* 4.5 10.1 - - + -
173A TYR* 4.4 25.1 - - + +
176A GLN* 4.5 10.8 - - + +
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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
----------------------------------------------------------
25A GLU* 2.8 45.6 + - - +
120A PHE* 2.9 19.7 + - + +
121A ARG* 3.3 18.8 - - + +
123A ALA* 1.4 71.4 - - - +
125A ARG* 1.4 63.9 + - - +
127A PHE* 4.2 5.8 - - - -
128A TRP* 3.2 68.9 + - - +
173A TYR* 4.4 22.8 - - + -
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG 2.9 16.5 + - - +
122A GLU* 2.6 27.2 + - - +
123A ALA 3.4 0.6 - - - -
124A ARG* 1.4 78.0 - - - +
126A ASP* 1.3 62.0 + - - +
128A TRP* 3.4 3.5 + - - +
129A ARG* 2.9 50.8 + - + +
118C ARG* 5.0 2.2 - - - +
122C GLU* 1.7 62.7 + - - +
125C ARG* 5.4 0.2 - - - -
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Residues in contact with ASP 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU 3.5 13.4 + - - +
123A ALA* 4.2 3.8 - - - +
125A ARG* 1.3 79.2 - - - +
127A PHE* 1.4 56.9 + - - +
129A ARG* 2.7 31.8 + - - +
130A GLY* 2.9 26.5 + - - -
169A ARG* 2.6 57.8 + - + +
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Residues in contact with PHE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 3.9 19.5 - + - -
21A ILE* 3.6 40.4 - - + -
123A ALA 3.0 24.3 + - - +
124A ARG 3.8 2.7 - - - +
126A ASP* 1.4 71.5 - - - +
128A TRP* 1.4 75.3 + + - +
130A GLY 3.6 0.5 + - - -
131A ALA* 3.1 19.6 + - - +
166A TYR* 3.6 34.4 - + - -
169A ARG* 3.9 15.7 - - + +
170A ALA* 3.5 42.6 - - + -
173A TYR* 3.8 28.9 - + + -
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Residues in contact with TRP 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 4.7 17.9 - - + +
22A GLU* 6.2 5.4 - - + -
25A GLU* 4.8 4.8 + - - -
124A ARG* 3.2 68.5 + - - +
125A ARG* 3.9 3.1 - - - +
127A PHE* 1.4 93.9 - + - +
129A ARG* 1.4 60.9 + - - +
131A ALA* 3.4 10.0 + - + +
132A GLU* 3.1 26.3 + - - +
173A TYR* 5.8 1.2 - - - -
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ARG* 2.9 30.6 + - - +
126A ASP* 2.7 34.9 + - - +
128A TRP* 1.4 76.8 - - - +
130A GLY* 1.3 50.6 + - - +
132A GLU* 3.4 16.5 - - - +
133A SER* 2.9 30.5 + - - -
169A ARG* 3.9 6.3 - - - +
118C ARG* 0.6 247.6 - - - +
119C GLY* 5.0 1.2 - - - +
122C GLU* 5.6 1.2 - - - +
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Residues in contact with GLY 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASP 2.9 14.5 + - - -
127A PHE 3.8 1.8 - - - -
129A ARG* 1.3 69.7 - - - +
131A ALA* 1.4 59.2 + - - +
132A GLU 3.3 0.2 - - - -
133A SER* 3.8 5.5 - - - -
134A LEU* 2.9 27.5 + - - +
162A ALA 4.8 1.7 - - - +
166A TYR* 3.7 16.1 - - - +
169A ARG* 3.5 28.5 - - - +
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 4.7 17.1 + - - +
127A PHE 3.1 13.9 + - - +
128A TRP* 3.4 15.2 + - + +
130A GLY* 1.4 74.1 - - - +
132A GLU* 1.3 52.3 + - - +
134A LEU* 3.2 6.1 + - - +
135A GLU* 2.8 36.9 + - - +
166A TYR* 3.7 20.2 - - + +
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A TRP 3.1 13.1 + - - +
129A ARG* 3.4 19.2 - - - +
130A GLY 3.3 0.2 - - - -
131A ALA* 1.3 77.5 - - - +
133A SER* 1.3 59.0 + - - +
135A GLU* 3.4 7.1 + - - +
136A ALA* 3.1 23.6 + - - +
114C LYS* 5.6 3.6 + - - -
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Residues in contact with SER 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG 2.9 18.0 + - - -
130A GLY* 3.8 9.2 - - - -
131A ALA 3.4 0.2 - - - -
132A GLU* 1.3 72.7 - - - +
134A LEU* 1.4 58.5 + - - +
136A ALA* 3.7 3.8 + - - +
137A ALA* 3.0 30.7 + - - +
162A ALA* 4.4 11.7 - - - +
169A ARG* 4.9 6.3 - - - -
114C LYS* 6.0 3.6 - - - +
115C GLU* 5.3 8.6 + - - -
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 4.4 1.1 - - - +
18A ARG* 4.2 19.1 - - - +
