Contacts of the helix formed by residues 116 - 138 (chain A) in PDB entry 4O46
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 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PRO* 4.7 18.7 - - - +
111A ASN 3.6 6.2 - - - +
112A CYS* 3.5 9.8 - - - +
113A SER* 2.7 54.3 + - - +
114A GLU 4.8 0.2 - - - -
115A THR* 1.4 72.7 - - - +
117A TYR* 1.3 62.6 + - - +
118A GLU 3.5 2.2 - - - -
119A SER* 3.7 16.8 + - - +
120A LYS* 3.2 23.7 + - - +
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Residues in contact with TYR 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 3.1 27.2 + - - +
115A THR* 3.0 34.6 + - + +
116A GLN* 1.3 68.3 - - - +
118A GLU* 1.4 64.8 + - + +
120A LYS* 3.3 7.4 + - + +
121A VAL* 3.0 30.0 + - - +
160A ILE* 4.0 13.5 - - + -
164A HIS* 3.3 68.2 + + + +
165A MET* 5.0 6.7 - - + -
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN* 4.5 12.3 + - - +
42A ARG* 4.4 11.9 + - - +
116A GLN 3.5 0.4 - - - -
117A TYR* 1.4 76.8 - - + +
119A SER* 1.4 57.5 + - - +
121A VAL* 3.4 2.3 + - - +
122A PHE* 2.9 30.5 + - - +
165A MET* 3.8 29.4 - - + -
169A HIS* 3.4 25.3 + - + +
171A ILE* 3.8 17.9 - - + +
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Residues in contact with SER 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU 4.8 5.7 + - - -
42A ARG* 3.4 24.4 + - - +
112A CYS* 3.7 18.2 - - - -
116A GLN* 3.7 17.6 + - - +
117A TYR 3.4 0.2 - - - -
118A GLU* 1.4 73.1 - - - +
120A LYS* 1.4 60.0 + - - +
122A PHE* 3.2 7.6 + - - +
123A TYR* 2.9 48.9 + - - -
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Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 5.0 12.2 - - + +
112A CYS* 3.8 20.5 - - + -
113A SER 5.7 0.7 - - - +
116A GLN 3.2 15.6 + - - +
117A TYR* 3.6 8.3 - - + +
119A SER* 1.4 77.8 - - - +
121A VAL* 1.4 55.9 + - - +
123A TYR* 4.0 2.4 - - - +
124A LEU* 3.0 43.6 + - + +
156A GLU* 5.5 1.8 - - - +
160A ILE* 4.0 24.2 - - + -
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TYR 3.0 20.5 + - - +
118A GLU 3.9 2.9 - - - +
120A LYS* 1.4 70.2 - - - +
122A PHE* 1.4 57.7 + - - +
124A LEU* 3.3 1.4 + - - +
125A LYS* 2.8 36.7 + - - +
157A ALA* 3.7 31.5 - - + +
160A ILE* 3.7 22.0 - - + -
161A SER* 3.8 13.7 - - - +
165A MET* 3.8 14.6 - - - -
171A ILE* 3.8 17.9 - - + +
175A LEU* 3.9 21.5 - - + -
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Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 3.4 62.8 - - + +
43A ASN* 4.1 20.9 - - - -
46A SER* 3.8 22.4 - - - -
118A GLU 2.9 17.9 + - - +
119A SER 3.2 4.5 + - - +
121A VAL* 1.4 75.7 - - - +
123A TYR* 1.4 63.1 + + - +
125A LYS* 3.5 13.9 + - + +
126A MET* 3.0 44.9 + - + +
171A ILE* 4.0 22.1 - - + +
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Residues in contact with TYR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.6 19.2 + - - +
42A ARG* 3.4 34.7 - - + +
45A LEU* 4.8 5.2 - - + -
104A LEU* 3.6 24.1 - - + +
108A LEU* 3.5 51.4 - - + +
109A ILE* 3.6 20.6 - - + +
112A CYS* 3.7 21.8 - - - -
119A SER* 2.9 34.9 + - - +
120A LYS* 4.2 1.6 - - - +
122A PHE* 1.4 76.6 - + - +
124A LEU* 1.4 61.8 + - - +
126A MET* 3.2 6.4 + - - +