130A GLY 2.9 19.9 + - - +
131A ALA* 3.4 5.8 - - - +
133A SER* 1.4 75.0 - - - +
135A GLU* 1.4 56.4 + - - +
137A ALA* 3.3 5.0 + - - +
138A LEU* 2.8 37.8 + - + +
159A LEU* 3.8 21.5 - - + -
162A ALA* 4.1 3.7 - - + +
163A ARG* 3.4 63.9 - - - +
166A TYR* 4.0 19.1 - - + -
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Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 5.5 4.7 + - - -
131A ALA 2.8 20.6 + - - +
132A GLU* 3.4 7.5 + - - +
134A LEU* 1.4 72.7 - - - +
136A ALA* 1.4 57.9 + - - +
138A LEU* 3.4 14.4 + - + +
139A THR* 2.7 35.2 + - - +
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 3.1 16.7 + - + +
133A SER* 4.3 4.0 - - - +
135A GLU* 1.4 73.4 - - - +
137A ALA* 1.3 55.2 + - - +
139A THR* 3.4 9.3 - - - -
140A HIS* 2.7 54.8 + - + +
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A SER* 3.0 21.4 + - - +
134A LEU 3.4 4.9 - - - +
136A ALA* 1.3 75.2 - - - +
138A LEU* 1.4 60.6 + - - +
140A HIS* 4.0 3.4 - - - +
141A ASN* 3.1 24.4 + - - +
155A ALA 4.9 3.0 - - - +
158A ALA* 4.6 3.8 - - + +
159A LEU* 4.0 22.0 - - + +
162A ALA* 3.5 24.5 - - + -
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 2.8 32.5 + - + +
135A GLU* 3.7 15.7 - - + +
137A ALA* 1.4 72.3 - - - +
139A THR* 1.4 54.8 + - - +
141A ASN* 3.6 5.3 + - - +
142A ALA* 2.8 37.3 + - - +
159A LEU* 4.1 18.2 - - + -
163A ARG* 4.0 22.2 - - - +
254B GLU* 4.2 4.7 - - - +
273B PHE* 4.3 15.3 - - + -
285B ARG* 3.8 29.4 - - - +
343B ASP* 3.8 20.4 - - - +
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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 GLU* 2.7 30.7 + - - +
136A ALA* 3.1 11.7 + - + -
138A LEU* 1.4 72.0 - - - +
140A HIS* 1.3 67.6 + - + +
142A ALA* 3.4 2.4 + - - -
143A GLU* 3.1 41.9 + - + +
273B PHE* 5.0 5.5 - - - -
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Residues in contact with HIS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 2.7 40.9 + - + +
137A ALA* 4.5 3.6 - - - +
139A THR* 1.3 82.9 - - + +
141A ASN* 1.4 57.6 + - - +
143A GLU* 4.0 7.5 + - - +
144A VAL* 4.1 12.1 + - - +
155A ALA* 3.9 22.2 - - + +
106C GLN* 6.5 0.9 - - + -
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Residues in contact with ASN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ALA 3.1 19.5 + - - +
138A LEU* 3.7 5.9 + - - +
140A HIS* 1.4 76.4 - - - +
142A ALA* 1.3 63.2 + - - +
144A VAL* 3.7 4.3 - - - +
152A ALA 4.5 0.2 - - - +
155A ALA* 4.7 7.4 - - - +
156A GLY* 3.6 21.0 + - - -
159A LEU* 3.5 28.7 - - + +
326B ARG* 2.6 53.4 + - - +
327B PHE* 4.4 2.2 - - - -
341B GLN* 4.9 0.2 + - - -
343B ASP* 3.4 32.7 + - - +
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU 2.8 20.5 + - - +
139A THR* 4.1 3.4 - - - +
141A ASN* 1.3 77.8 - - - +
143A GLU* 1.4 63.1 + - + +
144A VAL 3.5 5.4 + - - +
273B PHE* 3.9 24.9 - - + -
325B ARG* 3.5 12.0 + - - +
326B ARG* 5.0 0.7 - - - +
341B GLN* 2.8 41.5 + - - +
342B ALA 6.0 1.1 - - - +
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A THR* 3.1 32.8 + - + +
140A HIS* 4.0 4.2 + - - +
141A ASN 3.6 0.4 - - - -
142A ALA* 1.4 75.8 - - + +
144A VAL* 1.4 62.3 + - - +
145A PRO* 3.7 6.6 - - - +
283B TRP* 4.1 15.7 - - - +
325B ARG* 2.6 47.3 + - - +
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Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A HIS 4.1 12.6 + - - +
141A ASN* 3.7 11.0 - - - +
142A ALA 4.1 2.6 - - - +
143A GLU* 1.4 75.6 - - - +
145A PRO* 1.4 76.1 - - + +
146A ARG 3.9 1.0 + - - -
148A ARG* 4.0 10.3 - - + +
151A GLU* 4.6 6.1 - - + -
152A ALA* 3.7 39.7 - - + +
155A ALA* 5.7 1.3 - - + -
324B GLU 4.7 0.2 - - - +
325B ARG* 5.3 2.1 - - - -
326B ARG* 3.5 41.1 + - - +
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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