127A LYS* 2.9 27.4 + - - +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 4.2 27.1 - - + -
120A LYS* 3.0 27.2 + - + +
123A TYR* 1.4 71.7 - - - +
125A LYS* 1.4 60.2 + - - +
127A LYS* 3.3 14.6 + - + +
128A GLY* 2.9 23.6 + - - -
153A ALA* 3.5 27.3 - - - +
156A GLU* 3.6 43.7 - - + +
157A ALA* 3.6 19.7 - - + +
160A ILE* 3.7 20.2 - - + -
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Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 2.8 19.2 + - + +
122A PHE* 3.5 13.8 - - + +
124A LEU* 1.4 75.2 - - - +
126A MET* 1.4 54.7 + - - +
128A GLY* 3.2 2.9 + - - -
129A ASP* 2.9 58.9 + - - +
154A TYR* 3.6 9.4 - - + -
157A ALA* 4.1 0.8 - - - +
171A ILE* 4.8 7.2 - - + +
174A GLY* 3.8 16.6 - - - -
175A LEU* 3.9 43.1 - - + +
178A ASN* 3.5 19.2 - - + +
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Residues in contact with MET 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 4.5 18.4 - - + +
46A SER* 4.2 27.4 - - - +
49A TYR* 5.2 1.6 - - + -
100A VAL* 3.7 27.4 - - + -
104A LEU* 3.9 19.5 - - + -
122A PHE* 3.0 42.2 + - + +
123A TYR* 3.2 12.8 + - - +
125A LYS* 1.4 74.6 - - - +
127A LYS* 1.4 59.3 + - - +
129A ASP* 3.1 11.9 + - - +
130A TYR* 2.9 53.0 + - + +
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Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.7 21.2 - - + +
104A LEU* 3.7 6.7 - - + +
105A ASP* 2.7 38.3 + - - +
109A ILE* 3.8 15.5 - - + +
123A TYR 2.9 13.6 + - - +
124A LEU* 3.3 19.1 + - + +
126A MET* 1.4 74.7 - - - +
128A GLY* 1.3 61.3 + - - +
130A TYR 3.6 0.2 + - - -
131A TYR* 3.2 48.5 + - + -
149A SER 5.4 1.8 - - - -
153A ALA* 3.8 17.0 - - + +
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Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU 2.9 11.2 + - - -
125A LYS 3.2 4.0 + - - -
127A LYS* 1.3 77.0 - - - +
129A ASP* 1.4 53.9 + - - +
131A TYR 3.5 0.2 + - - -
132A ARG* 3.0 17.3 + - - +
150A SER* 2.8 29.3 + - - -
153A ALA* 3.5 15.0 - - - +
154A TYR* 3.3 20.2 - - - -
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Residues in contact with ASP 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LYS* 2.9 43.0 + - - +
126A MET* 3.1 13.0 + - - +
128A GLY* 1.4 75.0 - - - +
130A TYR* 1.3 61.0 + - + +
132A ARG* 3.1 10.3 + - - +
133A TYR* 2.9 51.2 + - + +
154A TYR* 2.7 26.2 + - - -
178A ASN* 2.8 26.3 + - - +
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Residues in contact with TYR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 4.1 4.0 + - - -
49A TYR* 3.3 8.8 - - - +
50A LYS* 3.2 32.9 + - + +
53A VAL* 3.7 22.7 - - + -
97A CYS* 3.7 21.0 - - + +
100A VAL* 3.7 36.6 - - + -
101A LEU* 4.1 23.8 - - + -
104A LEU* 5.0 0.2 - - + -
126A MET* 2.9 56.3 + - + +
129A ASP* 1.3 74.1 - - + +
131A TYR* 1.4 60.7 + - - +
133A TYR* 3.4 20.4 + + - -
134A LEU* 3.1 30.9 + - - +
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Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLN* 5.3 3.7 + - - -
101A LEU* 3.6 31.5 - - + +
105A ASP* 4.6 8.3 + - - -
127A LYS* 3.2 48.5 + - + +
130A TYR* 1.4 73.2 - - - +
132A ARG* 1.4 60.0 + - - +
134A LEU* 3.3 21.1 + - + +
135A ALA* 2.9 26.3 + - - +
146A VAL* 3.6 31.3 - - + +
149A SER* 3.6 36.2 + - - -
150A SER* 3.7 12.1 - - - -
106B ASN* 3.4 29.9 + - + -
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ARG* 4.4 4.6 - - - +
128A GLY 3.0 13.7 + - - +
129A ASP* 3.1 28.9 + - - +
131A TYR* 1.4 74.7 - - - +
133A TYR* 1.4 81.2 + - - +
135A ALA* 3.1 9.4 + - - +
136A GLU* 3.0 48.1 + - - +
150A SER* 3.8 9.2 + - - +
154A TYR* 2.9 18.9 + - - -
178A ASN* 3.4 21.4 + - - +
181A VAL* 3.8 22.2 - - - +
182A PHE* 3.8 30.5 - - + +
185A GLU* 5.1 1.4 + - - -
186A ILE* 3.7 18.8 - - + -
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Residues in contact with TYR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LYS* 3.3 25.7 - - - +
53A VAL* 4.0 18.2 - - + -
57A ARG* 3.4 48.3 + - - +
93A LEU* 3.8 17.1 - - + +
97A CYS* 4.0 9.4 - - - -
129A ASP* 2.9 40.3 + - + +
130A TYR* 3.7 41.0 - + - +
131A TYR 3.4 0.4 - - - -
132A ARG* 1.4 97.1 + - - +
134A LEU* 1.3 61.8 + - - +
136A GLU* 3.5 24.6 - - - +
137A VAL* 3.9 4.2 + - - +
178A ASN* 4.9 1.9 + - - -
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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
----------------------------------------------------------
93A LEU* 4.9 0.9 - - + -
94A GLU* 3.7 36.4 - - + +
97A CYS* 3.7 21.5 - - + -
98A GLN* 4.0 17.5 - - - +
101A LEU* 3.8 14.8 - - + -
130A TYR 3.1 15.3 + - - +
131A TYR* 3.4 32.8 - - + +
132A ARG 3.2 0.2 - - - -
133A TYR* 1.3 74.1 - - - +
135A ALA* 1.4 62.4 + - - +
137A VAL* 3.3 10.0 + - - +
138A ALA* 3.1 22.7 + - - +
142A LYS* 5.9 2.1 - - - -
146A VAL* 3.9 19.5 - - + -
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Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A TYR 2.9 13.6 + - - +
132A ARG* 3.1 13.2 + - - +
134A LEU* 1.4 72.3 - - - +
136A GLU* 1.4 65.2 + - - +
137A VAL 3.1 1.6 + - - -
138A ALA* 3.2 18.6 + - - +
143A ARG* 3.7 12.8 + - + +
146A VAL* 3.7 12.7 - - + +
147A VAL* 3.8 28.9 - - + +
186A ILE* 4.0 17.3 - - + -
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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
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57A ARG* 3.1 44.6 + - - +
60A TRP* 3.5 21.4 - - + -
61A ARG* 4.6 5.4 + - - -
132A ARG* 3.0 33.0 + - - +
133A TYR* 3.5 14.4 - - - +
134A LEU 3.3 0.4 - - - -
135A ALA* 1.4 75.9 - - - +
137A VAL* 1.3 60.9 + - + +
138A ALA 5.0 0.5 - - - +
185A GLU* 4.3 12.1 - - - +
186A ILE* 3.9 17.7 - - + +
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TRP* 3.5 44.4 - - + +
90A GLU* 3.7 31.3 - - + +
93A LEU* 4.3 26.7 - - + -
94A GLU* 3.8 23.9 - - + +
133A TYR 4.2 9.9 - - - +
134A LEU 3.3 13.4 + - - +
136A GLU* 1.3 78.8 - - + +
138A ALA* 1.3 64.1 + - - +
139A THR* 4.1 6.1 + - - +
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLU* 5.4 0.2 - - - -
134A LEU 3.1 17.7 + - - +
135A ALA 3.2 6.3 + - - +
136A GLU 4.9 0.7 - - - +
137A VAL* 1.3 81.3 - - + +
139A THR* 1.3 66.0 + - - +
142A LYS* 4.2 22.4 - - + +
143A ARG* 3.4 43.4 + - + +
146A VAL* 4.2 7.0 - - + -
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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) + - + + + + + -
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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